College of Science Theses and Dissertations
Permanent URI for this collectionhttps://hdl.handle.net/1969.6/1175
Browse
Browsing College of Science Theses and Dissertations by Type "Text"
Now showing 1 - 20 of 269
- Results Per Page
- Sort Options
Item Analyses of biological communities and development of indices of biotic integrity for monitoring tidal streams along the upper Texas coast(2020-05) Margo, Abraham; Pollack, Jennifer Beseres; Withers, Kim; Tolan, JamesTidal streams along the upper Texas coast are characterized by large heterogeneity in abiotic conditions and biotic communities, posing challenges to managers seeking to assess their ecological condition and develop effective management strategies. There is currently no standardized protocol for assessing ecological condition in Texas tidal stream systems. The goal of the current study was to create multimetric indices of biotic integrity (IBIs) from nekton and benthic macroinfaunal community metrics that were effective in discriminating between degraded “test” and non-degraded “reference” streams (classified by watershed land-cover data). Fifteen tidal streams were sampled twice per year in 2018 and 2019 to assess water quality, nekton, and benthic macroinfaunal dynamics. In order to create the multimetric indices of biotic integrity, multiple univariate metrics were assessed to determine the extent to which they differentiated between test and reference sites. Selected metrics were used as components in developing the multimetric IBIs, which give higher scores to samples that have similar biotic characteristics to our reference condition samples. Multivariate analyses provided a complementary approach to selection of IBI metrics by visualizing, comparing, and identifying community-level changes as well as taxa that associate with the test or reference condition. Results indicated that overall differences in biological communities between test and reference sites were often not extremely strong. Multivariate analyses indicated nekton communities exhibited stronger differentiation between test and reference samples whereas benthic macrofaunal communities were influenced more by year to year variations. However, several univariate metrics highlighted components of communities that did differ between test and reference sites, and these metrics were used to form the IBI. Comparing IBIs for both nekton and benthic macroinfauna can provide a more comprehensive understanding of biotic integrity in tidal streams than focusing on one or the other. Results should be interpreted with some caution but could help inform water resource management decisions that seek to support aquatic life use while balancing human needs for food, recreation, and industry.Item Analysis and applications of the weighted central direction method(2016-12) Choi, HaekyoungIterative methods yield an approximated solution to a given problem by producing a sequence of points that converges to the exact solution. Due to the effectiveness of these methods, they become one of the core mathematical procedures widely used in many major mathematical areas such as Differential Equations, Linear Algebra, and Matrix Analysis. The Methods of Alternating Projection, which we will use in this thesis, form a class of iterative methods based on the relevant projection algorithm introduced by John von Neumann. This outstanding algorithm received considerable attention by mathematicians which contributed to a number of different algorithms to solve several problems. Recently, two former graduate students at Texas A&M University-Corpus Christi, Melina Wijaya and Zulema Cervantes, introduced a couple of new algorithms in this area. Wijaya presented the Weighted Direction algorithm, and Cervantes introduced the Weighted Central Direction algorithm by combining the Weighted Direction and the Central Direction. The algorithm with the combination of two directions achieved a faster convergence than the algorithm with the Weighted Direction only. However, the Weighted Central Direction algorithm needs a parameter which depends on the size of the problems. This thesis carries two objectives. Firstly, study the role of the wide angle condition which guarantees the convergence in the Weighted Direction algorithm in order to analyze if this condition is necessary for the convergence of the algorithm. Secondly, improve the algorithms developed by Wijaya and Cervantes in order to obtain a faster convergence by finding an adequate ratio between the Weighted Direction and the Central Direction that is independent of the size of the problems.Item An analysis of emergency management agencies gis data for planning 9-1-1 services for the border counties of the lower Rio Grande Valley(2017-08) Nino, Orlando; Smith, Richard; Jeffress, Gary; Huang, YuxiaTexas 9-1-1 entities collect data that can be used to gain knowledge on 9-1-1 call patterns and trends. It is ideal to know these issues too efficiently maximize monies appropriated to local emergency management agencies. This research will analyze 9-1-1 calls and two police departments calls for service using Geographic Information Science (GIS). This information provided by multiple emergency management agencies to better plan 9-1-1 services in the border counties of the Rio Grande Valley. The data that was used is recorded daily by these agencies. Many emergency management organizations keep their own GIS data in-house and they need to be analyzed with 9-1-1 data. Analyzing various GIS databases can yield better results, in finding correlation within each dataset, hotspots and inadequate data collection. These results can then be used by the organizations that contributed the data and shared to all stakeholders.Item Analytic solutions for the harmonic potentials involving concentric layered dielectric spheres(2018-05) Cisneros, Frank; Palaniappan, Devanayagam; Sadovski, Alexey L.; Zimmer, BeateThe mathematical problem of a conducting spherical core of radius 𝑎 concentrically covered by a dielectric phase of radius 𝑏 placed in an arbitrary external electric field is investigated. The vector field equations for the electric field (Maxwell equations) and the boundary conditions are transformed to a scalar boundary value problem (BVP) in terms of the harmonic potential functions. The harmonic potentials denoted by Φ𝐼(𝑟,𝜃,𝜙) and Φ𝐼𝐼(𝑟,𝜃,𝜙) where (𝑟,𝜃,𝜙) are spherical coordinates, satisfy the Laplace equations in the regions 𝑏<𝑟 and 𝑎 < 𝑟 < 𝑏, respectively. General analytical solutions for the potentials in the two phases are determined in infinite series form using spherical harmonics methods. Exact closed form solutions are also derived via an alternative approach. The latter solutions contain integrals involving harmonic functions. Our general solutions are applicable for arbitrary external potentials disturbed by a conducting spherical core with a dielectric coating. Several illustrative examples are investigated and exact solutions for them are constructed using our general solutions. The non-dimensional parameter 𝑘= 𝜀𝐼/(𝜀𝐼+𝜀𝐼𝐼) , where 𝜀𝐼 is the dielectric constant for the region 𝑟 > 𝑏 and 𝜀𝐼𝐼 is the dielectric constant for the region 𝑎 < 𝑟 < 𝑏, influences the potential patterns in the case of externally imposed constant and linear fields. Our results for the source induced field indicate that the force is positive or negative depending on 𝑘 < 0.5 or 𝑘 > 0.5. Furthermore, the force is greater than zero when the core radius 𝑎 approaches the value of the outer radius 𝑏. We believe that our mathematical results are of interest where coated dielectric objects are exposed to external electric fields.Item Applicability of the microfragmentation technique to propagate corals in a fisherfolk community in the Philippines(2019-12) Broquet, Nicole C.; Scarpa, John; Siccardi, Anthony; Pollack, Jennifer Beseres; Vaughan, DavidCoral nursery implementation is becoming a highly prevalent method of coral restoration in the Philippines. These nurseries primarily focus on fast-growing branching corals and do not commonly include massive corals. This is due to the slow growth rate and morphology of these corals, which are not conducive to traditional nursery methods. Microfragmentation is a relatively new technique that has displayed positive results for massive coral propagation. This method utilizes small coral fragments (≈1-3 cm) that are mounted on platforms, then placed in ex-situ or in-situ nurseries. The fragments exhibit rapid growth, which decreases the duration of the nursery phase before transplantation. Though microfragmentation is becoming more practiced, there is no published literature specifically focused on this method in the Philippines. The present study aimed to determine if: 1) coral specimen (i.e., putative genotype) significantly influenced growth, and 2) this method was viable in a fisherfolk community in the Western Visayas of the Philippines. Five corals of opportunity (putative genotypes) of the lobe coral, Porites lobata, were fragmented with hammer and chisel by several volunteer fisherfolk. The fragments were cultured from April-August 2018 in an in-situ fixed-leg nursery at a depth of approximately 2m. Maintenance was performed weekly and measurements of growth (i.e., volume change) were conducted monthly. The fragments were then transplanted to a selected restoration site and monitored for one month. A hierarchical Bayesian log-linear regression model indicated that 59.7% of growth (volume change) variation was attributed to coral specimen (i.e., putative genotype) and 26.4% of growth variation was attributed to the individual fragment. Overall, the average monthly increase in particular specimen’s fragment volume was 23.5% per month (95% CI, 3.43% - 43.9%/month) with the greatest monthly increase for a specimen at 30.1% per month (95% CI, 19.3 – 40.3%/month). Mean tissue spreading was determined to be 43.24cm2 /month (95% CI 44.5 – 79.4 cm2 /month) and mean linear extension was estimated to be 1.55 cm/month (95% CI, 0.92 – 2.02 cm/yr). Though high growth rates for P. lobata were documented in this study, nursery maintenance was significant due to lack of resources and location of nursery. This method may be viable and highly beneficial in established coral nurseries in the Philippines, but may not be feasible in a remote fisherfolk communityItem Applying segmentation and neural networks to detect and quantify marine debris from aerial images captured by unmanned aerial system and mobile device(2018-08) Tran, Kieu; Conkle, Jeremy; Starek, Michael J.; Gibeaut, JamesMarine debris is a global issue with adverse impacts on the marine environment, wildlife, economy, and human health. Its presence on beaches may vary due to topography, hydrological conditions, proximity to litter sources, and the extent of beach use. Studies of these parameters on beach litter are essential for understanding spatial and temporal patterns; however, this work is labor-intensive and time-consuming. To overcome these obstacles while gaining higher spatial and temporal resolution data, two methods were developed (1) segmentation and (2) regions with convolutional neural networks (R-CNN) to detect and quantify marine macro-debris using high-resolution imagery. Data to develop and test the methods were collected using a small rotary Unmanned Aerial System (UAS) with an RGB sensor at various altitudes over a 100m section of sandy beach of Mustang Island, Texas. Images were processed through structure-from-motion photogrammetry to derive orthomosaics for each flight. Orthomosaics were then run through an image processing, and classification workflow developed for segmentation and delineation of imaged debris. The segmentation algorithm detected the most debris at the lowest altitude (215 of 341 total at 15m), with decreasing detections at 22m (101) and 35m (50). The second method applied deep learning object detection to smartphone images. Based on the dataset and the network architecture, R-CNN mean average precision can range from 31.4% to 66% (Girshick et al., 2014). Training for R-CNN consisted of three stages: extract region proposals, train AlexNet to classify objects, and train a bounding box regression model to locate the debris. Average precision for the Specifically Engineered Algorithm for Gathering and Understanding Litter Location (SEAGULL) detector was ~22%, meaning it has a low performance at detecting all the debris in the testing dataset and correctly predicting whether or not that region was debris or not. Object detection has been a challenging task for decades, and with a low overall debris detection accuracy, it needs to be further improved with the use of a larger dataset or adjusting the training parameters. Few studies have been published on this topic, but this work demonstrates that remote sensing with UAS has the potential to increase research efficiency.Item Assessing embryonic toxicity and end fates of nanoplastics in freshwater environments using gastropod Biomphalaria Glabrata(2022-07-22) Merrill, MacKenzie Leigh; Xu, Wei; Bahr, Keisha; Wagner, Daniel; Mozzachiodi, RiccardoThe wide use of plastics has resulted in not only the accumulation of macroplastic pollution in the aquatic environment but also plastic particles at micro and nano levels (MPs and NPs). Accumulation of these MPs and NPs have numerous adverse effects on the morphology, behavior, and reproduction of living organisms. In this study, we investigated the effects of NPs on the embryonic development of Biomphalaria glabrata, a commonly used gastropod in toxicology studies. This study identified the adsorption of NPs by the embryos of B. glabrata and showed evidence of NP absorption by the hatched juveniles. NP bioaccumulation subsequently triggered the alteration in the expression of several stress response genes, including heat shock protein-70 (HSP70), cytochrome P450 (CYP450), and macrophage migration inhibitory factor (MIF). With the influence of NPs, the hatching rates of B. glabrata embryos varied depending on the sizes of NPs. In addition, the NPs with mean diameters of 1.0 µm or 0.03 µm led to higher embryo mortality rates than 0.5 µm NPs. This preliminary study demonstrated the impact of NPs on the development of B. glabrata embryos. Further studies on the mechanism of NP toxic effects are desired.Item Assessing short-term sediment accretion rates and hydrological influences on a microtidal estuarine wetland: Mustang Island, TX(2015-12) Martinez, MelindaAs sea level rises there has been a growing concern whether salt marsh wetlands can withstand an accelerated rise in sea level by vertically accreting. Sediment accretion is a natural process that changes the elevation of the marsh surface relative to sea level. For a wetland to persist in the long-term, its accretion rate must at least match the rate of relative sea level rise. This study describes sedimentation rates in the estuarine wetlands located on Mustang Island, TX, a sandy barrier island. Sedimentation rates were measured bi-weekly from June 2014 to July 2015 using sediment plates and erosion pins, and over periods of 2.4 to 3.3 years (2012- 2014/2015) using horizon marker techniques. Water level loggers were used to assess hydrological controls on bi-weekly sedimentation patterns. Shallow cores (~15 cm) were collected from the horizon marker plots in August 2014 and July 2015. Vertical accretion rates were compared across different timescales including decadal rates determined using 137Cs from a previous study on Mustang Island, TX. Results indicated sediment accretion across the study area was not significantly influenced by hydrological patterns, with the exception of low marsh environments near tidal creeks (r2=0.52, p < 0.1). The most important factor in determining sediment deposition on sediment plates located near the main tidal creek was the number of flooding events, suggesting that deposition increases as frequency of flooding events increases. The total accumulation deposited on plates was dominated by inorganic sediments, suggesting there is a limit of detrital organic matter contribution for this area. Average vertical accretion using horizon markers was 8.15 ± 5.21 mm yr-1 in upland environments; 4.51 ± 5.21 mm yr-1 in high marsh environments; 3.36 ± 3.57 mm yr-1 in high flat environments; 11.92 ± 9.73 mm yr-1 in low marsh environments; and 1.88 ± 2.54 mm yr-1 in low flat environments. There was a significant difference in vertical accretion rates between both horizon markers and erosion pins, which provide annual-scale accretion rates, when compared to 137Cs, which provide decadal-scale accretion rates (p < 0.1). On average annual vertical accretion rates were 2.8 times higher than decadal rates. Differences between annual and decadal accretion rates are mostly attributed to shallow sediment compaction within the top 3 cm of the wetland surface. Variation in wetland vertical accretion rates increased significantly going from decadal (± 0.41 mm) to annual (± 2.87 mm) to annualized biweekly rates (± 9.60 mm). Annual-scale accretion rates measured using horizon markers in low marsh and upland environments appear to be keeping up with relative sea level rise (RSLR), which is 5.27 ± 0.48 mm yr-1 as measured since the 1950’s at a nearby tide gauge. However horizon marker vertical accretion rates in tidal flats and high marsh environments are not sufficient to overcome sea level rise. Vertical accretion rates were positively correlated with organic and inorganic accretion for all horizon markers (p < 0.1); however, the relative contribution of organic matter decreases as inorganic matter increases. Our findings anticipate environmental shifts in habitats with accretion rates below RSLR. Furthermore, vertical accretion was dominated by inorganic matter, making the wetlands reliant on constant wind and episodic storms to transport sediment to the area. Importantly, these data suggest that storm-induced sedimentation acts to stabilize coastal wetlands and helps certain environments cope with RSLR, but is not sufficient to prevent shifts in the relative composition of the wetland.Item Assessing the acute toxicity of photodegraded anthracene with in vitro and in vivo skin models(2022-07-20) Brzezinski, Molly; Xu, Wei; Seemann, Frauke; Conkle, Jeremy; Zhu, LinThe Gulf Coast of Texas is heavily inundated with petroleum refineries that release Polycyclic Aromatic Hydrocarbons (PAHs) into nearby waters, and these chemicals may pose a threat to human health when they interact with environmental conditions. PAHs are a group of hundreds of different chemicals, and the Environmental Protection Agency has identified 16 priority PAHs. Many of these chemicals are acute skin irritants and can cause skin, lung, bladder, and liver cancer with chronic exposure. Humans can be exposed when they interact with contaminated air, soil, and water. Recent studies have demonstrated that abiotic factors such as UV light, salinity, and pH can modify PAH structure, however, it is unknown how these modifications affect acute toxicity to the human skin barrier. The objectives of this study were to characterize the phototoxic effects of a priority PAH, anthracene by testing photodegradation treatments on cell culture and animal models. Gas chromatography and mass-spectroscopy confirmed the presence of 1,9-anthraquinone and phthalic acid, both known skin irritants, in photodegradation products. Keratinocyte cell culture was used to assess the impacts of photodegraded anthracene on cell migration, viability, and stratification development. We found that longer photodegradation times resulted in decreased cell viability and increased migration. A unique three-dimensional stratification assay demonstrated that photodegraded anthracene reduces differentiation in apical keratinocytes. Relative gene expression analysis suggests that keratinocytes bypass TLR-4 activation and utilize IL-1?, IL-1?, and TNF-? to produce an inflammatory response. Mus musculus studies indicate that extracellular matrix remodeling may be induced by 4, 8, and 24-hour photodegraded intermediates by keratinocyte-derived Il-1?, S100a9, Mmp1, and Connexin43. The results of this study indicate that photodegradation can produce intermediates that may elicit dermal inflammation, and the presence of these intermediates should be evaluated in bays with high foot-traffic.Item Assessing the influence of genotypic diversity on sulfur dynamics in the seagrass halodule wrightii using stable isotope analysis(2022-07-19) Girard, Allyson; Larkin, Patrick; Abdulla, Hussain; Felix, JosephCoastal development and other mounting anthropogenic pressures are threatening valuable seagrass habitats. The greatest risks posed to seagrasses are the effects of coastal eutrophication, which stimulates primary productivity and ultimately supplies abundant organic matter to marine sediments. The decomposition of this material is initially facilitated by aerobic microorganisms, depleting dissolved oxygen and generating anoxic conditions. Under these conditions, anaerobic microorganisms such as sulfate-reducing bacteria begin to dominate the degradation process, which reduce sulfate (SO42-) to sulfide (H2S) for energy production. The accumulation of H2S in marine sediments is problematic for seagrasses, as this molecule can be highly toxic. Yet, seagrasses can withstand relatively high concentrations of H2S in their environments. Stable isotope analyses have been used to investigate sulfide intrusion in seagrass meadows, as the unique isotopic signature of sediment-derived sulfur can be used to trace the uptake of H2S and its distribution throughout the plant. This technique has allowed the study of factors that may influence sulfide production and intrusion, such as reduced light availability, organic matter enrichment, and high temperatures. However, few studies have examined the biological or biochemical features that enable seagrasses to withstand relatively high sedimentary sulfide levels. One biological feature that may help confer resistance is population genetic diversity, which has been identified as an important trait in the survival and performance of seagrass meadows under environmental stress. In general, genetic diversity is thought to play an important role in population resistance to environmental disturbance, as a wider assortment of functional traits encoded at the molecular level results in a variety of phenotypes likely to possess morphological and physiological differences that are complementary. This genotypic complementarity may extend to biochemical strategies associated with tolerance to, or detoxification of, H2S. The purpose of this study was to determine whether sulfide intrusion differs between genotypes of the seagrass Halodule wrightii, a prominent species in the Gulf of Mexico. Further, as the sulfur isotopic composition of marine sediments and seagrass vegetation is known to exhibit high spatial variability, this study also sought to assess sulfide intrusion between populations from distinct sites along the Texas Gulf Coast. Stable isotope data was used to infer the proportion of sulfur in H. wrightii tissues that was derived from sedimentary sulfide, while total sulfur (TS) data was also considered to understand the extent of sulfur accumulation within the plant. H. wrightii genotypes were determined by screening each sample at a series of microsatellite loci previously identified for this species. Although no difference in sulfide intrusion was observed between genotypes, sulfide uptake and distribution was significantly different between the three study sites. The results offer important insight to the effect of local conditions on sulfide intrusion in seagrass meadows and may guide future investigations concerned with the influence of genotypic diversity on H2S metabolism in seagrasses.Item Assessment and valuation of nitrogen mitigation ecosystem services in natural and restored wetlands of the Texas coastal bend(2020-05) Hayes, Lydia; Hayes, Lydia; Zhang, Lin; Williams, Lauren; Zhang, Lin; Williams, Lauren; Reese, Brandi; Reese, Brandi K.Eutrophication leads to poor water quality, hypoxia, and biodiversity loss in aquatic ecosystems, which is a major issue in the Gulf of Mexico and its surrounding estuaries. It is largely caused by excess nutrients in aquatic environments. With population rising along the Texas coast, there is an increase in nitrogen-based nutrients output, through wastewater and agricultural runoff. It is critical to reduce nutrients input to nitrogen-limited waters to improve water quality and eliminate eutrophication. Wetlands are important ecosystems that offer many ecosystem services including nitrogen mitigation. Denitrification is the main pathway for removing excessive nitrogen-based nutrients in wetland sediments. In this study, nitrogen mitigation was quantified through potential denitrification measured in five wetland sites, two restored and three natural ones. Our results showed that the age of wetlands is a major factor regulating denitrification rates, with lowest average annual rates found in two restored sites, Egery Flats and the Nueces Bay restored marsh (11.46 and 10.85 kg N∙ha-2∙yr-1, respectively). Significantly higher rates were found in natural wetland sites, with mean annual rates of 22.5, 29.39, and 39.27 kg N∙ha-2∙yr-1 measured for the Aransas River Estuary, Oso Bay marsh, and the Naval Airbase Bridge, respectively. Temperature was another influencing factor for denitrification rates in three of the five sites. The seasonal denitrification rates measured in this study were used to quantify the economic value of nitrogen mitigation ecosystem services in the two restored wetland sites. The replacement cost was $36,565∙yr-1, and $8,125∙yr-1, for Egery Flats and Nueces Bay restored marsh, respectively, which is an equivalent value of $13.55∙kg N-1 removed.Item An assessment of seagrass evolutionary diversity in the Anthropocene(2021-08) Rock, Brianna Marie; Daru, Barnabas H.; Proffitt, Ed; Larkin, PatrickSeagrass meadows provide enormous ecosystem goods and services, ultimately establishing complex coastal habitats that support diverse collections of marine organisms. However, the future of seagrass communities under rapid shifts in climate in the Anthropocene—a period of pronounced human impact on biotic communities—has recently been questioned. Uncertainties from sampling biases present challenges to ecologists and evolutionary biologists in understanding species sensitivity to anthropogenic climate change. Here, we synthesize possible impediments that can constrain research to assess present and future seagrass responses to climate change. First, our knowledge of seagrass occurrence information is prevalent with biases, gaps and uncertainties that can influence inferences on species’ response to global change. Second, research on seagrass diversity has been focused on species-level metrics that can be measured with data from the present - but rarely accounting for the shared phylogenetic relationships and evolutionary distinctiveness of species. Third, compared to the mass production of species occurrence records, computational tools that can analyze these datasets in a reasonable amount of time are almost non-existent or do not scale well in terms of computer time and memory. These impediments mean that scientists must work with incomplete information and often unrepresentative data to predict how seagrass diversity might change in the future. In chapter one, we discuss these shortfalls and provide a framework for overcoming the impediments and diminishing the knowledge gaps they generate. Although climate change projections indicate significant threats to terrestrial biodiversity, shifts in species composition in marine environments might be equally profound. Here, we also explore how different facets of α-diversity (i.e., within all seagrass communities globally) and β-diversity (i.e., between seagrass communities) of seagrasses may respond to future climate change scenarios across the globe and compare them with the existing network of marine protected areas. By utilizing ensemble species distribution modeling under various scenarios of climate change, we observe widespread decreases in seagrass weighted endemism on a global scale. This projected loss in seagrass endemism will result in decreases in β-diversity within temperate regions resulting in the homogenization of seagrass communities in these regions. Regardless of the climate scenario, the hotspots and cold spots of these projected shifts in seagrass α- and β-diversity are predicted to occur outside the current network of marine protected areas, suggesting that these marine protected areas will be insufficient to safeguard the future of seagrasses. Our findings report species’ response for a group underrepresented in climate change assessments yet crucial in maintaining marine food chains.Item Assessment of Sulfide Intrusion and Genotypic Diversity in the Seagrass Halodule Wrightii from the Texas Gulf Coast(2019-12) Rubiano-Rincon, Sebastian; Larkin, Patrick D.; Coffin, Richard; Hu, XinpingSeagrasses are marine angiosperms that provide key ecological services to coastal areas. Unfortunately, seagrasses are experiencing a progressive decline, driven by natural and anthropogenic stressors, including sulfide (H2S) intrusion from high sediment sulfide concentrations. Seagrasses cope with sulfides through avoidance (reoxidation in the sediment) or tolerance (assimilation by tissues). Previous studies also suggested that seagrass response to environmental stress can be influenced and benefit from having genotypic (clonal) diversity. Although these mechanisms have been studied in some species, few have examined sulfide intrusion and its relation to genotypic diversity in seagrasses from the Texas Gulf Coast. In this study, we used stable sulfur isotopes and a microsatellite-based DNA marker assay to assess sulfide intrusion in the seagrass Halodule wrightii and investigate whether genotypic diversity plays a role in its response to sulfide stress. We found a gradient in δ34S values (-5.58 ± 0.54‰ to 13.58 ± 0.30‰), from roots to leaves, suggesting that H2S enters through underground tissues and is then distributed throughout the plant. The presence of sulfide-derived sulfur in varying proportions (15% to 76%) among the leaf, rhizome and root tissues indicates they are able to assimilate it into non-toxic, metabolic forms. Although sulfide intrusion did not significantly vary among the different genotypes (P > 0.05), this seagrass population had signs of being genetically diverse, indicating that it has the necessary genetic material to face and resist environmental stress. We hope that this study serves as the basis for further exploration of the genetics of sulfur assimilation and metabolism in seagrasses.Item Associations between chlorophyll and wind forcing in the Gulf of Mexico derived from satellite observations(2015-08) Trnka, Maureen C.The Gulf of Mexico supports many industries that rely on its natural resources. Primary production is required to sustain fish populations and contributes to ocean carbon exchange. Ocean color satellites make it possible to observe large geographic areas; however, an individual sensor has limited coverage. The GlobColour project merges observations from multiple satellites into a single product. The purpose of this study is to use GlobColour and QuikSCAT to investigate the seasonal and non-seasonal associations between chlorophyll and wind from 2000-2008 in the Gulf of Mexico. An overview of the Gulf of Mexico’s physical setting, circulation, and main features is presented. The Gulf is divided into: Interior Basin, West Florida Shelf, Louisiana-Texas Shelf, Tamaulipas-Veracruz Shelf, Bay of Campeche, and Campeche Bank. Phytoplankton biomass is discussed in the context of nutrient-transport mechanisms including coastal upwelling, Ekman pumping, horizontal advection, and vertical turbulent mixing. Seasonal associations are evaluated between chlorophyll and wind using Empirical Orthogonal Functions and Singular Value Decomposition. Chlorophyll has strong seasonal variability over the shelves. The interior variability of chlorophyll and wind speed is in-phase with annual periodicity, increasing in winter and decreasing in summer. Strong winter winds increase the upward turbulent transport of nutrients into the mixed layer. The northern chlorophyll variability has a dipole with increased anomalies over the Western Shelf and decreased anomalies around the Mississippi mouth; associated with intensified easterly winds. Non-seasonal anomalies of chlorophyll and wind are similarly investigated. Increases in wind speed are associated with chlorophyll increases over the Campeche Bank, Bay of Campeche, and West Florida Shelf; the mechanism is upward entrainment of nutrients by turbulent mixing. Northerly winds are associated with coastal upwelling in the Bay of Campeche, offshore advection in the west, and a chlorophyll dipole across the Mississippi mouth. The non-seasonal coupled patterns are predominantly intraseasonal and spatially coherent with interannual modulations. This study is the first to apply a merged ocean color product to research in the Gulf of Mexico. Overall, this project provides baseline information on the seasonal and non-seasonal variability of chlorophyll and winds, identifies statistical associations, and proposes dynamical mechanisms.Item Beach geomorphology and Kemp’s Ridley (lepidochelys kempii) nest site selection along Padre Island, Tx, USA(2018-05) Culver, Michelle F.; Gibeaut, James C.; Starek, Michael J.; Tissot, Philippe; Shaver, Donna J.The Kemp’s ridley sea turtle (Lepidochelys kempii) is the most endangered sea turtle species in the world, largely due to historic take of eggs at the primary nesting beach in Mexico, loss of juveniles and adults incidental to fisheries operations, and the limited geographic range of its nesting habitat. In the USA, the majority of nesting occurs along Padre Island in Texas. There has been limited research regarding the connection between beach geomorphology and Kemp’s ridley nesting patterns, but studies concerning other sea turtle species suggest that certain beach geomorphology variables, such as beach slope and width, influence nest site selection. This research addresses the literature gap by quantifying the terrestrial habitat variability of the Kemp’s ridley and investigating the connection between beach geomorphology characteristics and Kemp’s ridley nesting preferences on Padre Island, Texas, USA. Beach geomorphology characteristics, such as beach slope and dune peak height, were extracted from airborne topographic lidar data collected annually along the Texas coast from 2009 through 2012. The coordinates of observed Kemp’s ridley nests from corresponding years were integrated with the geomorphic data, which was then statistically analyzed using generalized linear models and random forest models. These models were successful in predicting Kemp’s ridley nest presence. The top generalized linear models explained 40-46% of nest presence variability with a relatively low prediction error. The final random forest model was superior in performance in comparison to the generalized linear models, with a true positive rate above 85%. Nest elevation, distance from shoreline, maximum dune slope, and average beach slope were the significant variables in the top two generalized linear models and the relatively most important variables in the random forest model, with elevation and distance from shoreline being the most influential in each. Kemp’s ridleys nested at a median elevation of 1.04 m above mean sea level and a median distance from shoreline of 12.79 m, which corresponds to the area directly below the potential vegetation line, which is defined as the lowest elevation where dune plants may persist. Kemp’s ridleys also exhibited a preference for a limited range of the study area and avoided nesting on beaches with extreme values for maximum dune slope, average beach slope, and beach width. This study provides new information regarding Kemp’s ridley terrestrial habitat and nesting preferences that have many applications for species conservation and management.Item Behavior of popular indices of genetic diversity in simulated expanding populations(2022-05) Bynum, Adam; Bird, Christopher E.; Sterba-Boatwright, Blair; Portnoy, DavidProtecting genetic diversity is an integral component of food security, fishery management, and biodiversity conservation, and thus the ability to model and predict the distribution of genetic diversity is valuable. Population genetic theory predicts that genetic diversity will be greatest in the largest populations at mutation-drift equilibrium, implying that efforts to preserve diversity would be best focused on keeping populations as large as feasibly possible. Natural populations, however, are rarely in equilibrium, because their sizes can fluctuate due to a variety of processes, e.g., populations that have had a recent bottleneck or invaded a new habitat. To predict patterns of genetic diversity in natural populations, it has become increasingly important to understand how populations behave in non-equilibrium scenarios. Here we report the effects of mutation rate (µ), initial population size (Ne0), and final population size (Ne1) on the genetic diversity in expanding populations using a Wright-Fisher forward time model built with SLiM2. Using a 300 bp sequence to simulate modern genome-wide surveys of genetic variation (RAD), a range of naturally occurring mutation rates, and population sizes, multiple models were created to cover a broad portion of parameter space, and six commonly reported measures of genetic diversity estimated. As previously reported, genetic diversity increased with increasing population size given a similar set of circumstances, but there are broad swaths of parameter space where small populations exhibit greater diversity than large populations, making historical context critical in population genetics analysis. Depending on population size and mutation rate, the different diversity indices (nucleotide diversity, gene diversity, number of haplotypes, effective number of haplotypes, number of heterozygotes, and number of substitutions) progressed towards equilibrium at different rates. Furthermore, different diversity indices had different levels of sensitivity to changes in diversity at different times. To better describe the change in diversity with time, logistic growth models were used to estimate the equilibrium diversity (Deq), initial diversity value (D0), amount of time required to reach halfway to genetic equilibrium (t50eq), growth parameter (Φ3), maximum rate of genetic diversity increase (r), and time required to reach 95% of the equilibrium value (t95) in populations that expand from Ne0 to Ne1. We employed both linear and non-linear model fitting and used AIC to identify the best models describing the logistic growth parameters with varying Ne0, Ne1, and µ. In most cases, the models fit the simulated data well as the relative bias is low, ranging from +/- 3%, but the models did not perform as well when Ne0, Ne1, and µ, are small, with relative bias as high as 20%. The best models were used to create a tool that estimates the diversity of a population given the time since the onset of expansion, Ne0, Ne1, and µ. The prediction model performed best when using the Ne0, Ne1, and µ used in the simulations but could give misleading diversities when interpolating, so a switch was created to restrict the tool to only accept the predefined set of parameter values. This tool can be used to get a rough approximation of how long it will take for genetic diversity to accumulate and determine why there might be deviations from the neutral expectation that large populations have more diversity without running time consuming simulations and subsequent analysis.Item Behavioral condition of red drum Sciaenops ocellatus fingerlings exposed to habitat structures and predators in rearing ponds(2017-08) Schacht, Tyler Hans; Withers, Kim; Vega, Robert R.; Scarpa, John; Proffitt, CharlesStock enhancement programs strive to propagate fish similar to their wild counterparts, but hatchery-reared fish are often deficient in their ability to detect and avoid predation. The objective of this study was to determine if the provision of complexly structured habitat would improve post-stocking survival of hatchery-reared red drum, Sciaenops ocellatus, when exposed to free-roaming predators. Experiments were conducted in 0.2 ha rearing ponds between July and December 2016 at the Coastal Conservation Association Marine Development Center in Corpus Christi, Texas. Three habitat treatments (non-vegetated [normal rearing], artificial seagrass, and artificial seagrass with predator exclusion cages) were used to assess if habitat complexity influenced growth and condition. Fish growth (TL) was affected by trial (i.e., seasonality; P < 0.0001) but not by treatment (P = 0.178). After rearing to the fingerling stage (36 days post-hatch), survival from predation was assessed by exposing red drum to free-roaming predators (pinfish, Lagodon rhomboides) in experimental “wild” ponds (0.2 ha) with artificial seagrass for 24 hours. In two trials, fish condition (K) differed significantly among treatments (P<0.0001) and was lower in the artificial seagrass treatment with predator exclusion cages compared to the other treatments. Red drum may have been more active and vigilant (“leaner”) when exposed to caged predators, while the fish in the unstructured habitat led a more sedentary life (“fat”). Overall, when exposed to free-roaming predators in a “wild simulation” fish reared in ponds with the addition of structured, complex habitat survived better. The results of this study suggest that the provision of complexly structured habitat improved behavioral mechanisms (i.e., foraging, predator-avoidance) that may increase post-release survival of hatchery-reared red drum.Item Benthic macrofauna community response to salinity in the San Antonio and Matagorda Bay systems, Texas(2017-05) Ehrmann, Hannah; Montagna, Paul A.; Pollack, Jennifer Beseres; Sterba-Boatwright, BlairThe aim of this study was to quantify the effects of salinity on ecosystem health in Matagorda and San Antonio Bay systems, using benthic macrofauna communities as biological indicators of ecosystem integrity. Benthic and discrete water quality samples were taken monthly at five stations in the San Antonio and Matagorda Bays. Benthic macrofauna community dynamics were linked to salinity to infer the effects of freshwater inflow on the estuarine biotic communities. The benthic communities were classified into two groups based on different salinity habitat zones when salinity was above or below 11. Benthic metrics were significantly correlated with salinity, one-month lag, or two-month lag salinity in all bays. Peak abundances were observed in Carancahua and San Antonio Bays when salinities were 5 and 7 respectively, and peak diversity was observed in San Antonio Bay when salinity was 4. Diversity (Hill’s N1) increased throughout the salinity gradient in Tres Palacios and San Antonio Bays, as did abundance in Tres Palacios Bay. Overall, salinity was a driving factor for these communities. There is a need for hydrological restoration in many areas, and resources for restoration have been made available by the RESTORE Act. However, only small flows may be available to be set aside to maintain ecological health. The present study gives evidence that benthic communities are supported by low salinity habitats within the upper reaches of the San Antonio and Matagorda Bay Systems.Item Biological productivity associated with the serpulid reefs of Baffin Bay, Texas(1997-08) Hardegree, Beau; McKee, David A.; Prouty, Jennifer S.; Tunnell, John W.; Dunton, Kenneth H.The upper Laguna Madre and Baffin Bay-complex has long been noted for its abundant finfish populations despite its generally persistent hypersaline condition. The purpose of this present study was to determine the contribution of the serpulid worm reefs to the productivity of Baffin Bay. The primary focus of this thesis was to test the hypothesis that fish were larger and found in higher concentrations near the serpulid worm reefs in Baffin Bay, and to quantify the abundances of potential prey items associated with the reefs. In addition, I measured the productivity (by O2 evolution) of the epiphytic algae growing on the reefs and compared it to published seagrass studies in the upper Laguna Madre. Lastly, I examined the dependence of consumers on carbon fixed by these primary producers using stable carbon isotope ratios as tracers. A total of 5,396 individuals representing 35 fish species, were collected by trammel net during the study. Seven fish species (Mugil cephalus = 27.3 o/q Pogonias cromis = 20.2 %, Cynoscion nebulosus = 15.2 %, Leiostomus xanthurus = 12.1 %, Arius felis = 10.7 %, Lagodon rhomboides = 2.3 %, and Sciaenops ocel/atus = 1.1 %) comprised 89.0 % of the total catch. The overall ichythyofaunal catch rate was not significantly different between reef and non-reef sites and only a seasonal effect in the catch rate data was observed. Seasonal differences can be explained by the recruitment of fish into the bay in Spring and Summer. These seasonal peaks can be attributed to three species: Arius felis, Pogonias cromis, and Leiostomus xanthurus. No strong evidence was found to support the hypothesis that larger fish congregate around the serpulid worm reefs.Item Biomimetic iron complexes for the oxidation of C-H bonds in hydrocarbons(2021-12) Le, Uyen; Prakash, Jai; Billiot, Fereshteh; Holubowitch, NicolasWith the rapid growth in transportation and industry, petroleum and other types of fossil fuels (coal, heavy oil) are heavily used for energy production. The consumption of these types of energy resources pose a serious environmental concern because of the production of greenhouse gases such as carbon dioxide, methane, nitrous oxide, and chlorofluorocarbons (CFCs) which are the primary reasons for climate change. This makes the development of cheaper and cleaner energy more important in modern society. Conversion of methane into liquid fuel such as methanol has become a promising goal for future petrochemical derivatives and decreasing petroleum dependence. Methane is the primary component of natural gas which is highly abundant on earth. Methane is used as a raw material to produce methanol which is further used as fuel to generate electricity. However, the conversion of methane into methanol is carried out at high temperature and pressure and this process is energy consuming. This makes methane oxidation catalysts high in demand. In recent decades, transition metal complexes have proven to be efficient and powerful catalysts for various oxidative transformations. Specifically, mononuclear and di-nuclear metal complexes now are widely applied as catalysts for the oxidation of organic substrates and water. Transition metals such as Mn, Fe, Co, Ni and Cu have been recognized as cheap, environmentally friendly and effective catalysts for C-H activation. Specifically, iron is the most attractive metal because it’s very inexpensive (most earth-abundant transition metal), displays high oxidation states (required in catalysis), and is relatively non-toxic. In this research, we will design and develop routes for synthesizing iron complexes that can serve as cheap and efficient catalysts for methane oxidation (or C-H activation). This is the foundation for future research aiming at converting inert hydrocarbons into useful petrochemical derivatives.