SHORT ORAL PRESENTATIONS
Development of an Autonomous Unmanned Surface Vehicle (USV)
Nolan Bell, Anjin Chang, Jordan Upshaw
In recent years, it has been challenging to monitor inaccessible areas, such as underwater, even though it can provide important and useful information in the fields of environment, ecology, and engineering. In this research study, an advanced Unmanned Surface Vehicle (USV) was developed to collect data more efficiently and safely in the water system. The USV platform is designed to operate for extended mission duration, allowing for large areas to be monitored autonomously. We adopted a catamaran with two parallel hulls of equal size as the body frame. Two motors were mounted on masts at the back of each hull for propulsion and steering by differential thrust. The propellers were installed above the water surface so that the UAV can be operated in extremely tough environments. A Pixhawk Cube with GPS was adopted to conduct autonomous operations. The advantages of the UAV is that it is capable of being scaled up or down easily and can mount different sensors for various underwater applications, such as image/video capturing, inspecting facilities, and 3D modeling.
Dermal exposure risk of Photodegraded Polycyclic Aromatic Hydrocarbons
Molly Brzezinski, Wei Xu, Leisha Martin
The community of Corpus Christi shares a coastline with a sprawling petroleum industry and is at risk of environmental exposure to a variety of petrogenic chemicals. Polycyclic Aromatic Hydrocarbons (PAHs) are a diverse group of pyrogenic and petrogenic chemicals that result from wild-fires, automobile exhaust, and oil refining processes. These chemicals are ubiquitous in areas of heavy industry and 16 high priority compounds have been identified by The US Environmental Protection Agency (US EPA) for their bioaccumulation and carcinogenic effects in occupational settings. UV radiation can enhance toxicity to aquatic organisms, however, we don’t yet understand if concurrent environmental conditions like sunlight and seawater can enhance acute toxicity with dermal exposure. Therefore, our study will use solar simulation to degrade 16 priority PAHs at environmentally relevant salinity and pH to test the effects on skin barrier function, direct cellular toxicity, and secondary cellular responses of the skin. We will use a 2D and 3D human skin cell culture approach and anticipate that each chemical will elicit a degradation dependent effect on cell migration and cytotoxicity.
Molecular assessment of environmental pollutant exposure during crucial innate immune system development windows in marine medaka (Oryzias melastigma)
Elizabeth DiBona, Marissa Brown, Frauke Seemann
The innate immune system is critical for pathogen defense, organism homeostasis and tumor suppression. Despite being a prominent target for environmental pollutants quantification of immune compromise is challenging due to complex interactions of multiple pathways. In-line with the ‘Developmental Origins of Health and Disease’ (DOHaD) hypothesis evidence is increasing that exposure to toxicants during critical phases of immune system development is associated with later-life immune disease susceptibility. Marine medaka (Oryzias melastigma) has previously been highlighted as a model for developmental immunotoxicity and critical developmental windows assessment. However, knowledge of onset and functionality of innate immune parameters such as, immune initiators (C1q, MBL, TLR-3, TLR-5, TLR5-soluble), mediators (IL-1β, MYD88, M-CSF), and effectors (LYZ) is still missing. To assess occurrence and functionality of selected innate immune genes, gene expression has been assessed during embryonic development (5-11 days post fertilization) with/without pathogen challenge. Results indicated a potential critical window of innate immune development between the oldest age group, 11 dpf, and 7 dpf. Observations of significantly decreased expression in 11 dpf when compared to 7dpf in the control group for immune initiators (C1q, TLR5-soluble) and immune mediators (MYD88, M-CSF) support this proposed critical window. Significant decreased expression of an immune initiator (C1q) for 11dpf compared to 7 dpf was also observed in the challenged group. Immune effector (LYZ) had a reverse trend of increased expression in 11 dpf compared to 5 dpf in the control group, indicating another potential critical window between 5 dpf and 11 dpf. The identification of molecular markers for developing innate immune response provides the baseline to identify susceptible developmental pathways and stages. Subsequent exposure experiments targeting these critical innate immune system development stages combined with later-life stage immunocompetence assessment will provide a high-throughput toolbox to assess immunotoxicity of common environmental pollutants.
Corals thriving in dynamic environments may hold key insights into future coral reefs
Ashleigh Epps, Keisha Bahr
Mystery corals found in the coastal bend could provide researchers with the insight they need to understand coral adaptation in the midst of climate change. The Texas coastal waters have dynamic, fluctuating environmental conditions and are heavily influenced by anthropogenic stressors; therefore, are not considered optimal conditions for corals. Nonetheless, cryptic coral species (Astrangia poculata and Oculina diffusa) have been documented in this ecosystem. This research aims to explore the strategies coastal bend corals utilize to cope with dynamic fluctuations in environmental conditions. We conducted extensive surveys throughout the coastal bend to document the environmental variability and potential survival strategies of these cryptic corals. Environmental data collection (i.e., temperature, salinity, etc.) was measured weekly by season followed by plankton tow surveys during the highest tide and lowest tide of the full moon cycle. Stable isotope analyses of coral tissue was processed to understand the feeding strategies used to overcome the dynamic fluctuations in the coastal waters. Corals were collected seasonally (n=16) and tissue extraction occurred to conduct stable isotope analyses, chlorophyl measurements, and zooxanthellae counts. It is hypothesized that during the summer months (i.e., June and July), autotrophy will be the primary feeding mechanism. When primarily autotrophic, the coral tissue isotope carbon (δ13C) ratios should be higher in comparison to the nitrogen (δ15N) ratios. Concurrently, plankton biomass observations will show higher abundance in phytoplankton than zooplankton. In the winter months (i.e., November and February), it is hypothesized heterotrophy will be the primary feeding mechanism, in which observations should shift to favor heterotrophic conditions. Understanding how corals exist by observing their nutritional intake in extreme environmental conditions could provide insights into potential phenotypic plasticity and adaptability to anthropogenic influence. These conclusions could support future coral reef conservation and management strategies where the adaptability of corals could lead to the restoration of degraded reef ecosystems.
Think globally, act locally: A risk and resilience assessment of coral reef watershed quality in Kāne‘ohe Bay, Hawaiʻi
Alexandra Good, Keisha Bahr
Human activity on land contributes to adverse consequences in the sea; therefore, land management actions could enhance coral reef resiliency. Over 60% of coral reefs are negatively affected by local human activities, and a land-to-sea approach is widely used to mitigate stressors at a local scale. Across the Hawaiian Islands, there is a significant positive relationship between watershed health and the adjacent reef. Coral reefs surrounding areas with high human population density are suffering from compromising sedimentation levels due to coastal development and land alteration. However, there is an extensive research gap in how key species respond to land-based sedimentation and how the impact will cascade with increased human pressure. Previous research in Hawai’i proved coral biological response to increased temperature and acidification levels is species-specific, and generalizations regarding community response to environmental change will not lead to effective conservation. Using the land-to-sea approach, this project aims to quantify the differences in the species-specific tolerance thresholds of Montipora capitata from two different watersheds in Kāneʻohe Bay, HI (low-impact vs. high-impact). This research aims to quantify the future anthropogenic influence on M. capitata by evaluating the interaction of local sedimentation and global ocean warming stressors at the organismal level. Due to our rapidly changing climate, predicting how future environmental parameters will affect critical reef-building species’ resiliency will generate efficient restoration and conservation of these critical ecosystems. This study will provide a substantial dataset for further developing models evaluating the future impact of local and global environmental stressors on coral reefs worldwide.
In silico computational chemistry to predict accessible and reactive areas for Benzo[a]pyrene metabolites in nucleosomes and DNA
Remi labeille, Frauke Seemann, Kelda Flores, Anthony Fieramusca, Erik Gonzalez
Benzo[a]pyrene (BaP) and its metabolite benzo(a)pyrene-7,8-dihydrodiol 9,10-epoxide (BaP-DE) have been observed to induce transgenerational bone impairment in fish through epigenetic profile modifications in the germ cells. It is hypothesized, that both DNA methylation and histone tail modifications are contributing factors to generate the observed transgenerational phenotype. To determine DNA loci and nucleosome molecule structures susceptible for BaP-DE binding, and subsequent changes of DNA methylation and histone tail modifications, a holistic in silico computational chemistry pipeline has been developed:
a) To provide insight how binding affinity to DNA hotspots will impact the DNA structure and gene expression, DNA methylation at CpG islands is analyzed for BaP-DE binding affinities. Model DNA sequences are created with Avogadro, using CG and AT base pairs alone and in combination to characterize the interaction and affinity with BaP-DE using AutoDock Vina and Abalone. Top-ranked sequences for binding will be analyzed for conformational changes impacting DNA re-/de-methylation, and thus, subsequently modifying gene expression.
b) To assess possible BaP-DE binding sites at the histone tails H3 and H4 and interference with post-translational modification (PTM) the software AutoDock Vina was employed. The BaP-DE/histone tail complexes are then examined for conformational and functional changes which may affect gene expression, using the molecular dynamics package (hybrid Monte Carlo approach) available in Abalone software.
Together, these in silico computational chemistry analyses will allow to identify priority sites for study in germ cells and osteoblasts in the biological Medaka fish model and enhance the understanding of epigenetic mechanisms involved in transgenerational inheritance.
Role of miRNA regulation in Benzo[a]Pyrene- induced bone deformities in Medaka fish
Rijith Jayarajan, Frauke Seemann, Ethan Constantine, Remi Labeille
Benzo[a]Pyrene (BaP) is an ubiquitously detected polycyclic aromatic hydrocarbon in the environment. It has been demonstrated that BaP can cause bone deformities in a transgenerational manner in Medaka fish (Oryzias latipes). Ancestral BaP exposure has been shown to alter the expression of microRNA (miRNA) - target gene pairs during bone development. In this study, a microinjection-based approach was used to screen the key microRNAs (miR214, miR199a, miR210) involved in BaP-induced skeletal defects. Custom made oligonucleotides for agonists and antagonists of each miRNA were injected at 3 days post fertilization (dpf). To visualize developmental changes, the calcified bone area and calcification intensity were assessed every third day until 30dpf in the control, miR-agonist, and -antagonist groups. A reduced bone calcification was observed upon miR199a agonist injection at 27/30dpf, indicative of its role during late bone development. miR214 agonist injection resulted in a significant difference calcification in the posterior vertebrate region at 9/12dpf which reveals the effect of this miRNA during early bone development. Injection of miR210 agonist or antagonist did not reveal any changes in bone calcification, but a high mortality rate was observed in miR210 injected fishes after 12dpf. The results indicate that increased concentrations of miR199a and miR214 may have a key role in transgenerational BaP-induced bone toxicity. The present study highlights two different developmental time points potentially crucial for normal bone development in vertebrates. Follow-up experiments will address molecular and cellular changes induced by overexpression of these two miRs.
Coastal cities seen as socio-ecosystems systems: challenges and opportunities in the face of climate change
Ulsia Marino, David Yoskowitz
This study analyzes the cities of the Gulf of Mexico as a socio-ecosystems system. This conceptual and methodological framework makes it possible to identify the threats and risks that coastal cities face as a result of the climate change, in particular, from the perspective of urban planning and management, where coastal ecosystems through the provision of ecosystem services and nature-based solutions can help to undertake adaptation and mitigation actions. This study is in the phase of identifying the conceptual and methodological framework. However, it proposes a working hypothesis, research questions, and some characteristics to select the coastal cities to analyze in Mexico, Cuba, and the USA: one in each country.
Assessing the effects of nocturnal training on long-term memory in the marine snail Aplysia californica
Robert Mueller, Riccardo Mozzachiodi
Long-term memory (LTM) is known to be modulated by circadian rhythms across different species. Previous research in the marine snail Aplysia californica revealed that circadian rhythms regulate a form of learned fear called long-term sensitization (LTS), which occurs in response to training with repeated aversive stimuli (Kandel 2001; Fernandez et al. 2003). LTS manifests as an increase in the duration of the defensive tail-siphon withdrawal response measured 24 hours after training. LTS is known to be regulated by the time of the day when animals receive training. Aversive training protocols conducted during the daytime (5 pm) induce robust LTS, whereas nocturnal training (11 pm) does not induce LTS (Fernandez et al. 2003). In addition to LTS, aversive training also alters an appetitive behavior by decreasing the animal’s motivation to feed. This decreased feeding motivation is measured 24 hours after training as long-term feeding suppression (LTFS; MacLeod et al. 2018). Unlike LTS, it is unknown whether LTFS is also modulated by circadian rhythms. This project will investigate whether nocturnal training affects the expression of LTFS similar to LTS by utilizing three different experimental groups; a diurnal trained group (5 pm), a nocturnal trained group (11 pm), and a control group (no training). If nocturnal training is not conducive for LTFS, this result would suggest that LTFS and LTS share common mechanisms. However, if LTFS is shown in the absence of LTS, this result would suggest that LTFS and LTS may be modulated by different mechanisms for LTM formation and retention.
Trophic niche responses to hypoxia and contaminant stressors in coastal fishes
Jacob Oster, Benjamin Walther
Recreational and commercial fisheries are important resources for coastal communities and estuaries provide important habitat for these fisheries, but if we don’t account for sub-lethal effects of disturbances, such as hypoxia or mercury in estuaries, we may overestimate the health of coastal fisheries. Anthropogenic stressors in coastal ecosystems, such as eutrophic hypoxia, are projected to increase in frequency and duration in the upcoming century. Long-term consequences of such stressors at sub-lethal levels are not well characterized at the species level and community level. These stressors could have interactive effects that may increase the susceptibility of organisms to other stressors, such as methylmercury; reduce their niche variation; and change links within food webs Therefore, I am using long term biomarkers in three coastal fish species to study sub-lethal disturbances. This work will use manganese:calcium ratios in otoliths to approximate lifetime exposure to hypoxia and mercury concentrations in eye lenses to assess lifetime exposure to mercury. To assess how these stressors impacted the individual, the condition factor and stable isotope ratios within muscle and liver will be measured to indicate changes in growth rate, fecundity, and trophic interactions as a result of the stressors. This study will elucidate the consequences of sub-lethal stressors at the individual organism level, within population variation, and across species to advise management efforts for fishes occupying similar niches to the ones in this study.
Hurricane/tropical storm rainwater chemistry in the US (from 2008 to 2019)
Yixi Qiu, Joseph David Felix
Rainwater chemistry of extreme rain events is not well characterized. This is despite an increasing trend in intensity and frequency of extreme events and the potential excess loading of elements to ecosystems that can rival annual loading. Thus, an assessment of the loading imposed by hurricane/tropical storm (H/TS) can be valuable for future resiliency strategies. Here the chemical characteristics of H/TS and normal rain (NR) events in the US from 2008 to 2019 were determined from available National Atmospheric Deposition Program (NADP) data by correlating NOAA storm tracks with NADP rain collection locations. It found that the average pH of H/TS (5.37) was slightly higher (p < 0.05) than that of NR (5.12). On average, H/TS events deposited 14% of rain volume during hurricane season (May to October) at affected collection sites with a maximum contribution reaching 47%. H/TS events contributed a mean of 12% of Ca2+, 22% of Mg2+, 18% of K+, 25% of Na+, 7% of NH4+, 6% of NO3-, 25% of Cl- and 11% of SO42- during hurricane season with max loading of 77%, 62%, 94%, 65%, 39%, 34%, 64% and 60%, respectively, which can lead to ecosystems exceeding ion-specific critical loads. Four potential sources (i.e., marine, soil dust, agriculture and industry/fossil fuel) were indicated by PCA. The PMF suggested that Mg2+, Na+ and Cl- were primarily marine-originated in both event types, while 36% more sea-salt Ca2+ and 33% more sea-salt SO42- were deposited during H/TS. Agriculture and industry/fossil fuel were the main sources of NH4+ and NO3-, respectively, in both rain event types. However the NH4+ contribution from industry/fossil fuel increased by 13% during H/TS indicating a potential vehicle source associated with emergency evacuations. This work provides a comprehensive assessment of the rainwater chemistry of H/TS and insight to expected ecosystem loading for future extreme events.
Post-release survival, growth and habitat preference of hatchery-reared Southern Flounder (Paralichthys lethostigma)
Andrew Ricken, Simon Geist, Ivonne Blandon, Chris Mace
Southern Flounder are an important target for recreational fishing. The Texas Parks and Wildlife Department (TPWD) Coastal Fisheries Stock Enhancement program is raising and releasing Southern Flounder to supplement natural recruitment in order to keep the population stable and ideally increase from current low levels. To increase the number of restocked fish the program is moving to an extended rearing season beyond the winter spawning season in the wild. This project will conduct mesocosm experiments during which Southern Flounder juveniles will be released into net pens installed in a known nursery habitat and measure weekly growth and condition and survival during different seasons of the year for 8-week periods. Parallel water quality parameters and prey availability will be assessed and correlated to the flounder data. To understand if a longer period of rearing at the hatchery before restocking would e beneficial, two different age/size classes will we investigated.
Shotgun sequencing EtOH preserved historical fish with whole genome amplification and repair mix yields no extra benefits
Roy Roberts, Chris Bird, Sharon Magnuson
Historical museum specimens are notorious for being difficult to sequence, but sequencing success unlocks a wealth of temporal and population genomic information. Additionally, next generation sequencing has made whole genome sequencing practical and cost efficient. Whole genome shotgun sequencing libraries were constructed from each of six historical (1907-1909, EtOH Preserved) and contemporary fish species from the Philippines. A mostly factorial design was employed to test for the effect of whole genome amplification (WGA/NoWGA), enzymatic repair (NEBNext FFPE Repair Mix), and mass of DNA at the onset of library preparation. In total, 144 libraries (62 WGA, 82 noWGA) were sequenced. After adapter trimming and quality filtering we found that sequence duplication in historical WGA libraries (~60-90%) was much higher than either historical NoWGA (40%) or contemporary libraries (20-50%). Further, historical WGA samples had higher proportions of contaminant DNA. The average fragment length of the historical NoWGA libraries (~80 nt) were much shorter than the other treatments (~471 nt). The NoWGA libraries had a higher proportion of reads filtered (median of ~8.1-8.5%) than WGA (median of ~1-4-2.5%) regardless of collection era. Despite several historical WGA metrics out preforming NoWGA, the high rate of duplication, amplification of contaminants, and library failure made it an inferior option to NoWGA. Further, DNA repair had no discernable benefits. Given differences in sequencing efficiency and fragment length, historical NoWGA samples required ~15x more DNA fragments in the sequencing reaction to obtain the equivalent depth of coverage to contemporary samples.
Planktonic larval ingress and vertical distribution in the Aransas Pass inlet system
Olivia Robson, Simon Geist
In Corpus Christi Bay there are several ongoing proposals for industrial developments, including four desalination plants. These developments are causing concern about the potential environmental impacts to the area. Many economically important species such as Red Drum, shrimp species, and Southern Flounder use the bay as a nursery ground thus making the estuary a critical habitat for their survival. The Aransas Pass inlet and surrounding shipping channels act as the main pathway these larvae enter Corpus Christi Bay and Mission Aransas NERR from their spawning areas in the Gulf of Mexico. Both larval fish and crustaceans are extremely sensitive to changes in the water column, like salinity and temperature, as they are still rapidly developing and growing. Larval organisms also participate in what is called daily vertical migration in which larvae move vertically in the water column based on the time of day and has been shown to be relevant even in a shallow inlet like Packery Channel in a previous project. This diel vertical migration is an important factor as salinity, temperature, and current can dramatically vary based on depth, especially in a narrow inlet system like the Aransas Pass inlet. Even though larval stages are a crucial step in an organism’s life history few studies have been. My research is focused on the collection and quantification of larval fish and crustaceans at discrete depths in the Aransas Pass Inlet System. This research will not only give us a better understanding of the various species who use the area as nursery grounds, but it will also serve as a baseline for environmental health before any proposed industrial developments commence.
Corals in crisis: how temperature and nutrient fluctuations affect physiological responses of corals and their microbiome in Kāne‘ohe Bay, Hawai‘i
Zoe Ruben, Keisha Bahr, Hussain Abdulla, Jeffrey Turner, Lee Pinnell
Coral reefs are the foundation to social, cultural, and economic life in Hawaiʻi; however, these reefs have not escaped environmental stressors that have ravaged coral reefs in other areas of the world. Kāne‘ohe Bay, Hawai‘i, represents one of the most studied estuarine coral reef ecosystems globally with well-documented anthropogenic disturbances. However, the mixed effects of thermal stress and nutrient loading on the coral microbiome (endosymbiotic algae, bacteria, archaea, viruses, and fungi) remain poorly understood. Therefore, this project will investigate how temperature and nutrients influence the coral microbiome across a spatial environmental gradient. Pairs of known bleached/non-bleached corals will be collected at two long-term monitoring sites within Kāneʻohe Bay, encompassing the natural spatial gradient of temperature and nutrient influence. Corals will be subjected to experimental treatments varying in temperature and nutrient levels for 30 days at the Hawaiʻi Institute of Marine Biology. Biological response variables will be measured, and coral fragments will be subsampled for future metabolomics and metagenomics analysis. It is hypothesized that: (1) corals subjected to a combined increase in temperature and nutrients will experience higher levels of bleaching and lower levels of survivorship, (2) corals exhibiting non-bleached phenotypes will show higher levels of survivorship than their bleached counterparts, and (3) there will be an observed shift in microbial community composition across corals due to these stressors. If validated, these findings will support that coral bleaching susceptibility is manifested throughout the coral microbiome, and the physiological response to stressors can be better understood to potentially mitigated.
Machine learning methods for the solution of differential equations
Pavithra Venkatachalapathy, S. M. Mallikarjunaiah
Solving Partial differential equations (PDEs) numerically is a demanding task. Although, there are classical methods such as Finite difference, Finite Element method (FEM), Finite volume Method to solve PDEs they have their own limitations. One such example is an issue with huge computational costs involved in simulating the crack propagation in brittle elastic solids. Further, not to mention a huge disadvantage in re - meshing and challenges in computationally modeling crack evolution in heterogeneous, anisotropic and 3D materials. In recent years, Deep Neural Networks (DNNs) have displayed an outstanding achievements in various field of science ad engineering such as Image classification, fault detection and also in the study of PDEs. A multilayer feed forward network with adequate number of hidden layer neurons can be used to approximate any continuous function. Consequently, neural networks have also tremendous merits in solving PDEs [2]. We use Artificial
Neural Networks (ANNs) to solve Fredholm second kid singular integral equation(FIE) from fracture mechanics. The idea, is to construct trial solution into two parts. The first part will satisfy the initial/boundary conditions and the second part implements feed forward neural network, and then train network to satisfy the integral equation. This construction is demonstrated successfully in [4]. Our work is structured as follows: a) Determine the trial solution. b) train the neural network to satisfy the integral equation. c) Optimize the parameters of neural network using Broyden - Fletcher - Goldfarb - Shanno (BFGS) algorithm. d) Analysis of Experimental results. e) The solution obtained will be tested against the numerical solution obtained by using collocation technique approach of solving FIE. f) Summarizing the list of future work.
3D scanning of limpet shells for volume characterization
Amanda Villarreal, Patricia Cockett, Ruby Mehrubeoglu
Limpets are bioindicators of their surrounding environment. Their physical attributes develop based on their environmental conditions. This research project focuses on determining the different limpet shell’s attributes based on their 3D scans.
Unlike geometric objects, calculating the volume of the shell cannot be found with a simple formula or other set rules due to the highly varying surface and shape parameters. Therefore, instead shell volume is computed using software tools that extract both 3D and 2D shell attributes. Previous work by our lab has identified and measured seven physical measurements scanning data and the MATLAB programming tool. These measurements include inner shell volume, outer shell volume, solid shell volume, major axis, minor axis, height, and peak shift.
The characteristics of the M series of shells are being collected at the moment by the structured-light 3D scanner. Each scan takes about an hour to complete, and alignment/fusion takes about two hours to complete. Once all the shells in the M series are scanned, this information will be uploaded to MATLAB to produce the physical dimensions of the shells. We report our preliminary work on these measurements.