Thesis and Dissertation Announcements

The Comparative Anatomy of Extrafloral Nectaries in the Cactus Family (Cactaceae)

Major Advisor: Dr. David E. Lemke

Committee Members:

Dr. Paula Williamson

Dr. Root Gorelick, Carleton University

Zoom: https://txstate.zoom.us/j/84512634250 

Extrafloral nectaries (EFNs) are specialized glands that unlike floral nectaries, which function primarily in pollination, are typically associated with plant defense, attracting invertebrates whose presence and activity can reduce herbivory. EFNs were first observed in cacti in 1837 and have been noted in at least 25 different genera. Morphologically, cactus EFNs have been categorized as belonging to one of four distinct groups: short, obviously modified spines (type 1 EFNs); nectaries that resemble ordinary spines with no readily apparent modifications (type 2 EFNs); nectaries associated with small foliage leaves occurring adjacent to an areole (type 3 EFNs); and nectar-secreting regions of epidermis situated below an areole (type 4 EFNs). Although the distribution of these morphological types has been examined, little is known of their anatomical structure. My study refines this previous classification scheme characterizing type 1 EFNs as short, blunt projections consisting of a basal vascularized stalk filled with subnectary parenchyma and a broad secretory head containing layers of nectary parenchyma. Secretion appears to occur through ruptures in the cuticular covering of the gland. Type 1 EFNs are the most diverse group, with forms that range from spine-like, with an elongated secretory head containing fiber-like cells, to more specialized examples with flattened secretory heads that only contain isodiametric secretory cells. These EFNs can be phylogenetically informative on a species level within genera. In type 2 EFNs, nectar is produced in an area of small, isodiametric cells with dense cytoplasm at the base of a spine, then transported upwards to the sites of secretion. Type 3a and 3b EFNs secrete nectar from stomata in foliage leaves or modified leaf tissue. These stomata are located over subjacent vascular tissue with type 3a EFNs being associated with vegetative tissue and type 3b EFNs located on the exterior of pericarpel. Type 4 EFNs are also associated with leaf tissue but secrete nectar though open pits in patches of dark-red epidermis that are connected to subjacent vascular tissue.

Bio:  Jackson Burkholder grew up attending Colorado Cactus and Succulent Society events, and what started as one or two small plants every year has turned into an obsession with desert flora. This inspired him to attend college at Colorado State University where he earned his B.S. in Horticulture with minors in Nursery & Landscape Management and Japanese. Outside of his studies, Jackson takes care of his large collection of primarily South American cacti and has been involved in multiple organizations focused on his favorite plants including the Cactus and Succulent Society of America and the International Cactaceae Academic Network.  In addition to botany, Jackson is also interested in photography and in repairing and restoring antique scientific equipment.  He was excited to join the Lemke Lab in 2019 and combine all his interests by studying plant anatomy.  After graduation he hopes to continue conducting botanical research either by pursuing a PhD or by working at a botanical garden.

Patterns of Macroinvertebrate Diversity and Composition in a Spatially Complex River Basin: Taxonomic and Functional Approaches

Major Advisor:  Dr. Weston Nowlin, Department of Biology, Texas State University

Committee Members: 

Dr. Benjamin Schwartz, Department of Biology, Texas State University

Dr. Mariana Perez, Department of Biology, Texas State University

Dr. Richard Johansen, U.S. Army Engineer Research and Development Center

Join Zoom Meeting: 

https://txstate.zoom.us/j/87913507951?pwd=5elb6MnknLFYclclh59XxhrbxzGrI9.1

Riverine benthic macroinvertebrate community composition and diversity respond to environmental gradients (i.e., climate, land use, water quality) and flow disturbances (i.e., frequency of drought or flooding).  There is a paucity of data exploring how larger-scale watershed and environmental gradients influence the taxonomic and functional trait composition and diversity of macroinvertebrate communities within a single large river drainage. In this thesis, I examined the relative strength of environmental drivers on benthic macroinvertebrate communities at multiple spatial scales using a spatially nested study design of 102 sites distributed throughout the Colorado River basin, Texas, USA; this basin includes the Colorado, Concho, San Saba, Llano, and Pedernales rivers. I assessed variation in local diversity (α-diversity) and between sites (β-diversity) at taxonomic and functional trait-based levels using distance-based redundancy analyses and variation partitioning. Spatial processes driving each of these were modeled using Moran eigenvector maps (MEMs). Taxonomic α-diversity differed among rivers, while functional trait α-diversity exhibited less variation. Across all sites and rivers, local-scale environmental conditions (i.e., canopy cover, water quality, and flow velocity) and broad-scale spatial structuring (determined via MEM vectors) explained the greatest amount of variation in macroinvertebrate community composition at taxonomic and functional trait levels. However, functional trait-based models explained considerably more variation than taxonomic-based models. Flow disturbance regimes had a relatively minor role in determining macroinvertebrate community composition. When b-diversity patterns across all sites and rivers were assessed, replacement was the main facet driving b-diversity both in terms of taxonomy and functional traits. These results indicate that local scale environmental conditions are important in determining macroinvertebrate composition, but larger-scale spatial structuring of communities (i.e., upstream to downstream) also plays an important role. Replacement was the more important component of b-diversity at both the taxonomic and functional trait levels, which might be due to the Colorado basin being a single hydrologically connected system, despite its relatively large size. Hydrological disturbance regime was found to have a relatively minor role in influencing the taxonomic and trait composition of macroinvertebrate communities and this lack of influence may be due to the way in which hydrological regimes were classified in this study and the relatively fast lifespans of many invertebrates. Overall, this thesis demonstrates that community composition at taxonomic and functional trait levels is influenced by environmental drivers at multiple spatial scales and that future studies should incorporate temporal dynamics of communities in order to forecast how communities respond to future environmental changes, such as climate change and land use practices.

Bio: Miranda Sams graduated from Cedarville University with a B.S. in Environmental Science. After working around the world with NGOs and environmental consulting agencies, Miranda decided to pursue a M.S. in Aquatic Biology. She started her M.S. in Dr. Weston Nowlin’s lab in the Spring of 2023. Beginning in August, Miranda will continue her work as a Ph.D. student in Dr. Nowlin’s lab. She enjoys all outdoor activities, traveling, and dancing.

An Evaluation of Enriched Aerobic Bacterial Communities Capable of Biodegrading TCE Under Different pH and Temperature

Major Advisor: Dr. Bob McLean

Co-Advisor: Dr. Sangchul Hwang

Committee Member: Dr. Manish Kumar

Zoom Link:
https://txstate.zoom.us/j/82081718008?pwd=YVU3aXlFS3kyS0VhZ21GdGtjSDB5Zz09

Trichloroethylene (TCE) is a widely used halogenated organic compound in industrial cleaning and degreasing. It frequently contaminates groundwater, soil, and the biosphere, and direct human exposure to TCE significantly affects multiple organs, including the heart, kidneys, liver, and central nervous system. As a priority pollutant listed by the US-EPA, various strategies have been implemented for TCE remediation. However, bioremediation stands out as a low-cost, sustainable, and eco-friendly technique for the complete mineralization of TCE. Global temperature increases have direct and indirect effects on the environment at macroscale, microscale, surface, and subsurface levels. Therefore, this study aims to investigate the effect of temperature and pH on TCE degradation using an enriched bacterial community. A sediment sample from the Concho River in San Angelo, TX, was collected based on urban runoff of oil, gasoline, kerosene, and other contaminants. This sample was used to enrich aerobic bacterial communities in an M9 minimal mineral salt buffer with TCE, followed by transferring the culture to fresh M9 salt buffer with TCE to obtain a stable, enriched aerobic bacterial community. This enrichment process indicated that the bacteria were potentially metabolizing TCE as a sole carbon substrate or surviving in its presence. Optical density was measured at 600 nm for turbid samples, and plate screening on M9 agar plates with inoculated bacteria and TCE was used to visually observe mixed cultures of different colony-forming units (CFUs). Experimental 5-day incubation periods were conducted with samples containing 1 g/L glucose, 0.5 g/L yeast extract, specific bacterial inoculum concentrations, and TCE concentrations diluted within the range of 0-25 ppb, spiked with 2 ppb 1-chlorobutane. Samples were analyzed for chlorinated volatile organic compounds using gas chromatography and mass spectrometry. Various parameters, such as temperature and pH shifts, were adjusted during each 5-day experiment to optimize environmental conditions for TCE biodegradation. The results indicated that the optimal environmental parameters for in situ bioremediation of TCE were 4% inoculum, 15℃, pH 6, with 40 mg/L TCE. Optical density proved unreliable for quantifying bacterial cell growth, so the IDEXX most probable number (MPN) analysis was used for bacterial cell count. Additionally, 16S rRNA amplicon sequencing was performed on Concho bacterial stock samples incubated at 25℃ for 24 hours, and on samples with 4% inoculum at 15℃, pH 6 in 40 mg/L TCE after 5 days to identify bacterial communities in stock growth and optimized environmental conditions. In the future, other remediation techniques such as biosorption (adsorption and absorption), physical removal of contaminated sites (ex situ), oxidation and reduction (venting and mineralization), in conjunction with bioremediation using bioreactors, could be employed to achieve the most effective results.

Bio: Joe Ball graduated at Texas State University with a B.S. in Microbiology. After working for Micro-Bac International that utilizes bacteria to degrade waste, Joe decided to pursue this type of research as a research assistant in Dr. Hwang’s Lab (HEDGE) in the Spring of 2023. The DOE project in HEDGE Lab aims to clean up the environment with multiple remediation techniques. Joe’s research goal is to find unique bacteria capable of biodegrading contaminants in the environment. Joe plans to get hired through the DOE to help them clean up their contaminated sites all around the nation.  

Analyzing Colony Structural Characteristics to Assess Establishment of Reintroduced Black-tailed Prairie Dogs (Cynomys ludovicianus) 

Major Advisor: Dr. Joseph Veech

Committee Members: 

Dr. David Lemke

Dr. Ivan Castro-Arellano

The reintroduction of a species to portions of its former range where it has become locally extinct presents many challenges. As such, there is a need to develop methods to monitor whether the species has established self-sustaining populations at the reintroduction sites. The black-tailed prairie dog (Cynomys ludovicianus; BTPD) has been extirpated from large portions of its historical range, particularly in Texas. Reintroduction of BTPD is an on-going task in their overall conservation. My study explored the structural spatial dynamics of BTPD burrows as a potential indicator of colony establishment. I used colony age classes as a surrogate for establishment phase in order to derive hypotheses in the context of selfish-herd theory. A selfish herd forms and is maintained when prey individuals at the center of a group are safer from predators that are more likely to detect and capture individuals on the margin. Each individual seeks to decrease its “domain of danger” by moving toward the center of the herd. In the case of BTPD, this should result in burrow densities and spacing patterns that reflect greater survival probability at the center of a colony, as would be most likely observed in an established colony. Further, BTPD activity should be most prominent at the center and other centerto-edge differences should exist. I mapped burrows and measured physical characteristics at 14 colonies throughout north and west Texas. I then used ANOVA to test for differences among colony age classes and zones (central vs. peripheral). Although not all hypotheses were supported, field mapping of both newly-reintroduced and well- established colonies revealed that well-established colonies exhibited a consistently high proportion (> 0.9) of active mounded burrows across both central and peripheral zones. Conversely, newly-reintroduced colonies showed a relatively greater proportion of these burrows in the central zone but significantly fewer in the peripheral zone, suggesting an increase in active mounded burrows as colonies mature, specifically towards the colony edge. Therefore, the proportion of active mounded burrows could serve as a practical indicator of colony establishment and inform management decisions, potentially reducing the need for ongoing intervention once parity between zones is observed. Additionally, I investigated the potential of satellite imagery for remote monitoring. Although the satellite imagery analysis was not definitive, it indicated that with further refinement, this technology holds promise for identifying BTPD colonies and assessing areas of activity. Overall, my study provides detailed knowledge of BTPD colony structural characteristics and suggests that monitoring of active burrows is a useful tool in assessing success of BTPD reintroduction.

Bio: Erin Berkenkamp is a dedicated researcher and Certified Associate Wildlife Biologist®. She earned her B.S. in Wildlife Biology from Texas State University in 2017. Since then, she has worked as a consultant, applying ecological principles to the conservation and management of wildlife species and their habitats. This experience inspired her research into the development and implementation of science-based conservation practices aimed at protecting vulnerable species and sensitive habitats, with a specific focus on species reintroduction as a habitat restoration strategy. Her research, focusing on black-tailed prairie dog (Cynomys ludovicianus) reintroduction monitoring techniques, underscores the importance of ensuring that conservation interventions are effective and adaptive. Erin believes these efforts are crucial for preserving biodiversity and ensuring a sustainable future for coming generations.

The Use of Mixed Diatom Cultures and the Influence of their Microbial Communities on the Treatment of Reverse Osmosis Concentrate 

Major Advisor: Dr. Keisuke Ikehata

Co-Advisor: Dr. Benjamin Schwartz

Committee Member: Dr. Jason Martina

Zoom Link: 
https://txstate.zoom.us/j/6627949450?pwd=c0Z4b3hPc1gxOFRzSW1KVHF2UUlLZz09  

More frequent drought conditions and a rapidly growing population have intensified the need for alternative water resources and integrated resource management. Desalination of brackish groundwater and wastewater reuse offer alternative sources of freshwater, in which the use of reverse osmosis (RO) is commonplace. However, the freshwater recovery in RO systems is limited by the presence of constituents like silica (SiO₂) and calcium, and the waste stream, RO concentrate (ROC), requires careful management. The use of a class of silica-based microalgae, diatoms, has been proposed to remove silica, calcium, and nutrients from ROC which would allow for further treatment of the ROC and increased freshwater recovery in RO systems. While this method has shown to be effective with multiple isolated diatom species, the use of mixed diatom cultures was previously untested. Mixed cultures of brackish diatoms were collected from coastal wetlands in southern Texas and tested for their ability to remove constituents from ROC compared to a unialgal culture that has been studied extensively. It was hypothesized that the abundant microbial community and increased diversity in the mixed cultures could lead to greater ecosystem function and robustness. The effect of major functional microbial groups in the diatom cultures on ROC treatment was examined through the use of antimicrobials and the resistance to invasion by competing green algae was studied. Further, the microbial communities present in the diatom cultures used for this process were analyzed for the first time through metagenomics and the relationship between biodiversity and ROC treatability was explored. This research demonstrated a greater efficiency in ROC treatment by various mixed diatom cultures compared to a unialgal culture, a greater robustness in one mixed culture, and the complex relationship between diatoms and other microbial groups.

Bio: Emma Clow grew up in the pacific northwest before moving to Arizona where she graduated from Arizona State University with a B.A. in Earth and Environmental Science and a minor in Biological Sciences. She moved to San Marcos, TX in 2020 before deciding to pursue her master’s degree in Aquatic Resources. Emma hopes to contribute to the responsible management and conservation of our most precious natural resource: water.

Exploring Outcomes from Participating in Outdoor Science Activities

Major Advisor:  Dr. Kristy Daniel

Committee Members:

Dr. Paula Williamson
Dr. Michelle Forsythe

Today’s youth often lack opportunities to participate in science practices outdoors. The purpose of this study was to capture fifth-grade student responses to an outdoor science activity booklet to discover what outcomes the students received from the activity. Further, I wished to understand to what extent are elements from an outdoor science activity about pollination transferable to differing topics of outdoor science activities. The booklets contained four post-activity questions to find what each student found most enjoyable, important, helpful, and what aspects made the participants feel most like a scientist. Student responses were deductively organized into categories and emergent themes to reveal that students most enjoyed taking part in outdoor science practices. Participants reported that science practices were the most influential elements of the outdoor science activities. Science practices were also most responsible for students to feel like scientists and led many students to enjoy the activities. Science content was most important and helpful and the hands-on data collection and analysis aspects of the activities were significant. Finally, being outside fostered enjoyment of the science activities. Short outdoor activities, such as Pollination Partners, promote children's scientific interest and identity development. Using what we learned through deductively coding student responses, we can implement tools children found beneficial into future science activities to ensure participants experience enjoyment, learning, and feeling like a scientist.

Bio: Carolyn is a researcher who is passionate about wildlife conservation, Texas endangered species, and biology education. She completed her BS in Environmental Science with a track in sustainability at Sam Houston State University before joining the Daniel Biology Education Research Group in the Fall of 2022 to pursue her MS in Biology. Her research seeks to understand what elements of outdoor science activities lead 8-12 year olds to feel like scientists. After her graduation, Carolyn will remain under Dr. Daniel’s supervision to work toward her PhD in Integrative Biology and Aquatic Resources. She looks forward to her PhD projects in which she seeks to further understand how community members interact with the 7 Principles of Leave No Trace.

The Role of IBR5 in Auxin-Mediated Protein Degradation in Arabidopsis

Major Advisor: Dr. Nihal Dharmasiri, Department of Biology, Texas State University 

Co-chair: Dr. Sunethra Dharmasiri, Department of Biology, Texas State University

Committee Member: Dr. Hong-Gu Kang, Department of Biology, Texas State University

The plant hormone auxin controls plant growth and development by primarily regulating cell division, cell elongation, and cell differentiation. These processes are regulated by the expression of auxin-related genes, which is achieved through the degradation of AUX/IAA repressors through the ubiquitin proteasome pathway involving the SCFTIR1/AFBs complex. This complex comprises the F-box protein TIR1/AFBs, along with ASK1, CUL1, and RBX1. Prior research found the involvement of IBR5 in the auxin response pathway since the primary root growth of ibr5 mutant lines showed resistance to auxin. The IBR5 gene encodes a dual-specificity phosphatase, which has an essential yet unknown function in the auxin signaling pathway. It was previously found that the localization of the auxin co-receptor TIR1 is affected in ibr5-1 null mutant, and two different reporters, GFP (Venus) and GUS that represent AUX/IAA repressors, showed contradictory results in their degradation pattern. Additionally, previous work indicated  that the overexpression of IBR5 stabilizes AUX/IAA proteins through an unknown mechanism. Here we show additional data to confirm that the difference in subcellular localization of these two AUX/IAA reporters lead to different pattern of repressor degradation. Furthermore, this work shows that wild type IBR5 protein interacts with several AUX/IAA proteins in-vitro, and this interaction is not dependent on auxin. Collectively these results suggest that IBR5 may sequester AUX/IAA proteins from degradation leading to the accumulation of repressor proteins in IBR5 overexpression background. In-depth future investigation is worthwhile to determine whether the phosphatase activity of IBR5 is necessary for the regulation of AUX/IAAs stability.

Bio: Emran is from Sylhet, Bangladesh, and completed his BSc in Biotechnology and Genetic Engineering from Sylhet Agricultural University, Bangladesh. He joined the lab of Dr. Nihal Dharmasiri at Texas State University to obtain his MS in Biology. His research focuses on revealing the molecular mechanisms mediated by IBR5, which is a dual-specificity phosphatase, to regulate the plant auxin signaling pathway. After his graduation, he will join the Molecular and Developmental Biology PhD program at Cincinnati Children's Hospital Medical Center. He is enthusiastic to become a molecular biologist who can contribute to disclosing molecular mechanisms involved in human diseases.

Enhancement of the Lateral Line System of Subterranean Salamanders (Eurycea)

Major Advisor: Dr. Dana M. García 

Committee Members:

Dr. Chris C. Nice
Dr. Pamela B. Hart, The University of Alabama

Join by Zoom:

https://txstate.zoom.us/j/88637178695?pwd=cituWXNEdGFjTDBkd0k5RGN0YlpIZz09&from=addon

The genus Eurycea inhabits a range of groundwater habitats including surface and subterranean. In contrast with their surface-dwelling relatives, subterranean Eurycea exhibit characteristics associated with life in perpetual darkness, including reduced pigmentation and eyes, raising the possibility that other sensory systems may be enhanced to enable subterranean salamanders to navigate their dark world. To test the hypothesis that subterranean Eurycea have a more extensive lateral line system, the mechanosensory neuromasts of the anterior lateral line (ALL) of three subterranean and four surface populations were quantified. Two subterranean populations have significantly more ALL neuromasts than all four surface populations. One subterranean population has significantly more ALL neuromasts than three of the surface populations but does not differ significantly from one surface population. Distribution of neuromasts among five craniofacial regions was analyzed. A PCA of these regions shows that mandibular and post-orbital neuromasts are especially strong contributors to the variation between surface and subterranean populations. Serendipitously, PAX6 was observed in the neuromasts of Eurycea, a novel localization of the transcription factor protein which is known to be involved in eye and central nervous system development. To determine if this protein plays a role in the expansion of the lateral line system in subterranean salamanders, PAX6 labeling in neuromasts was compared between one surface and one subterranean salamander at three stages of development. Fluorescence intensity of PAX6 labeling in neuromasts is significantly higher in the subterranean species at adulthood but not at one- or three-months post oviposition. These results suggest a correlation between the hypertrophy of the ALL system of Eurycea, a subterranean lifestyle, and the sustained presence of PAX6 in neuromasts into adulthood.

Bio: Brittany is from Montgomery, Texas. She became involved in research on the ocular development of subterranean salamanders as an undergraduate in Dr. Dana García’s NSF Summer Fellowship at Texas State University. Eager to expand on this research, she began her master’s degree in the Fall of 2022. Brittany enjoys benchwork as well as field work and hopes to put her passion and experience to work in a position in the US Fish and Wildlife Service.

A Study of Undergraduate Students’ Interpretations of Tree-Thinking by Using Eye Movements

Major Advisor:  Dr. Kristy Daniel

Committee Members:

Dr. Noland Martin
Dr. Cynthia Luxford
 
Tree-thinking is the ability to correctly understand, use, and generate phylogenetic trees. Unfortunately, students often face difficulties interpreting trees correctly for a multitude of reasons. The purpose of this study is to analyze the eye movement patterns of students to determine how introductory biology students visually access trees during interpretation tasks and identify areas in which they are struggling to interpret. I used an eye-tracking system to capture participants' eye movements (both fixation duration and counts) while solving tree thinking problems. I used the results to generate heat maps illustrating the major areas of the diagrams visually accessed when solving tree-thinking questions. By analyzing these eye movements, I have identified differences in eye movement patterns and time spent on tasks between participants who answered tasks correctly compared to participants who answered incorrectly. This study revealed that participants who misinterpreted the tree tasks were more likely to spend more time considering the task, were less focused within the tree diagram and attended to more distracting areas of the tree rather than informative features, spent more time trying to interpret the question of the task rather than the diagram, and were over-confident in their tree-thinking skills. While tree-thinking instruction has been expanded in introductory biology courses, more interventions are needed to enhance students' comprehension of phylogenetic trees. By identifying elements of these diagrams that are causing confusion and distractions for learners, we can begin focusing on how to adapt instruction in ways that enhance informative regions and promote more proficient tree-thinking.

Bio: Mallika is a research enthusiast who wants to explore new things. She completed her BSc and MSc in Zoology from Jagannath University, Bangladesh. Mallika joined the Daniel Education Biology Research group at Texas State University for her second Master’s in Biology in Fall 2022 under Dr. Daniel’s supervision. Her research project is visual assessments of college biology students' phylogenetic tree-thinking. After graduating, she will be pursuing her Doctoral program in the same research lab. 

Neuromodulation of Olfactory Immune Responses in Rainbow Trout (Oncorhynchus Mykiss)

Major Advisor: Dr. Mar Huertas  

Committee Members:

Dr. Dana Garcia, Texas State University
Dr. Lauren Fuess, Texas State University
Dr. Yuan Lu, Xiphophorus Genetic Stock Center, Texas State University
DR. Erika Calvo-Ochoa, Hope College 
 
Zoom Link: https://txstate.zoom.us/j/84687267464?pwd=eFlKSE5jNEpUTlk3b0hDQ1JCQkxjdz09

Meeting ID: 846 8726 7464    Passcode: 338248

Trout can smell viruses and the resulting olfactory signals can activate the fish brain immune system. Preliminary results in our laboratory showed that trout can also smell bacterial odorants with high sensitivity and its detection elicits an avoidance behavioral response, thus the trout olfactory immune function is likely tunned for a variety of pathogenic odors. However, the brain integration process for these olfactory immune responses is unknown. The integration of environmental signals within the vertebrate brain is mediated by different neuromodulators which subsequently trigger behavioral responses and immune system activation. I hypothesize that the integration of olfactory bacterial signals is mediated by brain neurosteroid neuromodulation, which leads to the activation of the neuroimmune system and results in the avoidance behavior in rainbow trout. To test our hypothesis, we will first measure neurosterodoigenic brain responses in trout after nasal exposure to inactivated Yersinia ruckeri by measuring mRNA expression of different neurosteroidogenic enzymes and neurosteroid production by ELISA. Second, we will do a detailed mapping of the olfactory-immune pathway by pinpointing the specific locations of neurosteroidogenic enzymes and activated immune factors in the rainbow trout brain using multiple “in situ” hybridization and spatial transcriptomics techniques. Preliminary results showed a time (15 mins, 4 hours, 24 hours, and 7 days after bacteria odor exposure) and location-dependent (nose, olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum) expression of several neurosteroidogenic enzymes, which were parallel to localized production of neurosteroids. Our findings indicate the involvement of neurosteroids in the rapid bacterial odor identification via the olfactory system in rainbow trout. Investigating the olfactory-immune brain pathway for bacterial odor detection in rainbow trout will help to understand the role of neurosteroids in olfactory processing. Moreover, it can help to identify specific targets of action that can contribute to designing a more effective nasal vaccine to treat enteric red mouth diseases caused by Y. ruckeri in rainbow trout.

Bio: Maruf is from Bangladesh and graduated with his bachelor’s from Bangabandhu Sheikh Mujibur Rahman Agricultural University in Bangladesh from the faculty of Fisheries before getting his Master’s degree in Marine Biology from the University of Texas Rio Grande Valley, Brownsville, TX. His love for biology and a desire to work on fish physiology led him to focus on fish physiology and olfaction in his Ph.D. degree. He is supported by his lab, friends, and family on his academic journey.

Nuclear tRNA-derived RNA fragments (tRFs) trigger immunity in Arabidopsis and potentially function as a mobile signal in systemic acquired resistance

Major Advisor:  Dr. Hong-Gu Kang

Committee Members:

Dr. Nihal Dharmasiri (Texas State University)

Dr. Sunethra Dharmasiri (Texas State University)

Dr. Sibum Sung (The University of Texas at Austin)

Dr. Joe Louis (University of Nebraska-Lincoln)

Zoom Link: https://txstate.zoom.us/j/89437707227

Plants respond to stress through rapid and extensive changes in gene expression, orchestrated by intricate modifications in chromatin structure. They also possess a unique long-distance immunity known as Systemic Acquired Resistance (SAR), which offers protection against future attacks, indicating the presence of delicate signaling molecules in these immune responses. However, the identity and mechanisms of these signaling molecules remain poorly understood.

Our research on effector-triggered immunity (ETI) to Pseudomonas syringae pv tomato (Pst) in Arabidopsis revealed the significant role of DCL1 (Dicer-Like 1) in modulating ETI, emphasizing small RNAs' (sRNAs) importance. Deep-sequencing of nuclear sRNAs preceding defense gene induction uncovered the rapid accumulation of a 31-nt tRNA fragment (tRF^31Asp2) in a DCL1-dependent manner. Remarkably, infiltration of Arabidopsis with tRF^31Asp2 alone induced over 500 defense genes and immunized the plants against Pst and aphids. Additionally, we discovered that tRF31^Asp2 exhibited sequence-specific binding to genomes, including those within defense genes, indicating that the interaction between the tRF and the genome likely triggers transcriptional activation. Furthermore, our investigation revealed that tRF^31Asp2 was mobile, with its mobility enhanced by avirulent Pst, and translocated to the nucleus of distal tissue. To further explore this intriguing observation, nuclear sRNAs were deep-sequenced in leaves neighboring those infected. As a control, DIR1, a lipid transport protein known to be involved in SAR and itself capable of movement within plants, was used. Surprisingly, 16-nt-long tRFs, particularly those generated from Asp-tRNA (tRF^16Asp), were induced by avirulent Pst in a DIR1-dependent manner, suggesting that these tRFs might be a SAR mobile signal.

My study identifies a potent candidate molecule that modulates transcriptional reprogramming in response to infection and signals from neighboring leaves. This groundbreaking discovery unveils a mechanism in which sRNAs carry precise targeting information, guiding essential transcriptome changes. This paves the way for a promising new technological approach, enabling the precise engineering of stress responses.

Bio: Dinesh was born in the far-western part of Nepal. He earned his B.S. Biotechnology degree from Purbanchal University, Nepal in 2011 and M.S. Biotechnology from the Bangalore University, India in 2016. He then moved to San Marcos for pursuing his Ph. D in plant molecular immunology lab of Dr. Hong-Gu Kang in Fall, 2017. After graduation, Dinesh plans to continue his passion for research. Apart from academics, he is passionate about sports. 

Major advisor: Dr. Dana M. García

Committee members:

Dr. Gar Yee Koh

Dr. Robert J. C. McLean

Join Zoom Meeting: https://txstate.zoom.us/j/88507100096?pwd=NHNIWU5DVzhZR3dCWGpoNUk3Z2pwUT09

Meeting ID: 885 0710 0096 
Passcode: Passcode115682

Vitamin D is an essential vitamin, and worldwide many people experience vitamin D deficiency, leading many individuals around the globe to suffer from different illnesses such as cardiovascular disease, tuberculosis, diabetes, and cystic fibrosis. Vitamin D is well known for its main function in maintaining bone health; however, in recent years vitamin D has been recognized for its function in autoimmune health, integrity of the gut barrier, and gut microbiome composition. In this study, I hypothesized that vitamin D supplementation through diet would have an impact on gut microbiome composition and gut integrity, in the latter case by influencing expression of mRNA encoding tight junction proteins ZO-1, occludin, and claudin. Using C57BL/6J mice as a model, I assigned mice to 4 diet groups as follows: 1) standard diet (AIG-93G purified diet; CTR), 2) CTR + antibiotics (AB), 3) CTR + 5000 international units (IU) of vitamin D3 (VD), and 4) VD + antibiotics (VD + AB). Antibiotics consisting of 0.5 g/L vancomycin, 1 g/L neomycin sulfate, 1 g/L metronidazole, and 1 g/L ampicillin were given in water throughout the experimental period. The microbiome was assessed using DNA extraction, 16s PCR sequencing, and analysis using microbiome analyst. The results indicated that the supplementation of VD via diet had a positive impact on gut microbiome composition, leading to an increase in representation of Firmicutes phyla in the VD group in comparison to the CTR, while also showing an increase in the Dubosiella newyorkensis species in VD. Furthermore, qRT-PCR suggested that vitamin D supplementation improved gut integrity, since ZO-1 and occludin genes having higher rates of mRNA expression in mice consuming a VD diet in comparison mice on the control diet. This study indicates that vitamin D supplementation can potentially be used as a treatment for certain illnesses by treating underlying causes such as gut dysbiosis and permeability of the gastrointestinal tract.

Bio: Ethan Constantine is from the Dallas TX area and graduated from Texas A&M University Corpus Christi in 2020 with a B.S. in Biomedical Sciences. In his free time, he enjoys working out, running, and trains in kick boxing and muay tai. After graduating from Texas State University, he plans to take a gap year before continuing his education.

Drawing as a Generative Learning Activity: An Exploratory, Qualitative Investigation on a Nature Journaling Seminar Course

Major Advisor: Dr. Kristy L. Daniel

Committee Members:

Dr. Carrie Jo. Bucklin

Dr. Paula S. Williams

Drawing encourages critical thinking skills by pushing learners to use discernment and prior knowledge of a subject matter to create an external representation of their mental understanding. While visual representations play a key role in science education, it is less common to prompt students to draw their own visual representations to communicate their uniquely constructed ideas. This exploratory, qualitative study investigated drawing as a generative learning activity in a nature journaling seminar course by examining students’ use of drawing techniques taught in class, as well as dissecting their reported reflections on how drawing impacted their journaling experience. The students (n=11) were required to complete a nature journal using prompts developed to encourage reflection, drawing technique practice, and scientific thinking. We coded and analyzed student responses for trends in drawing technique usage, such as hatching and use of color. Student drawings reflected a steady increase of technique usage as more techniques were introduced in class, with a decline once drawing instruction ceased. Students reported that the practice of drawing nature observations increased their mindfulness and attention to detail in their written entries. Our findings provide insight to the benefit of drawing practices in nature journaling, as well as the effects of drawing instruction on student perceptions. Teaching drawing techniques with instructional guidance can provide students with the opportunity to take an active role in their education and deepen their understanding of, and connection with, the natural world. 

Bio: Hannah Baratang graduated with two A.S. degrees in Chemistry and Organismal Biology from Central Texas College at the age of 17. She graduated with a B.S. in Biology from Texas A&M - Central Texas at the age of 19. She joined the Daniel Biology Education Research Group at Texas State University in the Spring of 2023 to pursue a M.S. in Biology under Dr. Daniel's supervision. Since joining the research group, she has been an active member of Research Rangers, developed and illustrated the Good Gall-y! outdoor science activity, and independently organized a series of live music events in the San Marcos DIY scene.

Optimizing Chitosan-Functionalized Hollow Silica Microspheres for Isolation and Concentration of Nucleic Acids

Major Advisor:  Dr. Shannon Weigum

Committee Members:

Dr. Adeyemi A. Olanrewaju

Dr. Manish Kumar 

This research investigates Wastewater-Based Epidemiology (WBE), a tool utilized for detection and concentration analysis of wastewater samples. WBE is useful for monitoring and management of public health threats like viral outbreaks such as COVID-19. In current research, the development of this assay uses the unique properties of hollow silica microspheres coupled with chitosan as a binding agent, a method effective in the detection of various RNA and antigens in wastewater samples. The utilization of hollow silica microspheres, selected for the high surface area and buoyant properties, aided by chitosan, creates an efficient and selective binding process. This combination can be manipulated for the sensitivity of detection but also supports the capture of a wide range of viral particles and RNA molecules. Capture of oligonucleotides is achieved by chitosan binding to the surface of the hollow silica microspheres. This thesis research served to find the optimal conditions for nucleic acid binding, isolation, and long-term microsphere stability when functionalized with chitosan. The preparation of functionalized microspheres has been reduced. The incubation time of functionalized microspheres with L-Cysteine has been reduced to 10 minutes under end over end rotation.  The optimal binding conditions of oligonucleotides has been found utilizing a surrogate. It was found that the functionalized microspheres can bind nucleic acids at saturation within 1 hour. The incorporation of reduced incubation times has reduced the overall protocol by over 24hrs. A protocol has been developed to stabilize microspheres after lyophilization and storage. The addition of Trehalose, a cryoprotectant, increases stability after lyophilization and storage. SEM or Scanning electron microscopy was used to image the chitosan shell on the hollow silica microspheres. The functionalized microspheres containing various treatments applied was examined for disruptions in the chitosan surface and binding kinetics. The implications of this research are vast and transformative. By increasing efficiency and stability and reducing sample preparation costs, this research increases access to WBE for public healthcare and diagnostic testing. The adoption of methods can aid in early outbreak detection and the assessment of community health, therefore contributing to more informed and effective public health strategies and interventions.

Bio:  Omari began undergraduate studies at Southern Methodist University. He then finished his B.S. in Biology at the University of Houston. In the fall of 2022, he joined Dr. Weigum’s Optical Biosensors and Nanomaterials lab. After Graduation he plans to further his studies and pursue a joint MD/JD program.

Optimization of Molecular Buoys for use in the Isolation and Amplification of SARS-CoV-2 RNA from Wastewater

Major Advisor:  Dr. Shannon Weigum

Committee Members:

Dr. Rodney Rohde

Dr. Kelly Woytek

Wastewater based epidemiology (WBE) is an emerging tool used in the surveillance of viruses and viral diseases, such as SARS-CoV-2 and COVID-19. WBE comprises wastewater sampling and processing, isolation of target viruses and purification of target viral nucleic acids, and quantification through molecular means such as RT-qPCR. Isolation and purification are crucial steps in estimating viral loads and positivity rates in a given watershed. Current CDC-recommended methods in viral isolation can be costly, time consuming, or are otherwise inaccessible for widespread use. Our aim is to develop a rapid and accessible bio-separation method using inexpensive materials. In the present work, hollow silica microspheres, or “molecular buoys”, were functionalized with chitosan, a cationic polysaccharide, to capture nucleic acids in diluted stool. Scanning electron microscopy (SEM) was used to examine chitosan surface loading and fluorescently-tagged DNA aptamer (a surrogate oligonucleotide) diluted in stool was used to examine nucleic acid binding capacity. In addition, optimization of nucleic acid capture, reduction of assay time, and limit of detection (LOD) were explored. Under SEM, we observed shell formation on the surface of chitosan-functionalized microspheres that was absent in non-functionalized microspheres. Additionally, optimization of the assay wash protocol reduced assay time, bringing total assay time to around 35 - 40 minutes. Finally, a preliminary LOD was found to be 40 copies/uL in diluted stool. These findings suggest that functionalized hollow silica microspheres may be an effective, low-cost, and rapid method in the isolation of viral nucleic acids for use in WBE.

Bio:  Alexandra received a Bachelor of Science in Biology from the University of Missouri-Columbia in 2021. She then moved to Austin and worked in a contract lab for a year. She joined the Optical Biosensors and Nanomaterials lab, lead my Dr. Shannon Weigum, in August 2022. After graduation, Alexandra plans to continue her education and pursue a career in virology. 

A Prototypical Thermal-Preference Assessment Device for Studying Factors Affecting the Thermal Biology of Small Aquatic Animals

Major Advisor: Dr. David Huffman, Department of Biology, Texas State University

Committee Members: 

Dr. Shannon E. Weigum, Department of Biology, Texas State University

Dr. Alan W. Groeger, Department of Biology, Texas State University

Randy Gibson, Supervisory Biologist, San Marcos Aquatic Resources Center

Zoom link: https://txstate.zoom.us/j/85811727971pwd=M3ozWmFrL3A4ckhxbzBJRWlGVnZvUT09

Passcode 205373

Come see the Thermal Preference Assessment Device (TPAD) I have created for studying the thermal biology of small aquatic organisms such as Melanoides tuberculata. The TPAD was created in response to my review of prior thermal biology studies which revealed a wide range of thermal-gradient device designs and operational theories, many of which were plagued by design flaws that would prevent the formation of a stable, linear gradient. This, coupled with a ubiquitous lack of published performance data and assembly documentation would render replicating these devices difficult at best. The goal of this study was to design and build a proof-of-concept device capable of generating customizable, stable, thermal gradients for use in thermal biology studies, which conformed to the following specifications; 1) quick generation of stable, linear thermal gradients with extremes of 10 °C to 30 °C for at least 24 hours; 2) precise temperature controls, allowing the thermal gradient to be moved back and forth in the trough; and 3) free, unobstructed movement for organisms of varying size classes and modalities within the Testing Arena. The TPAD is driven by a novel counter-current exchange system, powered by computer-controlled thermoelectric Peltier heater/coolers. The Peltier units heat and cool water running counterflow through two pairs of vertically stacked exchange conduits. The exchange conduits are designed so that every segment serves as an individual heater/cooler for the water at that point, with the output temperature increasing incrementally from one end of the Testing Arena to the other. The TPAD was shown to be capable of producing a linear thermal gradient suitable for testing many small organisms of conservation concern from local waters and then maintaining the gradient for 24 hours. The Testing Arena was found to comfortably house organisms including M. tuberculata and Cambarus spp., though there were shaded areas which were favored by cover-seeking organisms. I think, despite not reaching all our original goals, that the TPAD demonstrates the potential of the counter-current exchange model as a refined method of conducting thermal preference tests. Work on the TPAD Design Phase II, a larger, more flexible, and more efficient model based on the success of Phase I, is already underway.

Bio: Matthew Tanner Donelon is from Georgetown, Texas. He graduated with a B.S. in Wildlife Biology from Texas State University in 2019, where he realized his love for innovation in wildlife management strategies. After graduation, Matthew will pursue work as an environmental consultant or engineer.