UNDERGRADUATE RESEARCH FORUM

APRIL 16, 2021

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Freshman Research Initiative Poster and Oral Presentations

Poster Presentation Categories: Poster Presentation Categories Poster #

▶ Astronomy, Mathematics, and Physics 1–10; 113–122 ▶ Biochemistry 11–26 ▶ Biological Sciences 27–56; 102; 106; 108 ▶ Chemistry 57–67 ▶ Computational Biology / Computational Biochemistry / 68–78 Computational Chemistry

▶ Computer Science 79–84 ▶ Human Ecology 85–112 ▶ Molecular Biology 123–139 ▶ Neuroscience 140–158

Oral Presentations

▶ Group 1 159–179 ▶ Group 2 180–200

Alphabetical Index of Authors Undergraduate Research Forum 2021 - Schedule of Presenters

College of Natural Sciences Texas Institute for Discovery Education in Science

Virtual Undergraduate Research Forum

The University of Texas at Austin April 16, 2021

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Freshman Research Initiative AUTONOMOUS ROBOTS Full Stream Name: Autonomous Intelligent Research Stream Poster Robotics Presentations Principal Investigator: Peter Stone Research Educator: Justin Hart The Freshman Research Initiative The goal of this stream is to create a system of fully (FRI) offers first year students the autonomous robots inside the new Gates complex opportunity to initiate and engage in to aid people inside the building. Students will learn authentic research experiences with about and contribute to cutting-edge research in faculty and graduate students in areas artificial intelligence and robotics. such as chemistry, biochemistry, Students in the Autonomous Intelligent Robotics stream are designing software for a system of robots nanotechnology, molecular biology that will exist within the new Bill and Melinda Gates and computer science. Computer Science Complex. The stream’s goal is to enable robots, and associated software agents, to FRI spans three semesters of interact with building visitors and residents. integrated coursework and laboratory FRI students are working on a different autonomous research in newly renovated, robotics challenge, namely the multi-robot interactive dedicated research labs. Students system. Topics include indoor navigation, wifi localization, human interaction, activity recognition, move through the program in cohorts multi-robot coordination, and many others. of about 30. Students emerging from This is a large programming project in which students FRI have experience with experimental experience many CS ideas that they can learn in detail techniques, lab work, and a deep as juniors or seniors in the Department of Computer understanding of the scientific Science. These include: software engineering, threads, message passing, distributed computing, process and sometimes publications. real-time systems, and AI algorithms. Additionally, students with engineering backgrounds can apply control theory and other engineering principles to the APTAMER design and control of the robots. Students also learn Full Stream Name: Aptamer about, and often contribute to, cutting-edge research Principal Investigator: Andrew Ellington in robotics and autonomous agents. Research Educator: Gwen Stovall BEHAVIORAL NEUROSCIENCE How can we use biochemistry and nucleic acids for Full Stream Name: Behavioral Neuroscience drug development and sensor applications? Principal Investigator: Nigel Atkinson Research Educator: Thilini Wijesekera The Aptamer Stream uses oligonucleotide chemistry, in vitro selection methodology, and The Behavioral Neuroscience stream, students will biochemistry to develop novel therapeutics, learn behavioral analysis, concepts in neuroscience, diagnostics, and molecular sensors. The tool of and genetics. Specifically, we will use the Drosophila choice for the development of these applications is an melanogaster model system and simple behavioral «aptamer,» an oligonucleotide binding species. In the assays to study the effects of alcohol and Stream, students use the methods of in vitro selection neuroimmune signaling. Many effects of alcohol on methodology to identify aptamers against a variety of behavior and health may arise from an effect on the targets and develop their downstream application. For neuroimmune system. We will first examine the effect example, aptamers targeting the precursors of of alcohol on agression (male-male fighting over disease states could offer inhibitory functions, thus resources), circadian rhythmicity and sleep, voluntary serving as therapeutics to alleviate disease. Still alcohol consumption, leraning, alcohol tolerance other aptamers against disease biomarkers (defined as alcohol-induced alcohol resistance), could be used in the development of disease and alcohol withdrawal systems using behavioral diagnostics. Additionally, some aptamers may serve assays and statistical data analysis. Then, we will use as gene regulators (such as synthetic riboswitches) Drosophila genetics (mutants, transgenes) to identify or for targeted drug delivery (such as nanoparticle genes and neural circuits that produce the alcohol adjuncts). response. Students will have the opportunity to propose experiments of their own design!

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BIG DATA IN BIOLOGY blot analysis. The students will get equipped with Full Stream Name: Big Data in Biology the laboratory techniques that could be applied in Principal Investigator: Hans Hoffman & Vishy Iyer any field of biological science. In particular, students Research Educator: Dhivya Arasappan in the Biobricks stream will apply these techniques in studying the biochemical activities of proteins How can we detect meaningful patterns from involved in RNA translation in A.thaliana. In one terabytes of sequence data? project, we are focused on examining the biochemical activity of a Cullin-based ubiquitin ligase (E3) called Advances in Next Generation Sequencing BPM3 in translation regulation in A.thaliana. BPM3 (NGS) technologies allow us to generate data has been shown to target transcription factors that at unprecedented speed and throughput. As a are involved in seed sizing and flowering time for consequence, we can now study biological systems at ubiquitin dependent degradation to regulate its the level of whole genomes and whole transcriptomes protein level. However, recent studies suggest that instead of at the single gene level. Importantly, this BPM3 may regulate protein level of its target by technology not only impacts research, but also inhibiting translation through its interaction with how medical care is provided; hospitals will soon eukaryotic initiation factors. Our current goal is to be generating sequence data for every patient who examine the direct impact of BPM3 on translation walks in the door in an effort to customize diagnosis using an in vitro translation system derived from and treatment to that patient. However, the biggest wheat germ. Our second project is focused on challenge for utilizing the power of such data is our elucidating the functional difference between eIF4G limited ability to quickly and reliably obtain insights and eIF-Iso4G in A.thaliana. Although eIF4G and its from this data. isoform, eIF-Iso4G, exhibit the same translational function in plants, the structural divergence of eIF- Iso4G, containing more substrate binding domains BIOACTIVE MOLECULES (FRI & ARI) compared to eIF4G, suggests it may have additional Full Stream Name: Synthesis and Biological functions in the cell. To study the binding partners Recognition of eIF-Iso4G, we have created a fusion protein called Principal Investigator: Stephen Martin Neddylator-Iso4G, to apply the Neddylator system to Research Educator: Elizabeth Ilardi identify novel binding partners of eIF-Iso4G. As the demand for therapeutic drugs increases, how are researchers working to better understand molecular interactions? BIODIVERSITY Full Stream Name: BioDiversity Discovery An understanding of the way proteins, enzymes, or Principal Investigator: David Hillis & David other macromolecules interact with small molecules Cannatella is integral to the process of drug design. The vast Research Educator: Thomas Devitt majority of drugs bind to such macromolecules initiating a biological response. In order for a The Biodiversity Discovery stream is interdisciplinary compound to be considered an efficient drug, it must and develops skills relevant for a variety of careers bind well, or with high binding affinity. Research in our in science. It is well suited for students interested in laboratory is focused on the design and synthesis of ecology, evolution, natural history, medicine, molecular small molecules that exhibit high affinities and biology, animal behavior, environmental science and specificities for selected macromolecules using genomics. Research occurs in the lab and in the field. laboratory techniques relevant to synthetic organic In the lab we measure and catalog specimens, map chemistry. and analyze distributions, and use molecular genetic tools to uncover evolutionary history and relationships between species. Outdoors we visit a variety of sites in the Austin area including two UT field stations – BIOBRICKS the Brackenridge Field Lab and Stengl Lost Pines Full Stream Name: Biobricks for Molecular Field station where wecollect specimens and make Machines observations about ecology and behavior. Students Principal Investigator: Karen Browning can choose among projects related to their interests Research Educator: Soo-Hyun Yang such as on systematics, taxonomy, GIS and spatial The teaching goal of the Biobricks stream is to ecology, genomics and molecular ecology. We work train undergraduate students to learn and master with a wide variety of taxa and are currently focusing the molecular and biochemical concepts of DNA on species found within Central Texas. cloning, recombinant protein expression and purification using the E.coli system, and western

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BIOPROSPECTING increase dramatically in the next 50 years. Increasing Full Stream Name: Bioprospecting: Isolation demands for energy put pressure on fossil fuel of Biologically Active Natural Products from resources, the burning of which contributes to Endophytes climate change. Energy options such as wind, Principal Investigator: Jenny Brodbelt solar, and tidal are promising energy alternatives Research Educator: Kasia Dinkeloo to conventional fossil fuels. Also exciting is the potential societal-scale transition from conventional What biologically active compounds can be obtained internal combustion engine-based vehicles to from endophytes present in native Texas plants? electric vehicles. However efficient energy storage The primary objective of the Bioprospecting stream is technologies are critical for effective utilization of to isolate, characterize, cultivate, process and screen these energy resources and complete electrification unique fungal endophytes from Central Texas for the of vehicles. Lithium-air battery and fuel cells are discovery of compounds with potential therapeutic promising candidates for energy storage, but applications.The stream will span multiple sub- scientific challenges exist to realize its full potential. disciplines of biology and chemistry. Our primary One such challenge is the need to find an effective focus is mycology, molecular biology, and organic catalyst for both the oxidation and reduction chemistry. reactions for the charging and discharging that occurs at the cathode in both technologies. While working towards the primary objective, we also investigate questions regarding the ecology of fungal The Computational Materials stream is a collaboration endophtyes. between the Department of Chemistry and the McKetta Department of Chemical Engineering. One primary research goal of the stream is to identify promising new inexpensive catalyst materials for BUGS IN BUGS the cathode in lithium air batteries and fuel cells Full Stream Name: Microorganisms in Bees and that increase electrical efficiency. Student’s results Other Insects will create a database to identify emerging trends. Principal Investigator: Nancy A. Moran Another primary research goal of the stream is Research Educator: Jo-anne C. Holley investigate computational methodologies used Symbiotic microorganisms have major effects on to model these materials. Students will have the their host nutrition and susceptibility to disease opportunity to write their own computer programs and toxins. In this stream, students explore the gut for determining the structure of materials and even microbiota and pathogens of insects to understand improve current methodology. how they affect the health and function of their hosts. An emphasis is be placed on ecologically important insects such as honey bees and other DISCOVERING SIGNALS pollinators. These are of current interest due to their Full Stream Name: Sarah Simmons Cell Signaling roles in agricultural and natural systems and to their Principal Investigator: Stanley “Stan” Roux widespread population declines. We focus on local Research Educator: Greg Clark Texan bees and wasps because they are abundant and biologically diverse. Different species can have How does the environment impact what cells do? different diets, social structure, and nesting habitats. All these can influence the microbes they associate A recent exciting discovery in plants is that ATP with, as well as many other ecological factors. is released into the cell wall during plant growth where it plays a major role in controlling how fast cells grow. Students in this stream carry out never- done-before experiments on this topic and discover COMPUTATIONAL MATERIALS significant new findings on how extracellular ATP Full Stream Name: Computational Materials controls growth. They learn methods of experimental Principal Investigator: Graeme Henkelman & design, data gathering, data interpretation, and data Gyeong Hwang presentation, and they learn principles of stimulus- Research Educator: Ray Chai response coupling that apply equally well to animals and plants. Specifically, students will do their What new materials can increase the performance of experiments on extracellular ATP signaling in root alternative energy technologies? hairs, an agriculturally important model system for studying plant growth. The world’s energy demands are expected to

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DISCRETE MATHEMATICS ENERGY ANALYTICS Full Stream Name: Geometry, Symmetry, Groups Full Stream Name: Energy Analytics and Fields Principal Investigator: Michael Pyrcz Principal Investigator: Michael Starbird Research Educator: Jesse Pisel Research Educator: Mark Daniels Can we use modern big data analytics and machine This stream will explore the following questions: learning to improve characterization and modeling for improved utilization of subsurface resources? What are transformations in the plane? What is an isometry? Recent numerical developments and improved How can we classify all the possible symmetries of computational resources have led to a rapid plane figures? expansion of big data analytics and machine learning implementations. These technologies are disrupting What sorts of combinations (groups) of symmetries many industries. Oil and gas has a long history can we see in a given plane figure? (In answering with big data from seismic surveys, production this question, we are introduced to permutations, monitoring, remote sensing and well-based the symmetry groups, and the finite symmetric and data. Additionally, there are various physics-based dihedral groups.) engineering and stochastic statistical workflows. What happens when we combine (compose) two or There is an opportunity to adapt and tool big more symmetries? data analytics and machine learning to optimize subsurface development to maximize the value What sets of symmetries can be used to generate all of national energy resources and to minimize the symmetries of the plane? environmental impacts. What is the difference between groups, rings, and fields as algebraic structures? FISH BEHAVIOR While exploring these questions, students will quickly Full Stream Name: Measuring the coevolution of run into fundamental questions about what it means cognition and behavioural trade-offs in fish to do mathematics: how can we define the terms Principal Investigator: Molly Cummings we are using to make sure everyone has the same Research Educator: Mary Ramsey understanding? How do you convincingly show that you know something must be true, rather than Fish are smart! But are some smarter than others? just seeing that it’s true for some specially chosen And what does personality and/or social interactions examples? How do we communicate mathematical have to do with it? ideas to others? We take a comparative approach to ask two primary questions: DIY DIAGNOSTICS (1) Do learning capabilities vary predictably between Full Stream Name: DIY Diagnostics species with different types of social interactions? Principal Investigator: Andy Ellington Research Educator: Timothy Riedel (2) Is there a relationship between an individual’s learning abilities and other behavioral attributes? Be a part of the ongoing revolution of do-it-yourself Is cognitive performance linked to activity, anxiety, (DIY) health diagnostics! This new stream will design exploratory, mate choice, and/or sociability and develop inexpensive andeasy-to-use medical behaviors? diagnostic tests intended for the patient to use at home. This democratization of diagnosis will save Students will conduct experiments with local time and money and help combat the growing cost of and semi-wild fish populations to test how social health care. Concurrent with developing diagnostic interactions influence four spheres of animal tests, we will be building virtual interfaces to tap behavior: mate choice, sociality, anxiety/exploration, into the power of medical and social data sets for and general learning ability. improving patient health. This stream is open to developing diagnostic technology utilizing any tools available including, but not limited to, biochemical tests, electronics, robotics, and large data sets including social networks.

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FUNCTIONAL GENOMICS GEOMETRY OF SPACE Full Stream Name: Functional Genomics Research Full Stream Name: Geometry of Space Principal Investigator: Vishy Iyer Principal Investigator: Karl Gebhardt Research Educator: Dia Bagchi Research Educator: Shyamal Mitra

How can we use genome sequences to better In the Geometry of Space stream, students will understand the function and evolution of organisms begin to understand the large-scale structure of at the molecular level? the universe through a study of the distribution Next generation sequencing technologies explore the of galaxies and clusters of galaxies using algorithms molecular biology of organisms on a genomewide developed in computational geometry and applying scale. These cutting edge methods enable high techniques in data analytics. The galaxy data will resolution inspection of whole-genome regulatory be obtained from the Hobby Eberly Telescope Dark interactions and gene expression. The Functional Energy Experiment (HETDEX), the Sloan Digital Genomics Research Stream combines molecular Sky Survey (SDSS), and from the NASA/IPAC experimentation and creative computational Extragalactic Database (NED). analysis to engage significant novel research into We will use computational geometry to obtain the size the mechanistic understanding of transcriptional and center of clusters of galaxies and data analytics regulation as well as the evolutionary underpinnings to determine member galaxies and outliers. We will of molecular behavior. compute the velocity dispersion of he clusters and their mass-to-light ratio. Specifically, one of the questions that we will try to answer is - are there GENE NETWORKS interconnections between clusters and are the Full Stream Name: Vertebrate Interactome clusters themselves clustered to form superclusters? Mapping We will provide 3-dimensional maps of the Principal Investigator: Scott Stevens distribution of galaxies. Research Educator: Al MacKrell This is observational cosmology that is direct and Students in the Vertebrate Interactome Mapping intuitive. The concepts in astronomy that we are (VIM) Stream investigate the ribonucleoprotein dealing with are simple but deep. Through our course complexes (RNPs) that facilitate mammalian gene work we will develop the necessary programming expression. RNPs can regulate splicing to create and data analysis skills. The results of this study will multiple mRNAs from a single gene, and control deepen our understanding of the large-scale structure the stability, cellular localization and translation of of the universe and the geometry of space that we live mRNAs produced. We want to understand what in. RNPs do and how they function. To do this, we are studying the function of DExH box RNA helicases, proteins that function in gene expression by GLOW WORMS remodeling ribonucleoproteins. We are also studying Full Stream Name: Glow Worms the diverse collection of G patch domain containing Principal Investigator: Daniel Dickinson proteins found in human cells. Proteins in this Research Educator: Ryan Doonan family are frequently observed interacting with DExH proteins and regulating their specificity and activity. The Glow Worms stream involves CRISPR “knock- Our primary approach involves the expression of in” technology to add a fluorescent protein tag affinity tagged proteins in mammalian cells, which (such as GFP) to any gene of Caenorhabditis permits the tag-mediated purification of complexes elegans, a microscopic roundworm. This allows that contain the protein. We use this approach to the expression of the gene, and the behavior of its understand the functions of these proteins in normal protein product, to be observed in living animals cells, and their role in the pathology of cancer and without the need for overexpression (see the movie for an example of a worm embryo expressing two developmental defects. tagged proteins, one green and one magenta). C. elegans is one of the most widely used animal model organisms, particularly in the fields of genetics and developmental biology.

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LUMINATORS By doing this, we reprogram bacteria to serve a Full Stream Name: Functional Materials Based on purpose of our choosing. Previous examples of this Metal Complexes approach include creating bacteria that are addicted Principal Investigator: Richard Jones & Emily Que to caffeine, and using these bacteria to accurately Research Educator: Lauren DePue measure the caffeine content of beverages. Students will first learn how to do this sort of genetic The Functional Materials Stream focuses on the manipulation and then move on to conduct research development of new functional materials. Students on an already existing project or begin a new project. are involved in ongoing research in photoluminescent Students from this stream will have the opportunity lanthanide coordination complexes. Recently, the to compete on the UT Austin iGEM team. research in these novel functional materials has attracted a great deal of interest because of their potential applications in photovoltaic devices (solar cells, which would relieve our emerging local, national, NANO CHEMISTRY and global energy crisis), fluoroimmuno-assays, Full Stream Name: Nanomaterials for Chemical laser systems, bioprobes, and optical amplification. Catalysis The students will learn how to design and synthesis Principal Investigator: David Vandenbout and luminescent metal complexes and study the Richard Crooks relationship between the photophysical properties Research Educator: Tony Dylla and their coordination structures determined by X-ray crystallography. How do you make new types of nanoreactors? In this Research Stream, students use cutting edge technology to synthesize nanoparticles using MAGNETIC MATTER combinations of metals including copper, gold, Full Stream Name: Electronic and Magnetic platinum, palladium, and nickel. The particles act Materials Research like “nanoreactors” to catalyze chemical reactions. Principal Investigator: John Markert Nanoparticles are tiny, around one billionth of a Research Educator: Matt Dwyer meter across, but they hold huge potential for use in biosensors, drug synthesis, fuel production, How do you create materials with new electronic and environmental remediation, and specialty chemical magnetic properties and structures? production. Our goal is to identify the best chemical This Research Stream focuses on materials physics catalysts that could eventually be used in these and the design and development of materials for applications. use in data storage, optics, sensors, and optical and infrared astronomy. Students will learn new materials synthesis via solid state reaction, followed PLANT PATHWAYS by structural, microscopic, magnetic, thermal, Full Stream Name: Epidermal Cell Fates and and superconducting characterization of the Pathways materials. Students may also perform cantilever Principal Investigator: Alan Llyod micromagnetometry, interferometry, and magnetic Research Educator: Tony Gonzalez resonance microscopy. How is a cell’s fate determined? This stream uses a comprehensive genetics approach MICROBE HACKERS to investigate developmental mechanisms that lead Full Stream Name: Hijacking Microbial Factories to cell fate decision events and the regulation of organ for Synthetic Biology differentiation pathways. Students will design and Principal Investigator: Jeffrey Barrick pursue experiments using a broad range of genetic Research Educator: Dennis Mishler strategies such as classical, molecular, forward and reverse genetics. In the process students will learn Microorganisms are the unparalleled masters of how to clone genes, engineer DNA, generate mutant building and breaking down chemical compounds. and transgenic organisms, document and analyze Can we reprogram bacteria so that they perform data, and more. While this lab focuses on a plant functions that are beneficial to society? molecular/genetic model, all the technologies learned Microbe Hackers conducts research in the field in this stream are common to research in all modern of synthetic biology. We manipulate the DNA molecular/genetic model organisms. instructions for bacteria through genetic engineering.

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PRACTICAL SENSORS (ARI) ROBOT LEARNING Full Stream Name: Practical Molecular Sensors Full Stream Name: Robot Learning from Principal Investigator: Eric Anslyn, Andy Ellington Demonstration and Interaction & Richard Crooks Principal Investigator: Scott Niekum Research Educator: Pedro Metola Research Educator: Rudolf Lioutikov

This stream will focus on the implementation of How can robots be easily programmed by non-expert several sensing protocols in existing analytical users in homes and workplaces? How can robots learn devices to further their potential, as well as explore to interpret and generalize human demonstrations? a new approach to selective molecular recognition. There will be three distinct branches of research. Currently, most robots are programmed meticulously The first project will involve the adaptation of an by robotics experts in a controlled laboratory electrochemical analytical method on a paper setting—a model that is obviously not scalable to large- platform for the determination of hormones in scale deployment. Robot learning from demonstration biological media. In the second project the students has emerged as an alternative paradigm for teaching will use the in vitro technique of aptamer selection robots new tasks by simply showing them what to (SELEX) to find those nucleotide compounds that do, rather than by writing code. Thus, learning from bind to receptor-analyte complexes as a means demonstration research tries to answer the question: to impart to them selectivity or enhanced binding “How can robots learn to interpret and generalize abilities against targets like polysaccharides and human demonstrations?” Solving this core research nerve agents. The students in the third project of this problem will enable the next generation of personal stream will be tasked with translating colorimetric robots to revolutionize the home and workplace in assays into a handheld spectroscopic device with the coming years. goal of utilization in enology field tests and rapid drug This research stream will place students at the analysis. cutting-edge of robot learning from demonstration research, working with robots to perform complex manipulation tasks, such as autonomously building QUANTUM COMPUTING IKEA furniture. Students will be given instruction in Full Stream Name: Harnessing Quantum Physics three core areas of robotics: manipulation, perception, for Computation and human-robot interaction. Additionally, students Principal Investigator: Brian La Cour will learn and practice programming skills via hands-on Research Educator: Noah Davis mini-projects in each of these areas. After these key competencies have been acquired, students will devise Quantum computers promise to revolutionize and implement research projects in the area of learning computing as we know it. How do they work and what from demonstration. are they really good for? In this FRI stream, students will learn about quantum computing and explore how they may be used to SUPRA SENSORS solve real-world problems. The work will consist Full Stream Name: Supramolecular Sensors of a combination of both computer simulation and Principal Investigator: Eric V. Anslyn hardware experimentation using the small state of Research Educator: Diana Zamora-Olivares the art quantum computer available through the IBM Quantum Experience. Students will engage in hands- In the Supramolecular Sensors Stream, students on learning and research using actual hardware that take on the challenge of constructing differential may be accessed locally or remotely. Research topics array sensors that can be ultimately applied to many will include the following: (1) understanding how fields such as homeland security, food industry, quantum systems can be used to store and process environmental science, and clinical diagnostics. information, (2) understanding and implementing The current project of the whole stream is the quantum algorithms to solve specific problems, and construction of peptide-based sensors that can be (3) methods of protecting quantum information using used to differentiate two types of samples, wine quantum error correction. Students will benefit from varietals, and protein kinases. The wine sensors work a background in basic linear algebra, familiarity with a via the indicator displacement assay, a technique high-level programming language, and an introduction pioneered by Dr. Eric Anslyn and his research group at to modern physics. the Department of Chemistry and Biochemistry. The kinase biosensors work via a fluorescence-enhanced mechanism that is displayed when the biosensor is recognized by the protein kinase.

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URBAN ECOSYSTEMS VIRTUAL CURES (FRI & ARI) Full Stream Name: Urban Ecosystems Full Stream Name: Virtual Drug Screening Principal Investigator: Advisory Council Faculty Lead: Walter Fast Research Educator: Mary Poteet, Stuart Reichler, Research Educator: Josh Beckham Ruth Shear Can new drugs be identified from virtual libraries of Can we discover ways to decrease the stress of drug-like molecules? human presence on local ecosystems to promote sustainability? Identifying new drug leads using traditional methods is an expensive and time consuming process. This Understanding the function of urban ecosystems can research stream uses both computational and wet lab help build more sustainable cities as well as to provide techniques to discover new drugs. First, a molecular areas of beauty and relaxation for urban dwellers. docking program is used to sift through libraries of In this multidisciplinary research stream, students chemical structures and predict which ones may bind use techniques from chemistry, biology, molecular to a protein that is a potential drug target. Results biology, microbiology, ecology, environmental are analyzed with a molecular graphics program. science, geological science, and social science to Students will learn how to run Virtual Drug Screening study urban ecosystems. We currently focus on the software and will use molecular graphics programs to Waller creek watershed which includes most of the UT interpret the results. Then DNA cloning and protein campus, and with more than 50% impervious cover, expression protocols are implemented in the lab to it is the most densely developed urban watershed in test the top potential drugs in enzyme assays. Austin. Leveraging the restoration work by the City of Austin and the Waller Creek Conservancy, this watershed provides an ideal testing ground to study WHITE DWARF STARS urban ecosystem functioning and its response to Full Stream Name: Exploring the Universe with restoration. Our current research includes identifying White Dwarf Stars and quantifying contaminants in the creek, localizing Faculty Lead: Don Winget contamination sources, and evaluating how stressors Research Educator: Mike Montgomery from urbanization and climate change affect ecosystem function. Our students engage in real- What can white dwarfs tell us about exotic processes world research and problem solving with faculty, staff, in stars? and community stakeholders, like the City of Austin, the University of Texas, The Nature Conservancy, and Students in this stream will make astronomical the Waller Creek Conservancy. observations of pulsating white dwarf stars and those in close binary systems. They will analyze the data and participate in building theoretical models through which we will explore physical processes in stars (e.g., convection, crystallization, and diffusion) as well as various relativistic effects (gravitational radiation, doppler beaming). In addition they will perform numerical experiments to study how pulsations allow us to “see beneath the surface” of these stars.

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Poster Presentations

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Using HETDEX to classify Lyman-Alpha high-redshift galaxies

Presenter(s): Sarah Bruce, Valentina Tardugno Poleo, Abriana Himanog, Nick Davila, Thomas Maina Collaborator(s): Óscar Chávez Ortiz, Gene Leung, Steve Finkelstein Department(s): Department of Mathematics; Department of Astronomy; Department of Physics

This research aims to examine very distant, Lyman-alpha emitting galaxies from the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) survey to better understand their contribution to the reionization of the intergalactic medium. HETDEX is an unbiased, large-area, multifiber, spectroscopic survey that collects spectra from millions of galaxies through Lyman-alpha emission using Visible Integral-Field Replicable Unit Spectrographs (VIRUS). We use Elixer Plots, a classification tool, to examine images, spectra, and fitting parameters, and distinguish between distant Lyman-alpha emitting galaxies, nearby galaxies, and noise in the North Ecliptic Pole (NEP) and Spitzer/HETDEX Exploratory Large-Area (SHELA) fields. Of the 330 NEP sources, we found 143 (43%) to be potential distant galaxies. Of the 150 SHELA sources, we found 76 (51%) to be potential distant galaxies. Utilizing the selected galaxies, we can analyze the physical properties of Lyman-alpha emitters, searching for correlations between galaxy properties and Lyman-alpha emission strength. Our results will inform us of the types of galaxies responsible for reionizing the universe at earlier times.

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The orbital properties, internal motions, and origins of the

120-Myr-old Pisces-Eridanus Stellar Stream

Presenter(s): Alice Burington-Luna Collaborator(s): Madeline Lucey, Keith Hawkins Department(s): Department of Astronomy: The University of Texas at Austin

Gaia DR2 has recently revealed the nearby 120 Myr old Pisces-Eridanus (Psc-Eri) stellar stream orbiting the Milky Way. Studying stellar streams similar to Psc-Eri can help us understand the evolution of the Galaxy and the nature of star formation. In this work, we use Gaia astrometric data to perform orbit integration of the stream members throughout its formation (t=-100Myr to t=500Myr) using the python package galpy. We also created 3-dimensional quiver plots of its structure and motion at multiple time periods to understand the internal kinematics of the system and determine its morphology at birth. The preliminary results of its structure at birth address the current debate of whether the stream formed as a spherical or cylindrical cluster.

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Conditions for planet formation within binary star systems

Presenter(s): Shannon Fitton Collaborator(s): Benjamin Tofflemire, Adam Kraus Department(s): Department of Astronomy; University of Texas at Austin

This project focuses on determining the best conditions for young binary star systems to retain their protoplanetary disk, such that exoplanet formation is favorable. Binary systems are a common outcome of star formation, however our understanding of planet formation in the binary environment is only now being explored. Since detecting protoplanetary disks is more feasible than detecting exoplanets themselves, creating a model showing the likelihood of the presence of exoplanets within binary systems provides clearer insight on what the ideal conditions are within the stellar pair to make such detections. However, binaries have lower disk occurrence rates than single stars, though it is unclear what properties of the binary are responsible for the retention of protoplanetary disk material. To investigate the conditions necessary for protoplanetary disk retainment, a list of candidates was compiled creating subcategories to include systems with and without disks, and once the systems are vetted as being gravitationally bound, they are run through LOFTI--a program that calculates orbital constraints for a stellar binary and fits orbital parameters to the system. The resulting information is then compiled such that the key differences in the orbital parameters between disk bearing and non-disk bearing binaries can be observed. These differences will allow for the calculation of the statistical probability for a particular binary system retaining its protoplanetary disk, and therefore the likelihood of exoplanets being present.

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Recognizing Indigenous contributions to science

Presenter(s): Aubrey Medrano Collaborator(s): Megan Raby Department(s): Department of Astronomy; Department of Latin American Studies

Works and studies detailing the history of physics and astronomy often exclude indigenous Latin Americans from their narratives, and this exclusion from the history of science contributes to indigenous exclusion from modern universities and scientific institutions. Past and current efforts to include indigenous people in scientific endeavors haven’t been efficient because of a lack of focus on how indigenous science is known and practiced in comparison to Western methodologies. This work advocates for educational efforts in these fields to include the discussion and analysis of how different cultures interact with and interpret knowledge as a means of increasing the representation of indigenous people in physics and astronomy. A literature review focused on indigenous Central American scientific interactions with Western entities and societies, with an emphasis on physics and astronomy, illuminates how indigenous science has been minimized and how to best increase the representation of indigenous scientists. By connecting indigenous scientific development missing from the history of science to the known timeline of human scientific development, the need to expand historical science records is demonstrated. By exploring why and how this history has been excluded from scientific accounts, scientists interested in increasing the accessibility of their field can better understand the barriers keeping indigenous people from physics and astronomy today. Armed with a deeper and more empathetic comprehension of the obstacles facing indigenous scientists, Western professionals can better approach removing those barriers for a more diverse and complex field.

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Determining the active galactic nuclei (AGN) fraction at MUV=-23 to

determine the SHELA Field AGN UV Luminosity Function at z~3

Presenter(s): Daniel Mock Collaborator(s): Steven Finkelstein, Adam McCarron, A. Medrano, D. White, D. Davis, I. Laseter, R. Ramachandran Department(s): Department of Astronomy

The shape of the AGN luminosity function at high redshift has been hard to determine, as previous studies have been limited by small amounts of high quality spectra and/or by the small area of their surveys. The shape of this luminosity function at the faint end has implications for the contribution of AGNs to the ionizing budget during the epoch of reionization. Recent work in the HETDEX/SHELA field at z=4 has shown that the faint-end slope of the AGN luminosity function may be steeper than previously thought, but this result is degenerate with the shape of the bright-end of the galaxy luminosity function. This degeneracy can be broken by using spectroscopy to empirically measure the AGN fraction amongst objects at MUV = -23. We tackle this problem at z~3, where spectra from the Hobby Eberly Telescope Dark Energy Experiment (HETDEX) probe AGN-sensitive rest-ultraviolet emission lines. Here we present a sample of 573 spectra for objects at z~3 across the 24 deg^2 of the HETDEX survey in the SHELA field. We used an affine invariant Markov chain Monte Carlo (MCMC) Ensemble sampler to extract information from the spectra. We also use a t-distributed Stochastic Network Embedding (tSNE) algorithm with a sample of known galaxies, AGN, stars, and low redshift galaxy interlopers to classify the 573 objects. We find that these methods allow us to classify AGN at a fairly high confidence, and future work will soon allow us to directly measure the AGN fraction at the proper magnitude.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 6

Determining membership of stars in open star clusters

Presenter(s): Neel Nagarajan Collaborator(s): Chris Sneden Department(s): Department of Astronomy

Astronomers often want to study star clusters and measure various properties like age, metallicity, etc. However, we must first define a cluster by identifying exactly which stars are members of the cluster we are looking at. In order to be a member, a star must have formed at roughly the same time as all the other cluster members and must have formed from the same molecular cloud of gas. I use the principle that stars which are members of a cluster move around the galaxy in a similar way, and so they should all be a similar distance from us and shift a similar amount in the sky every year. In astronomy language, these stars should all have the same proper motion and parallax. I looked at two open star clusters- NGC 752 and NGC 6791 and downloaded the stars’ data from GAIA, and processed the data using the above principle to come up with a list of cluster members. Finally, I used the idea that if I am successful in determining which stars are members, those stars must form the characteristic Hertzsprung-Russell (HR) diagram distribution when plotted on a color magnitude diagram (CMD). I got highly accurate results for NGC 752 as its CMD plot closely matched the HR distribution. For NGC 6791, the result was not quite as accurate, partly due to the great distance between the cluster and us and the high presence of dust between us and the cluster. The effect of the great distance was that for many dim stars, the uncertainties in the data were too large and those stars had to be filtered out separately. Nevertheless, my CMD for NGC 6791 did look similar to a published CMD for the cluster, indicating that my algorithm was useful even for more distant clusters.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 7

Evidence for a buried AGN in an extremely bright dusty galaxy

Presenter(s): Pranav H. Premnath Collaborator(s): Justin Spilker, Caitlin M. Casey, Mark Gurwell Department(s): Department of Astronomy

We present preliminary results of a submillimeter spectral line survey of a strongly lensed dusty star-forming galaxy (DSFG) at z ? 2, near the peak epoch of cosmic star formation. We use data from the Submillimeter Array, which recently completed a systems upgrade that substantially increased the instantaneous bandwidth. Focusing on the brightest spectral lines of CO and atomic carbon, we characterize the interstellar medium properties of this galaxy. We find highly excited CO and [CI] emission, and a large [CI] line ratio implies a higher excitation temperature than other extreme high-redshift sources. Based on this evidence, we infer that the source likely hosts a dust-obscured active galactic nucleus similar to other well-studied DSFGs.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 8

Reference star differential imaging of the PDS70 System with

HST/WFC3 images

Presenter(s): Aniket Sanghi Collaborator(s): Yifan Zhou, Brendan P. Bowler Department(s): Department of Astronomy

The direct detection technique has enabled high contrast imaging of extrasolar planets and has contributed to giant leaps in characterizing exoplanet atmospheres, constraining mechanisms of planet formation, and studying system architecture. The task of imaging an exoplanet is extremely challenging, as the light from a planet is around a million times fainter than that observed from the planet’s host star. The ultimate goal for direct imaging surveys is to detect and characterize a true Earth analog outside our Solar System. While rapid improvements in instrumentation and post-processing techniques have contributed to a steady rise in the number of directly imaged exoplanets, we are still limited to detecting widely separated self-luminous giant exoplanets. We present a new image processing technique for detecting exoplanets in Hubble Space Telescope observations. While the most commonly used technique of angular differential imaging is successful in ground-based observations of exoplanets, it is inherently difficult to perform with space-based telescopes such as Hubble, leading to low observing efficiency. We demonstrate the applicability of reference star differential imaging, a mechanically easier and relatively time-inexpensive technique, to Hubble Space Telescope images of the star PDS70 to uncover the planet PDS70b. Our high-fidelity detection of this young planet enables detailed characterization of its formation processes. Our technique will improve the Hubble Space Telescope’s performance in directly imaging exoplanets and will be directly applicable to the upcoming James Webb Space Telescope observations to characterize different exoplanetary systems.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 9

Imaging and spectroscopic programs for James Webb space telescope

Presenter(s): Raghav Venkataramanan, Aubrey Medrano Collaborator(s): Steven Finkelstein Department(s): Department of Physics

The James Webb Space Telescope (JWST) will bring about a dramatic improvement in sensitivity and angular resolution in the infrared. In this poster, we present two research projects related to preparations for NIRSpec (spectroscopy) and NIRCam (imaging) observations that will be performed as part of the CEERS survey. First, for the spectroscopic program, we are conducting target validation by visually inspecting data obtained using the Hubble (visible) and Spitzer (infrared) Space Telescopes in order to create a sample of high-redshift galaxy targets. A typical inspection involves studying a spectral energy distribution, photometrically-determined redshift, and a residual map, which models all sources imaged by Spitzer individually and subtracts them from the overall image. So far, we have completed over 700 inspections for redshifts z=6-11. Through this work we are building a sample of high-fidelity targets that will allow us to spectroscopically study a large number of galaxies in the early universe. In the second project, within the imaging program, we test how well JWST will be able to recover the observed physical sizes of galaxies as a function of their stellar mass. We make use of simulated galaxies from the SIMBA SPH simulations and use snapshots covering z = 3-9 to find the distribution of masses in all the galaxies. We use the Python Line Of Sight Extinction by Ray-tracing software to create image stamps of these galaxies in the NIRCam filters, choosing resolved galaxies to measure half light radii and investigate a size-mass relationship for each redshift. We then include these galaxies in a set of simulated NIRCam data being prepared for the CEERS team. We measure the goodness of fit of the galaxy radii from the SIMBA simulations to those we calculate the NIRCam datasets to explore how well the CEERS observations will constrain size-mass relationships at z > 3.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 10

Determining the efficiency of HETDEX's emission line discovery

algorithm using Markov chain Monte Carlo methods

Presenter(s): Delaney White Collaborator(s): Steve Finkelstein, Adam McCarron, Dustin Davis, Oscar Chavez, Gene Leung, Daniel Mock Department(s): Department of Astronomy; Department of Physics

The Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) takes advantage of the Hobby-Eberly Telescope at McDonald Observatory to map the three-dimensional positions of more than a million galaxies and will ultimately revolutionize our understanding of dark energy. HETDEX has an algorithm for detecting spectral emission lines, but it fails to detect faint emission features, a flaw we are hoping to improve with this analysis. Furthermore, verifying the catalog of known detections would give scientists confidence that they are studying real features. I extracted data from HETDEX based on a GOODS-N continuum catalog with ~60,000 known galaxies. To detect emission lines, I applied an automatic line-finding code I created that uses a Markov chain Monte Carlo Ensemble sampler. My results will test the HETDEX detections and quantify how detection efficiency of the HETDEX line-finding algorithm depends on a target’s brightness. Quantifying the missing features will allow collaborators to improve the HETDEX algorithm and improve the detection rate, which increases the galaxy sample for useful statistical inference. My early results not only verify that HETDEX fails to detect faint features, but that it could also be improved by searching for broader and narrower features than it currently does.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 11

Searching for potential small molecule Inhibitors for main protease in

SARS-CoV-2 by virtual screening

Presenter(s): Jadelynn Aki Collaborator(s): Josh Beckham Department(s): Freshman Research Initiative; Department of Molecular Biosciences; College of Natural Sciences

The advent of the Coronavirus disease 2019 (COVID-19), a member of the coronavirus family caused by SARS-CoV 2, threatened global health and was responsible for the most recent pandemic. The medical and scientific community made history by creating a vaccination for COVID-19 in less than a year; however, some viral mutations emerged making it more contagious, hence the urgency of finding a therapeutic drug for COVID-19. Viral proteases are well-validated drug targets, and the main protease is not an exception. The main protease is an excellent candidate as it cleaves the polyprotein of the virus into individual, functional proteins, and the proteolytic release is a process that is essential to the replication cycle. The uniqueness of this enzyme compared to human proteases also contribute to its potential as a drug target. Structure-based computational methods identified specific ligands that can bind to the target protein and become potential inhibitors of the COVID-19 main protease. Virtual screening with the molecular docking program GOLD docked novel compounds into the target protein to examine their binding interactions. Of the positive controls docked, Ritonavir ranked the highest with a score of 93.3 in GOLD. Various compound libraries consisting of 74,388 ligands (NIH Clinical Collection, MayBridge HitFinder 9, ChemBridge Library, In-house collection, CNS, Microformats, Novacore, and a large ZINC library) were screened in GOLD with scores ranging from 23.85-113.71. Additional library screenings will be performed to further discover promising novel ligands which can be evaluated for their inhibitory properties through biological assay testing.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 12

Identification of novel inhibitors for lethal factor in Bacillus Anthracis

by structure-based virtual screening

Presenter(s): Sofia Alvarez, Mahima Singeetham Collaborator(s): Josh Beckham Department(s): Biology; University of Texas

Anthrax is an infectious disease caused by the gram positive, rod shaped bacteria bacillus anthracis. It can be transferred through cattle from bacterial spores found in soil within farming regions of central and South America and sub Saharan Africa. Although the infection rate is minimal, anthrax can cause severe symptoms like itchy blisters/bumps, painless ulcers with black centers, and can lead to death if left untreated. Currently, there is no vaccine or formal treatment for this virus, which poses a threat to agricultural workers and the general population because of its potential to be utilized as a bioweapon. The risk of warfare enforces the need for developing inhibitors that can render the virus harmless and/or kill it. A possible target for this is Lethal Factor, a toxin produced by anthrax that cleaves the N-terminal of mitogen-activated protein kinase kinases. By itself, Lethal factor is not harmful but when paired with one of the other two toxins like the protein antigen and/or the edema factor, it amplifies its virulence and protein production. In order to identify novel inhibitors, virtual screening software such as GOLD and ICM was run to screen multiple libraries containing thousands of ligands that yielded a ranking of high scoring drug compounds. Overall, large libraries HF9 and Zinc generated the top ligands with scores ranging from 80-90, suggesting high binding affinity to the active site and hypothetically suppressing its functionality. The next step would be to put these drug compounds to the test in a wet lab setting through an enzymatic assay to confirm or refute the results from the virtual simulation.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 13

The separation of functionality in the CDX2 protein to stop inhibition

of ATM kinase DNA repair

Presenter(s): Payal Amin Collaborator(s): Soo-Hyun Yang Department(s): Biology; FRI Biobricks Stream

This study serves to identify the site within the homeobox domain of CDX2 that can separate its two functions of transcription and ATM Kinase inhibition, by working on E241V, a mutant gene coding for the CDX2 protein which contains multiple modifications to its primary structure. If expressed, the E241V gene may gain an altered function of the CDX2 protein in that it is unable to inhibit ATM kinase while maintaining its transcription abilities. The mutant E241V gene was inserted into the pDESTMBPHis vector and replicated in BL21 (DE3) Codon Plus E. coli cells through cell transformation. The expression of the proteins within the transformed bacterial culture was then induced using an allolactose, IPTG. In order to analyze and confirm the successful expression of the mutant CDX2 protein, an 8% sodium dodecyl sulfate-polyacrylamide gel was utilized to confirm the identity of the CDX2 protein. After being purified using MBP-affinity chromatography, the presence of the purified CDX2 mutant was confirmed through a subsequent 8% sodium dodecyl sulfate-polyacrylamide gel, which allowed for a visualization of the extent of protein purification through the intensity of the bands. Additionally, the characteristics of the mutant were further analyzed by quantifying the mutant gene using both BSA dilutions and a previously quantified CDX2 mutant, T194D. The E241V mutant was found to have a concentration of 1.739 µM. Furthermore, a DNA Binding Assay was used to visualize the binding of the CDX2 mutant to DNA, which confirmed the transcriptional functionality of the E241V mutant gene.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 14

Characterizing the PurR mutation in caffeinated coli strains

Presenter(s): Aneesa Bhakta, Alexa Burchak, Antara Gupta Collaborator(s): Mina Kim Department(s): Department of Molecular Biosciences

While sequencing strains of Caffeinated Coli, we found a serine to proline mutation in PurR, a repressor protein responsible for regulating xanP, guaA and several other genes in the purine biosynthesis pathway. Caffeinated Coli is a collection of strains of E. coli that are reliant on the xanthine salvage pathway to convert xanthine and xanthine alkaloids, such as caffeine, to guanine due to the deletion of guaB, a gene vital to the de novo synthesis pathway. Since the PurR mutation was present in all strains of Caffeinated Coli, it is likely that this mutation had a beneficial effect on Caffeinated Coli function. Therefore, it is important to identify the origin of this mutation in the progenitor strains to document when this mutation developed. Through our research, we hope to determine when the PurR mutation first appeared in our progenitor strains and classify not only how the PurR mutation affects purine biosynthesis, but also how it impacts evolutionary fitness. Once we receive Next Generation Sequencing results for all of our strains, we can begin to identify when the PurR mutation first appeared during the process of evolving the Caffeinated Coli strains by comparing the NGS data to a reference sequence from the E. coli genome. We have also designed plasmids with GFP reporter genes inserted downstream of putative PurR binding sites that are found within the xanP and guaBA promoters to test for differential gene expression in cells containing or lacking the PurR mutation. The PurR mutation is of great interest because it illustrates how the Caffeinated Coli strains are evolving in response to their genetic engineering. What we learn from this one evolutionary process may be generalizable to other organisms undergoing sudden alterations to their genomes.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 15

Identifying the active site on the CDX2 homeodomain responsible for

ATM-MRN inhibition

Presenter(s): Nia Choi Collaborator(s): Soo Hyun Yang,Tanya Paull Department(s): College of Natural Sciences; Freshman Research Initiative Biobricks Stream

Ataxia-telangiectasia mutated (ATM) kinase is vital in DNA DSB signaling and repair. ATM was identified in patients with Ataxia-telangiectasia (A-T), a neurodegenerative disease where A-T defective cells are unable to activate cell-cycle checkpoints and respond to DNA damage. ATM is activated in the presence of DSBs through its interaction with Mre11/Rad50/Nbs1 (MRN) which further activates downstream repair proteins. While the interaction between ATM and MRN is crucial to initiate the DSB repair signaling pathway, it is unclear how ATM-MRN interaction is regulated in cells. The caudal-type homeobox transcription factor-2 (CDX2) is a member of the homeobox transcription family that is expressed specifically in human intestinal epithelial cells. Recent studies have found that CDX2 inhibits this ATM-MRN interaction via its homeodomain. The goal of this project is to identify the active site on CDX2 responsible for ATM inhibition but separate from its transcription activity. The experimental aims of this study are 1) to introduce a point mutation within the CDX2 homeodomain via site-directed mutagenesis, 2) to examine the effect of the CDX2 mutation on its transcription activity, and 3) to examine the effect of the CDX2 mutation on ATM-MRN interaction. Overall, these experimental aims can help identify a separate-function mutation of CDX2 which will allow us to study the physiological effects of ATM inhibition by CDX2 in response to DSBs in human epithelial cells.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 16

Finding novel inhibitors of SARS-CoV-2 main protease

Presenter(s): Ji Min Chon, Jeff Huynh Collaborator(s): Josh Beckham Freshman Research Initiative; Department of Molecular Biosciences; Department. of Chemistry; College of Department(s): Natural Sciences; The University of Texas at Austin

SARS-CoV-2, or the causative agent of the 2019 coronavirus disease, has caused a global health crisis and is noted to be the most significant outbreak of the 21st century. The lack of therapeutic options and significant mortality rate make this disease a pressing candidate for drug discovery. One promising drug target is the main protease (denoted as Mpro) due to its importance in viral replication in the early stages of infection. The enzyme cuts the polyproteins translated from viral RNA to produce functional and mature viral proteins. In addition to this target protein’s essentiality, its highly conserved active site and dissimilarity to human proteases make Mpro a worthwhile target. Virtual screening was used to identify top compounds that may serve as potential hits for later biochemical assays. The molecular docking program GOLD docked and gave predicted binding via a GOLD score for several control compounds against the 6WTT crystal structure of Mpro to test the validity of this method. The positive control GC-376 was docked in a similar conformation to its x-ray crystallography pose and ranked high with a GOLD score of 87.53. Several compounds were selected from over 200,000 in various compound libraries such as: the NIH Clinical Collection, Maybridge HitFinder 9, and ZINC ChemBridge Library. Further screening was done on larger compound libraries from Maybridge and ZINC, which had score ranges of 58.43-98.24 and 52.5-106.78, respectively. Another docking program, ICM, was used in parallel on the same libraries to identify candidate compounds using an alternative scoring algorithm. From these collective results we are able to better visualize the binding interactions that are predicted to inhibit the functions of Mpro and compare the scoring algorithms of two virtual screening programs. We plan to screen more ligands to identify novel scaffolds that can contribute for further research against Mpro.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 17

Intrinsic hydrolysis of GTP in HRas

Presenter(s): Danielle Landry Collaborator(s): Jackson Fink, Lauren Webb Department(s): Department of Chemistry

Small monomeric GTPase proteins regulate many biological functions such as signal transduction at membranes, cell proliferation, cell differentiation, division, and more. These proteins act as a switch that controls cell signaling by cycling between “active” and “inactive” conformations. One particular superfamily of interest is the Ras family of GTPase proteins, which function as signal transductors at cellular membranes that control cell division. Specifically, p21 H-Ras (Ras) is a common oncoprotein related to pancreatic cancer, non-small cell lung cancer, and colon adenomas. Drugging this protein has proven to be extremely difficult, as GTPase proteins all have similar structures and functions making targeting a specific protein in the various superfamilies difficult. Ras has been thoroughly investigated and several specific oncogenic amino acid mutations have been identified at G12, G13, and Q61. These mutations cause Ras to be stuck in the active signaling confirmation resulting in uncontrolled cell growth. Residues Q61 and Y32 interact at the active site and have been implicated in the proposed mechanism of intrinsic guanosine triphosphate (GTP) hydrolysis to guanosine diphosphate (GDP) as stabilizers of an intermediate hydronium ion while a catalytic water performs the hydrolysis reaction. Previously, intentional mutations were made to Q61 through site directed mutagenesis to measure the different rates of hydrolysis of each mutant and compare it to the wild type protein. These results suggest a relationship between the amino acid’s ability to contribute to the stabilizing hydrogen bonding network and the protein’s intrinsic rate of hydrolysis. To further investigate this, the same set of kinetics experiments are been repeated on the associated Y32 residue. These results will help elucidate the specific electrostatic environment around the active site of hydrolysis to aid in therapeutic drug discovery.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 18

Developing an antibody against CDHR3 to prevent RV-C infection

Presenter(s): Kaitlyn Lee Collaborator(s): Soo Hyun Yang, Karen Browning, Jason McLellan Department(s): Department of Integrative Biology; Biobricks for Molecular Machines; Department of Molecular Biosciences

Rhinovirus is one of the many viruses that causes the common cold. There are more than 160 types of rhinoviruses. Specifically, rhinovirus-C has been shown to be detrimental to children’s respiratory systems, causing several diseases such as asthma, bronchitis, and pneumonia. There has not been any developments of vaccines or antiviral therapies to help young children, who are most susceptible to RV-C infection. Current studies have shown that RV-C has a high affinity for Cadherin-related family member 3 (CDHR3). CDHR3 are membrane receptor proteins highly expressed in the airway epithelial tissues in human cells. Each protein consists of six domains. The transmembrane domains, Domains 1 and 2, are exclusive docking sites for the RV-C virus. RV-C binds to the CDHR3 receptors to infect the human cells. CDHR3 is capable of replicating RV-C, however, inhibiting the interaction can prevent RV-C infection of human cells. The purpose of this project is to develop an antibody against CDHR3 in order to prevent the binding of RV-C. First, CDHR3 will be expressed and purified. However, CDHR3 is insoluble, making it difficult to purify the protein to further obtain a crystal structure and to create antibodies. The first experimental aim of this study is to introduce a point mutation on Domains 1 and 2 of CDHR3 via site-directed mutagenesis to increase the solubility of CDHR3. Once CDHR3 is soluble, the next aims are to purify the CDHR3 homogeneously, create antibodies against the purified CDHR3 protein, and identify antibodies that exhibit strong inhibition of RV-C binding to CDHR3. Once a soluble CDHR3 is secured, further investigation of the protein can be done in order to develop an antibody against CDHR3. An antibody can be further enhanced to create vaccines and antiviral drugs to prevent RV-C infection, especially for young children who are of higher risk.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 19

Developing a biomarker diagnostic panel for Melanoma

Presenter(s): Rory Malek, Julia Zheng, and Maria Nguyen Collaborator(s): Timothy Riedel Department(s): Freshman Research Initiative DIY Diagnostic Stream

Melanoma is the deadliest form of skin cancer with 80,000 diagnosed cases in 2017 in the U.S. Diagnostics for melanoma involve the histological examination of biopsies and lack any widely-used biomarker alternatives. To address this, a biomarker assay was developed targeting secreted phosphoprotein 1 (SPP1), a hyperexpressed gene in melanomas, using loop-mediated isothermal amplification (LAMP), an assay that uses pH indicators to visually convey pH changes caused by DNA amplification. Five primer sets based upon the gene’s cDNA were tested on controls. Multiple LAMP trials were run for two primer sets, 1 and 5, with and without loop primers. Four samples were run per trial, and a positive test result was considered when two samples amplified. The sensitivity and specificity for primer set 5 was 100% and 20% without loop primers and 66.7% and 100% with loops, respectively. The sensitivity and specificity for primer set 1 was 100% and 0% without loops and 100% and 66.7% with loops, respectively. Only primer set 1 with loops produced significant results (n=7 trials, p

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 20

Using virtual screening to identify novel inhibitors for the Enoyl-Acyl

carrier protein reductase (InhA) in Mycobacterium tuberculosis

Presenter(s): Sarah Mayberry Collaborator(s): Josh Beckham, Walter Fast Department(s): FRI Virtual Cures Stream

Mycobacterium tuberculosis causes the highly infectious disease Tuberculosis, an airborne illness which still remains in the top 10 causes of death worldwide despite antibiotics and a vaccine, largely due to the recent antibiotic resistant tuberculosis strains. InhA, the enoyl-acyl carrier protein reductase, is an advantageous drug target due to its essentiality in m. tuberculosis, as it catalyzes the enoyl-acyl carrier protein double bond reduction, an essential precursor to create mycolic acids for cell wall fatty acid biosynthesis. Although there are current antibiotics for this drug target, many of these once-effective treatments are losing efficacy to the antibiotic strains, creating a need for novel InhA inhibitors. Using an x-ray crystallography structure of the enzyme, numerous large libraries of compounds were virtually tested against InhA using the virtual screening program GOLD (cite gold). This computational process, producing docking estimations and relative binding scores for each compound, quickly narrowed down the list of potential inhibitors for InhA. After analyzing these compounds using Lipinski’s data and the docking conformations in the molecular visualization program PyMOL, novel inhibitors for InhA that show great promise for inhibition were noted for further wet-lab research in drug discovery.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 21

aptamer research

Presenter(s): Taylor Oliphant Collaborator(s): Gwendolyn Stovall, Andy Ellington Department(s): FRI Aptamer Stream

The goal of this project is to create an aptamer database that would enable researchers to have easy access to the full knowledge of aptamer research. This aggregation of data also works to preserve aptamer research and ensure it is available for long term use. Data is collected through PubMed, added to a spreadsheet, and peer reviewed before it is added to the database. Currently, the database contains over 900 peer reviewed sequences, with more awaiting review.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 22

Virtual screening of possible small molecule inhibitors of a subtilisin-like protease from Pseudogymnoascus destructans, the causative agent of white nose syndrome in bats

Presenter(s): Marie Pearce Collaborator(s): Josh Beckham, Walter Fast Department(s): ARI Virtual Cures Stream

White nose syndrome is a lethal disease caused by the fungus Pseudogymnoascus destructans, which has been spreading across North American bat populations since late 2006. The fungus grows on external tissues of bats such as their wings, noses, and ears, and typically infects them during their torpor, or hibernation. This disease is a major concern as declining bat populations have significant impacts on the agriculture industry due to bats' role in pest control. In this study, a subtilisin-like protease (SP2) has been chosen as a target for drug discovery in P. destructans; SP2 is a secreted protein that degrades collagen and allows the fungus to grow on bat tissues. An SP2 homology model was created based on other serine proteases available in the PDB and used to screen for possible small molecule drug leads. Two structures were used for screening to account for different conformations of the catalytic histidine in the enzyme active site. Nearly 15,000 compounds were screened for each structure on three different screening softwares: GOLD, ICM, and VINA. Over 50% of the top fifteen scoring ligands matched between the two structures. This may suggest that although the histidine is integral to catalysis, it is not important in ligand binding and the different conformations do not significantly impact ligand affinity. Overall, the top scoring ligands across the different docking programs were variable; however, one ligand was a top five hit for both structures in both GOLD and VINA dockings. This ligand will be focused on for experimental testing in the future to see if it maintains its affinity in vitro.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 23

Affordable-SELEX: a novel methodology for developing aptamers

and acquiring 21st century laboratory skills

Presenter(s): Gautam Rangappa Joanna Lee, Sakif Islam, Maanasa Lanka, Miriam Jaime, Lalitha Kaligotla, Cate Naukam, Gwendolyn Stovall, Collaborator(s): Andy Ellington Department(s): FRI Aptamer Stream

Aptamers, synthetically derived RNA or DNA molecular recognition elements, are increasing in demand for biosensors, diagnostics, and therapeutic technologies. Aptamer selection processes oftentimes require specialized equipment and training which causes them to be restrictive due to their high-cost burden. To counter the aforementioned issue, the Aptamer Lab of the Freshman Research Initiative at the University of Texas at Austin has altered traditional SELEX processes to create a SELEX methodology that is more affordable, easy to execute, and able to be performed in parallel. Researchers performing aptamer selections with the “Affordable-SELEX” method could discover novel aptamers that have the potential to advance modern scientific applications. Currently, we as a team are writing a manuscript detailing our adapted SELEX method for publication in the Journal of Visualized Experiments (JoVE). By marketing our research lab’s “Affordable-SELEX” method, our intent is to provide individuals interested in aptamer research an easily accessible way to begin rounds of selection. In the wide body of aptamer literature, many publications that are available do not provide a comprehensive protocol on how to perform aptamer selections. Through outlining our distinct bead-based and filter-based protocol utilizing video and written formats, we hope to provide interested researchers with a cost-efficient way to execute aptamer selections at large scale. Although the proposed protocol requires more effort to customize selection conditions compared to other methods, researchers are able to foster essential research techniques through this unique learning experience.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 24

Development of an aptamer database

Presenter(s): Brandon Ta Collaborator(s): Gwendolyn Stovall, Andy Ellington Department(s): FRI Aptamer Stream

The novel use of aptamers as a means of developing and improving tools in diagnostics, detection, therapeutics, biochemical assays, and many others, has quickly grown since the molecules were first developed and coined in 1990. Aptamer literature continues to build upon itself, looking to recursively improve selection methods and further research once aptamers are characterized for usage. However, the lack of an efficient database to access previous research has made it difficult for researchers to use aptamers in subsequent research. This project aims to develop a comprehensive aptamer database through extensive literature review of aptamer research of the past 30 years. The work will improve upon previously attempted databases by including additional relevant information such as the selection conditions of the aptamer, which can be used to set up or improve future methods of aptamer research. The aptamer database will also include analysis of sequence data in order to determine any motifs or significant repeats that can be used in future research. Combining this information with that of previously existing databases will allow for improved future work in the field of aptamer research. Currently, the database contains over 1000 sequences with relevant information over 30 years of aptamer research.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 25

In silico selection of an aptamer

Presenter(s): Justin Vu Collaborator(s): Gwendolyn Stovall, Andy Ellington Department(s): FRI Aptamer Stream

Aptamers are short-stranded oligonucleotides that can bind to targets, such as proteins, with high affinity and specificity. These sequences can help with diagnostic, therapy, drug delivery, or as a sensor for other molecules. Typically, to find an aptamer against the proteins of the virus, a selection of RNA against the target must be performed. This is called SELEX, Systematic evolution of ligands by exponential enrichment, which allows for the finding of aptamers against targets by continuously filtering RNA sequences by the target and seeing which one binds effectively. This process is begun with a pool of RNA that contains up to 1014 random RNA sequences (Lakhin, 2013). However, this process can take up to 2 years to finalize a product that can be found. Due to concern for safety, time, as well as cost, in silico selection has been proposed. In silico selection makes use of computer simulation to generate random sequences and compare them to the target by looking for thermodynamically favorable spots on the target, where the free energy would be low, as well as looking at favorable spots based on electronegativity. This selection can be summarized in a few steps: first, the generation of an RNA library, then the creation of 3D models of the target as well as binding ligand sites, and finally, screening of the molecules with selected RNA, also known as docking. Progress has been started with looking into RaptRanker, a program that takes HT-Selex data and looks for sequences that fit wanted parameters, such as length and primers. This is similar to making a doped pool, which can be used to find an aptamer much faster. As for molecular docking, AutoDock is being looked into to find ligand binding spots. This finds likely binding areas of molecules using already found data on the Protein Data Bank, in the form of pdb files. Lakhin, A. V., Tarantul, V. Z., & Gening, L. V. (2013). Aptamers: problems, solutions and prospects. Acta naturae, 5(4), 34–43.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 26

Individual and sex Differences in egg yolk proteome

Presenter(s): Andy Zhou Collaborator(s): Rebecca L. Young Department(s): Department of Mathematics; Department of Integrative Biology

Maternal effects in many bird species are in part mediated by proteins deposited in the yolk of their eggs. The differential deposition of such proteins can lead to phenotypic and fitness differences in offspring. This differential deposition can be observed through patterns in the yolk deposits in the egg and may also affect gene expression. We propose that chickens exhibit maternal effects which can present itself through differences between offspring in yolk protein presence and abundance, egg yolk growth patterns, and gene expression in early embryonic tissue.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 27

Negative Aptamer Selection against SARS to increase the specificity

of a SARS-COV-2 Aptamer

Presenter(s): Iqra Ahmad Collaborator(s): Gwendolyn Stovall Department(s): Freshman Research Initiative Aptamer Stream

Despite widespread transmission and potentially severe effects, the newly found SARS-COV-2 virus that causes the disease COVID-19 has proven difficult to detect due to a limited access to testing and the lack of accurate tests. Specifically, serological tests are being used as an effective diagnostic tool to detect the presence of Immunoglobulin G and Immunoglobulin M in serum (Interim Guidelines for COVID-19 Antibody Testing, 2020). However, due to the large class of coronaviruses, false positives are common because these antibodies often have difficulty distinguishing between SARS-COV-2 and other closely related coronaviruses. An aptamer, a DNA or RNA sequence that binds to a protein target, such as the SARS-COV-2 nucleocapsid protein, with high binding affinity can prove to be beneficial in producing an effective diagnostic test that detects the virus through protein presence. To improve the specificity and remedy the inconsistencies in developing an aptamer diagnostic test, negative selection is a technique that can be performed and incorporated into the SELEX (Sequential Evolution of Ligands by Exponential Enrichment) selection process to remove RNA species that have affinity for structurally similar non-target material (eg. SARS and MERS coronaviruses). Negative selection is conducted by alternating between the filter and bead-based method (toggle selection) thus allowing for the selection of a durable in vivo aptamer that will tightly and specifically bind to the nucleocapsid protein of SARS-COV-2 and not have any interactions with other coronaviruses such as SARS. After analyzing about 25 papers over the SARS-COV-2 viral structure and the complications with current testing, a working protocol for negative aptamer selection against SARS was created and will aid in solidifying the selection protocol necessary to generate a SARS-COV-2 nucleocapsid aptamer diagnostic test in wet lab.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 28

Phytoremediation of polyethylene terephthalate constituents in

Arabidopsis Thaliana

Presenter(s): Matthew Clark Collaborator(s): Tony Gonzalez Department(s): FRI Plant Pathways Stream

Despite an incremental shift to more sustainable plastic use, pre-existing, non-degradable plastic polymers generate a growing environmental footprint. One major plastic that pollutes the Earth’s aquatic and terrestrial environments is Polyethylene Terephthalate (PET). A two-enzyme system for depolymerizing PET into its constituents has been identified in the novel bacterium Ideonella sakaensis. In addition, there is evidence that the plastics’ constituents, Ethylene Glycol and Terephthalic Acid, despite being susceptible to biological degradation, are toxic to human populations. With this, should I. sakaensis’ two-enzyme system be used in open environments—rather than isolated processing facilities—PET’s constituents would need to be isolated to mitigate deleterious effects. Many plants are already being used for environmental remediation purposes, though the current research emphasizes heavy metal remediation and does not demonstrate phytoremediation potential of Ethylene Glycol and Terephthalic Acid. We propose the use of the plant model organism Arabidopsis thaliana to sequester Terephthalic Acid and Ethylene Glycol into plant vacuoles to minimize the impact on human populations. Firstly, we would determine the threshold toxicity of PET’s constituents (in A. thaliana). Then, we would use a candidate gene approach to identify and characterize genes that influence the plant’s resistance to Terephthalic Acid and Ethylene Glycol. This work will not only increase basic knowledge in plant biology, but will also provide future avenues for biotechnology, namely phytoremediation.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 29

Using virtual screening to identify novel inhibitors of SARS-Co-V-2

main protease

Presenter(s): Ting Cui Collaborator(s): Josh Beckham Department(s): Freshman Research Initiative; Virtual Drug Screening lab

The SARS-CoV-2 stands for severe acute respiratory syndrome coronavirus 2, which is the strain of coronavirus that causes the COVID-19 disease around the world. People infected with the virus will have symptoms of varying degrees, some just have a fever or a mild cough, some will develop pneumonia, and some will be more serious and even die. Coronaviruses are enveloped positive-stranded RNA viruses that replicate in the cytoplasm. Viral proteases play a critical role in the life cycle of many viruses by affecting the cleavage of high-molecular-weight viral polyprotein precursors to yield functional products. Through this research, by using computers to sift through the libraries of chemical structure to efficiently find the molecules of potential drug candidates which inhibit the target enzyme.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 30

Rearing environment affects mate choice preferences in Xiphophorus

Nigrensis fish

Presenter(s): Kayla Daly, LuLu Eisenberg Collaborator(s): Molly Cummings, Mary Ramsey Department(s): Department of Integrative Biology; Freshman Research Initiative

Female mate choice is an important facet of sexual selection and evolutionary processes such as speciation and sexual dimorphism. Depending on the system, female mate choice can be genetically fixed or can instead be plastic with inputs from experience-based and/or social learning. Understanding the relative contributions of developmental experiences in establishing female mating preferences is important for further illumination of the distinction between genetically-determined and learning-based preferences. Poeciliidae is a family of live-bearing freshwater fish with a wide array of mating systems and male phenotypes. This experiment used Xiphophorus nigrensis, a poeciliid species with genetically determined alternative male phenotypes, including a larger, ornamental courting male, a smaller coercive male, and an intermediate type with attributes of both the courting and coercive phenotypes. Females prefer larger courting males, and previous research suggests this preference is strengthened as females become older and more experienced. The experimental design consisted of juvenile females being raised in controlled social environments comprising five different treatment groups: all large males, all small males, large and small males, all intermediate males, and no males present. All treatment groups also included adult model females. This study tested whether the social composition of X. nigrensis rearing environments influenced adult mating preferences by tracking female behavior when shown animations of courting and coercive males on opposite sides of the experimental tank. The results showed no difference across background for overall willingness to associate with males, although they did find that virgin females significantly preferred to associate with the large male over the small male. The results found no preference for the large male for any of the male-exposed backgrounds. These findings indicate that controlled exposure to discrete male types did not influence mating preferences in this experiment, which carries implications for the understanding of preference behavior and sexual selection.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 31

Improving the efficiency and investigating the cooperative abilities of

the caffeinated coli bioassay

Presenter(s): Hannah Engebretson, Anna Helmers Collaborator(s): Mina Kim, Dennis Mishler, Jeffery Barrick Department of Integrative Biology; The University of Texas at Austin; Austin, TX Research conducted in the Department(s): Microbe Hackers Freshman Research Initiative stream, College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA

The ‘Caffeinated Coli’ bioassay is a system that uses a genetically modified strain of Escherichia coli to measure the concentration of caffeine. These bacteria lack the guaB gene, so they cannot perform the de-novo guanine synthesis pathway necessary to synthesize genetic material. When ?guaB is transformed with the pDCAF plasmid containing N-demethylase genes from Pseudomonas putida, the bacteria can demethylate the three methyl groups on methylxanthines into xanthine, rescuing the pathway. Pathway restoration results in a proportional relationship between caffeine concentration and growth. This system was expanded into a suite of eight plasmids with different combinations of the N-demethylases that demethylate specific methylxanthines. Preliminary results indicated that the plasmids could partially demethylate methylxanthines and release them back into their environment, allowing another strain to finish demethylation to restore their guanine synthesis pathway. Our goal is to determine if strains can collaborate, if so which ones, and the mechanism in which they do so. Plate and liquid tests in which a pair of strains are grown together in the presence of a methylxanthine cannot fully demethylate independently but could if they collaborate are used to reach our goal. Cooperation could increase the bioassay’s marketability by decreasing the number of plasmids required to perform the bioassay making it less expensive to produce. A drawback of the bioassay is that it’s viable at 30°C while the optimum growth temperature of E. coli is 37°C. This decreased temperature could hamper the efficiency of the bioassay by limiting or slowing bacterial growth. We plan to evolve all of the strains to be thermally stable at 37°C by gradually growing them at increasing temperatures starting at 30°C. Maximizing growth in the least amount of time decreases the bioassay’s required time, increasing its efficiency.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 32

The gut microbial communities of Texan large carpenter bees

Presenter(s): Sarah Hatcher, Anna Pham Collaborator(s): Jo-anne Holley Department(s): University of Texas at Austin; Painter Hall

Many social bee species, such as Apis mellifera and Bombus spp., can maintain a core gut microbiota through their close and consistent interactions with each other. This core gut microbiota is extremely important for their health, such as providing improved immunity and nutrition. This study investigated whether solitary bee species native to Texas, in particular those in the genus Xylocopa (carpenter bees), have any relationships with certain bacterial groups like social bees. We predicted that there would be mostly environmentally derived bacteria, but also some species-specific bacteria due to unique nesting practices between species. Specimens from the genera Andrena, Diadasia, Habropoda, Megachile, Svastra, and Xylocopa were collected. Their gut microbiome compositions were then assessed through metagenomic sequencing of the 16S rRNA V4 hypervariable region. Also, whole genome sequencing was performed on bacterial communities isolated from the genera Xylocopa to better understand the metabolic benefits the bacteria were providing to the host. The majority of the solitary bee species microbiome consisted of an abundance of Lactobacillus and environmentally derived bacteria. Moreover, X. micans, X. mexicanorum, and X. tabaniformis parkinsoniae all contained a relatively high amount of Orbaceae, Bifidobacterium, and Bombiscardovia. Through a Bray-Curtis analysis, it appeared those three species have very similar gut microbiota compositions. This suggests the potential of a core microbiota in those species of carpenter bee, even though they lack the consistent social interaction like social bees. Thus, indicating the presence of some alternative mechanism of bacterial acquisition.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 33

Caffeinated coli educational kit

Presenter(s): Cristhy Herrera, Yuyin Jiang, Ren Smith Collaborator(s): Dennis Mishler Department(s): Department of Molecular Biosciences; Norman Hackerman Building; The University of Texas at Austin.

Experiments involving synthetic biology are not commonplace in Texas High Schools. Although considerable efforts have promoted biotechnology access across the state, the distribution of these courses is heavily skewed mainly due to costs associated with such programs. The Caffeinated Coli Educational Kit can help reduce barriers to science education and expand the field of synthetic biology through experiential learning. This kit is modeled after the previously developed Caffeine Bioassay, which uses various strains of ?guaB E. coli to measure a series of methylxanthine solutions. Developing this biological kit entails preserving reagent viability throughout transportation from a lab-facility to schools. The primary steps of kit development required testing the best suitable antibiotic for the experiment, which was kept at room temperature to accommodate equipment available to schools. In conjunction with reagent testing, a curriculum to accompany the kit was developed to ease integration into already-existing curricula.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 34

Galápagos blackberry problem: A novel approach to rubus niveus

management in the Galápagos Islands

Presenter(s): Sarah Hollis Collaborator(s): Kenneth Young, Megan Raby Department(s): Biological Sciences

Rubus niveus, known commonly as blackberry or mora, is a non-native invasive species found in the Galápagos Islands that some have called the “worst weed” in the Galápagos. R. niveus prevents the growth of other species in areas it has taken over, while its large persistent seed bank makes it difficult to eliminate from an area without continual intensive maintenance. This thesis examines the potential of a collaborative approach to invasive species management involving local populations and the support of the local agricultural industry in eliminating the threat that Rubus niveus poses to native and endemic species as well as to the livelihoods of landowners. The current standard of management relies on the application of herbicides and manual removal, a difficult and costly task given the distribution and resilience of the plant. In order to properly combat Rubus niveus, a new approach is needed. The methods I use to develop this new approach include a literature review of the works surrounding Rubus niveus, the history of conservation in the Galápagos, and recent literature regarding agriculture in the Galápagos. By supporting the local agricultural industry, landowners have the resources they need to control Rubus niveus, thus reclaiming their land for agricultural purposes and providing a buffer for the protected park lands of the Galapagos National Park from invasion. In the long term, supporting local agriculture will also prevent the introduction of potential invaders by reducing dependence on imported goods from mainland Ecuador. Instead of focusing on methods to directly manage Rubus niveus, supporting landowners so that they have the ability to control the weed themselves creates a better infrastructure for dealing with invasive species in a way that benefits both the interests of conservation of the Galapagos National Park and the economic interests of landowners.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 35

Testing the relationship between boldness, anxiety and sociability

behaviors in G. affinis fish

Presenter(s): Nour Kassem, Claire Marrone, Jennifer Nguyen Collaborator(s): Nidhi Kuchimanchi, Mary Ramsey Department(s): Department of Integrative Biology; Freshman Research Initiative

Previous research has indicated preservation of individual differences in stress coping strategies and behavioral syndromes across much of the animal kingdom. Two main strategies, proactive responses involving bold and aggressive behaviors, and reactive responses involving risk aversion and shy behaviors, have been identified in coping with stressful situations, such as exploration of novel environments and objects. However, it remains unclear how these coping styles influence other behaviors. Our study aims to determine whether proactive and reactive boldness tendencies predict baseline anxiety, exploration, and sociability responses among Gambusia affinis fish. G. affinis are members of the poeciliidae family, small live-bearing freshwater fish. G. affinis are extremely invasive, so they’re expected to show more proactive strategies, which makes them a useful model system when studying behavioral differences in bold and shy individuals. In order to construct proactive and reactive behavioral profiles of G. affinis, focal individuals were placed in a boldness assay consisting of four conditions: an open field and object presentations including a plant and a plain or shiny novel object (PVC tube or fishing lure). The resulting behavioral measures were then compared to levels of anxiety, which was measured in the scototaxis assay using preference for a light or dark environment, and preference for spending time with a conspecific shoal group, which was measured using a sociability assay. We found consistent levels of anxiety and exploratory responses across boldness and scototaxis contexts. We also found that individuals who spent more time interacting with the shoal during the sociability assay displayed more anxious behavior during the open field condition of the boldness assay. Analyzing the relationship between proactive or reactive coping styles and behaviors such as anxiety, exploration, and sociability within G. affinis will allow us to draw conclusions on how responses to stress may contribute to individual variation in behavior.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 36

Does monk fruit discourage a dysbiotic gut?

Cat Tran, Shreyaa Hari, Cassidy Edwards, Jaycee Morales, Jessica Turk, Tho Lam, Mia Fuentes, Kyahria Presenter(s): Thomas Collaborator(s): Katie Hansen, Manya Iyer College of Natural Sciences: Freshman Research Initiative Nutrigenomics stream; Biomedical Engineering Department(s): Building; University of Texas at Austin

Known as the second brain, the human gut microbiome is a novel area of research because of scientists’ growing discovery on how the microbiome secretes short-chain fatty acids (SCFAs) to regulate appetite, gluconeogenesis, insulin secretion, and chronic inflammation. Luo han guo fruit, or Monk Fruit Extract (MFE) is a natural, non-nutritive sweetener (NNS) that has been previously observed to decrease insulin resistance, increase SCFA production, and enhance blood-glucose regulation, indicating that this sweetener could delay progression or prevent several metabolic diseases. Enterobacter cloacae, a gram-negative bacteria, has the ability to secrete fragments of lipopolysaccharides (LPS) past the epithelial lining of the intestines and into the bloodstream. In addition to its association with increased risk of insulin resistance and metabolic disease in rats, the LPS secretion also implies that E. cloacae may be associated with chronic, low-grade inflammation, leading to many inflammatory/autoimmune diseases. Thus, this experiment aims to find the correlation, if any, between MFE and bacterial growth of E. cloacae. The low and high monk fruit concentration values for experimentation were 0.0038837mM and 0.06mM, respectively. A bacterial assay was performed using a spectrophotometer set at 600 OD to measure bacterial growth. Preliminary research indicates that the relationship between monk fruit concentration and E. cloacae growth is inverse, where higher concentrations of monk fruit lead to lower growth of enterococcus. The low concentration group showed a 15% decrease in growth, and the high concentration group showed a 60% decrease in growth when compared to the control group. An ANOVA with a post hoc Tukey test indicated statistically significant data, suggesting that monk fruit may have an ability to reduce the risks of E. cloacae. Given these results, future research will explore the relationship between MFE and E. cloacae and its ability to regulate gene expression of LPS pathways.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 37

The environmental aspects of human impact toward urban ecosystems

Presenter(s): Katherine Le, Elizabeth Chandler, Mindy Vu, Madison Lee Collaborator(s): Stuart Reichler, Elizabeth Chandler, Mindy Vu, Madison Lee Department(s):

An urban ecosystem is the intersection of all of the plants, animals, and microbes, that interact within the urban environment. By increasing the number of students who can collect data and thereby widening the number and geographic distribution of study sites, the Habitat Scouts project aims to deepen our understanding of urban ecosystems.Additionally, with the limits on groups due to the current pandemic, our project has created a way to collect research in the outdoors individually without the need of the lab. For this descriptive study, a selection of urban greenspaces were chosen. Data was collected on aspects observed within each greenspace including: human use and impact, air quality, GIS such as iTree Canopy, and insect and tree biodiversity. Although this data is still in the collection process, eventually more in depth analysis will allow us to gain insight into the impact of urban greenspaces on the overall environment.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 38

Impacts of aspartame on E. cloacae, a marker for gut dysbiosis

Presenter(s): Tia Leary, Antonio Terrazas, Peiru Liu, Albert Lin Collaborator(s): Katie Hansen, Vincent Pham, Kara Rogers Department(s): Freshman Research Initiative Nutrigenomics Stream, College of Natural Sciences

The gut microbiome contains a large variety of bacteria which helps maintain functions in the digestive system, the immune system, and even the neural network. Research has shown that obese individuals tend to have a lower gut microbiome diversity, which can be associated with glucose intolerance, weight gain, and changes in short-chain fatty acid production. Non-nutritive sweeteners (NNS) are low-calorie sugar substitutes with little to no nutritional value. However, their effects on the human body, especially the gut microbiome, are still under investigation and have shown contradicting effects. Specifically, aspartame has been found to disrupt the balance and diversity of the gut microbiota. The consumption of aspartame has produced inconsistent results in humans, showing no effects in some studies and changes to the gut microbiome in others. The goal of this investigation is to identify if aspartame can impact the diversity of the gut microbiome. In particular, we are interested in potential impacts on Enterobacter cloacae, one of the markers of a dysbiotic microbiome. The production of lipopolysaccharides has been tied to obesity, inflammation, and liver disease. For this study, E. cloacae was incubated in the presence of 0.2% Aspartame and 1.0% Aspartame, and impact on growth was measured using a Tecan plate reader at 600nm. The results of this experiment showed an increase in E. cloacae growth with both 0.2% aspartame and 1.0% aspartame. An ANOVA with post-hoc Tukey test showed these differences to be significant. Since E. cloacae has been shown to increase inflammation and risk for obesity, the impact of aspartame on the gut microbiota warrants further investigation. The next steps of this investigation would be to examine the effects of NNS on gene expression patterns in these pathways associated with lipopolysaccharides produced by E. cloacae.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 39

The gut microbiota of the Mexican honey wasp

Presenter(s): Alexia Martin, Isaac Miller Collaborator(s): Jo-anne Holley Department(s): Texas Institute for Discovery Education in Science

In recent years, the gut microbiota has become a popular topic in pollinator research due to the benefits of mutualistic bacteria to insect health; however, most studies have concentrated on honeybees with little research done on native bees and wasps. Previous research on honeybees indicated that eusocial and swarming behaviors assisted in the establishment of a stable gut microbiota. Mexican honey wasps, like honeybees, are eusocial insects that form colonies through swarming, feed on honey, and provide a valuable economic service by pollinating avocados. Because of the behavioral similarities between honeybees and honey wasps, it was believed that honey wasps would also have a core gut microbiota. Data analysis was performed on gut bacterial sequences isolated from individually caught and nest-dwelling Mexican honey wasps to: (1) determine if a core microbiota existed within the species, and (2) compare the potential microbiota to the gut bacteria of native Texan wasps. The results of this analysis confirmed the presence of a core gut microbiota within the Mexican honey wasp. The identified bacteria consisted mainly of Lactobacillus and Bifidobacterium species, with the relative abundances of each bacterium within specimens differing between nests. Additionally, the bacterial species found within Mexican honey wasps differed from those found in native Texan wasps, indicating species exclusivity. This study is important because it provides a novel discovery that fills a gap within entomological literature and opens the door for future research into the relationship between Mexican honey wasps and their gut bacteria.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 40

Is colonization of invasive species associated with human population density? An investigation into the Non-Native Species within Central Texas.

Presenter(s): Kaden Green, Teresa Martinez Collaborator(s): Kaden Green, Teresa Martinez Department(s): Department of Molecular Biosciences; Austin, Texas

Extensive research has been done on the permanent negative effects of humans on their surrounding environment. In the present study, we delved into better understanding of whether human population density is associated with the artificial dispersal of invasive species. In other words, are invasive species associated with human population density? To test this question, we investigated the invasive plant species richness in three creeks located at different distances from an urban downtown area. We found that the number of invasive species in an ecosystem increases as distance from urban centers increases (one way ANOVA, F2,27=7.287, P=2.947x10-3). These results imply that there is indeed a significant association among the number of invasive species in an ecosystem and that ecosystem’s proximity to urban centers, which have an assumed abundance of human population and activity. Further studies must be done in order to assess how this dispersal occurs.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 41

Stevia concentrations on Enterobacter cloacae growth and gut

dysbiosis: is a no-carb sweetener really the easy way out?

Presenter(s): Poorna Menon, Donya Yazdi, Leslie Mui, Karen Yao, Riley Perugini, Connie Mai, Nitya Gudipaty Collaborator(s): Joie Zhang, Kara Rogers, Katie Hansen Department(s): FRI Nutrigenomics Stream

A societal push towards healthy lifestyles and diet culture has led companies to create FDA approved, low-calorie nonnutritive sweeteners to replace sugar. However, recent research shows that this switch may have adverse effects on the gut microbiota, leading to dysbiosis, obesity, and metabolic disease. The long-term safety and health benefits of stevia, a natural sweetener, needs more research before it can be considered a healthy sugar alternative. Enterobacter cloacae, a bacterial species which thrives in individuals with gut dysbiosis, was cultured in lysogeny broth (LB) and treated with stevia. A bacteriostatic assay was conducted in a 96 well microplate with stevia at concentrations 0.065% and 0.26%. Plates were read at 600nm after 15 hours. A low concentration of stevia was shown to increase the amount of E.cloacae bacterial growth, as it had a higher absorbance of 1.14 compared to the average absorbance of 0.653 of the positive control. However, a high concentration of stevia was shown to decrease bacterial growth with an average absorbance of 0.561. When comparing the LB/E.cloacae blank, LB/E.cloacae/0.26% stevia and LB/E.cloacae/0.065% stevia solutions, a one-way ANOVA test and Tukey post hoc analysis yielded p

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 42

Analyzing the DNA Barcode Gap

Presenter(s): Yusuf Mufti Collaborator(s): Justin Havird Department(s): Department of Integrative Biology

DNA barcoding is a powerful tool that allows researchers to easily characterize and identify species by sequencing a single gene, with the mitochondrial Cytochrome Oxidase I (COI) being the most common. The difference between intra and interspecific genetic variation, or the barcoding gap, is what determines if identification can reliably occur with a species using DNA barcoding. Mutation rate is known to affect the ability for a barcode gap to form. The mitochondrial enzyme alternative oxidase (AOX) is a secondary oxidative pathway to the classical cytochrome pathway present in many animal species. AOX is known to decrease the production of reactive oxygen species (ROS) and therefore slow mitochondrial mutation rates. Therefore, it is reasonable to assume that the presence of AOX would stymie the formation of the barcoding gap in a wide variety of species. Using COI data for a number of AOX and non-AOX bearing species, we compared the sequences to determine if the amount of variation differs across groups and if we can therefore point to the enzyme AOX as a potential roadblock to the effectiveness of DNA barcoding.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 43

Are anxiety responses consistent over time and context in G. affinis

fish?

Presenter(s): Nhu Nguyen, Mowna Ravipati Collaborator(s): Mary Ramsey, Molly Cunnings Department(s): FRI Fish Behavior Stream

Anxiety is a behavior that is seen in many species. Specifically, anxiety exists in animals when they are responding to novel environments where there could be dangers such as predators, or other stresses such as social competitions and scarcity of resources. The anxiety levels can be measured in different types of assays, where each examines different states of anxiety such as responses to novel objects, or immediate or acute fear to predators. If the assays do not measure the same state, then the animals would have different anxious responses across all different types of assay. A group of animals that are used to study behavioral neuroscience is fish, specifically the Poeciliidae family. Gambusia affinis, a species of the Poeciliidae family, is an invasive species, which is previously found to have individual variation in anxiety responses. Their behaviors such as their preference in dark vs white environments (scototaxis), whether they swim near the edge of the tank (thigmotaxis) or explore in open water, and whether they stay near the bottom of the water or near the top (water column analysis) are used to measure their anxiety responses in two distinct assays, scototaxis and water column analysis. All of these behaviors measure the fish’s anxiety levels, therefore this experiment will determine whether the anxiety measures are consistent across all three assays. The data from the experiments showed that the anxiety measures are not consistent across all three assays, even though all of them are specifically designed to measure the fish’s anxiety levels. It is important to study how anxiety works in order to develop anti-anxiety drugs for humans. Researchers can also apply this knowledge when further investigating a different question, such as the side effects of different drugs due to the different anxiety targets.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 44

Impact of glyphosate on cucumber beetle gut microbiota

Presenter(s): Wyatt Peters Collaborator(s): Jo Anne Holley, Nancy Moran Department(s): FRI Bugs in Bugs Stream

Microbial symbionts help mediate metabolic processes and detoxification in many insect species, especially herbivorous insects who rely on microbial symbionts to efficiently digest plant matter. Based on the negative impacts of glyphosate in other herbivorous beetle species, the cucumber beetle, a species of chrysomelid, may also be directly impacted by glyphosate due to its increasing prevalence in agriculture. Previous research has documented the presence of a microbiota in cucumber beetles, but the impact of glyphosate on this microbiota has been largely unexplored. First, cucumber beetle individuals will be gathered in an area free from glyphosate pollution, then individuals will be placed into two groups, one control, and one where the specimens are treated with glyphosate. An analysis of their microbiota will be conducted using DNA extractions, PCR, and sequencing to determine bacterial species present in wild-caught beetles and treated beetles. Data will then be compared between the groups to determine how glyphosate impacts the gut microbiota of cucumber beetles. It is expected that glyphosate will disrupt the growth of some species, thus changing the relative abundance of the gut microbiota and potentially altering beetle behavior upon exposure to the herbicide.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 45

Testing motivation and problem-solving in two poeciliid species:

Detour performance varies by species and developmental background

Presenter(s): Ishani Purohit, Ashley Itzep Collaborator(s): Molly Cummings, Madison Schumm, Mary Ramsey Department(s): FRI Fish Behavior Stream

Cognitive flexibility is an aspect of cognitive ability that reflects how well an individual can innovate solutions to novel problems. Variation in problem solving ability can be due to noncognitive factors such as motivation to engage with the task as well as cognitive/innovation abilities. Cognitive flexibility can be assessed through a detour task. Detour is the experiment of looking at how animals solve a problem regarding a barrier in order to reach a social reward, if any is given, looking closely at their cognitive flexibility when it comes to problem solving We then did a test performance in a detour task with two poeciliid species, Gambusia affinis and Xiphophorus nigrensis. They are members of the poeciliidae family, a group of freshwater live-bearing fish. G. affinis are highly invasive with an exclusively coercive mating system and X. nigrensis has a complex mating system with genetically determined male types with distinct mating strategies. We tested detour performance with a female social reward in wild-caught G. affinis females and female X. nigrensis raised in 5 controlled social backgrounds, two large courting males, a large courting and small coercive male, two small coercive males, intermediate males and all female tanks. We found that detour performance difference by species and developmental background. X. nigrensis fish were more likely to solve than G. affinis. Although there were no species or developmental differences in solving speed, we found that X. nigrensis were more motivated to reach the transparent barrier than G. affinis fish, it was seen that this was driven by females raised in the absence of the coercive male phenotypes (LL, all female).

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 46

Differential gene expression analysis of in vivo and in vitro Klebsiella

pneumoniae strains

Presenter(s): Noor Radde Collaborator(s): Renee Fleeman, Cory DuPai, Bryan Davies Department(s): Department of Molecular Biosciences

Klebsiella pneumoniae is an opportunistic pathogen that can cause fatal nosocomial infections in healthcare settings. Antibiotic-resistant strains of classical K. pneumoniae have only become responsive to last-resort antibiotics. Conventional antibiotics are becoming increasingly futile as bacteria continue to develop resistance, and pharmaceutical companies no longer pursue developing antibiotics. Alternative strategies to the use of conventional antibiotics are challenged with the task of identifying new gene targets that provide virulent strains with an advantage in vivo. An exciting strategy is to develop drugs to inhibit the virulence approaches K. pneumoniae uses to persist within the host. We analyzed the differential gene expression of in vivo and in vitro conditions using 80 Klebsiella pneumoniae strains to identify potential gene targets that are upregulated in virulent strains in vivo. The differentially expressed genes (DEGs) were further characterized using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Interestingly, a majority of the DEGs were downregulated in the virulent strains while in vivo and contributed to numerous significantly underrepresented KEGG pathways and GO terms in those strains. Some significantly upregulated DEGs were identified as potential gene targets that are known to contribute to virulence from other species that also persist within the host.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 47

Lost in translation: the use of bioacoustical analysis of advertisement call structure to describe species of the Eleutherodactylus subgenus Syrrhophus

Presenter(s): Mattie Sherwin, Arya Anagol Collaborator(s): Thomas Devitt, David Hillis, David Canatella Department(s): FRI Biodiversity Stream

Within the broad genus of Eleutherodactylus frogs, species delimitation has remained a challenge due to the elusiveness of species and their close resemblances. DNA sequencing data reveals their genetic divergence, but clear distinctions of species differences are necessary for proper identification of individuals and to explore potential mechanisms of speciation. Morphological depictions of frogs are undeniably crucial for this task, but their advertisement calls, essential for reproduction, provide key insight into species and possibly evolutionary differences. While utilization of bioacoustical analysis of frogs has assisted with delimitation before, few descriptions of calls from frogs of the Syrrhophus subgenus of Eleutherodactylus exist. Here, we evaluate qualitative and quantitative data of Syrrhophus call parameters in conjunction with DNA sequencing data to depict intraspecific and interspecific variation that complement genetic differences. Call structure disparities between species in our study, such as the pulsed calls of Eleutherodactylus marnockii and multi-note calls of Eleutherodactylus cystignathoides, reaffirm species boundaries and support usage of bioacoustical analysis for delimitation. Intraspecific variation among separate populations of species E. marnockii and E. nitidus for parameters like intercall interval duration supplement DNA evidence that suggests the presence of cryptic species awaiting recognition. These variations of call structure found within species will help expand the Syrrhophus subgenus and understanding of the biodiversity of its geographical range. Our findings supplement species distinctions already defined through genetic data, but also increase the volume of information surrounding a relatively understudied characteristic of frogs.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 48

Determining the mechanism and function of extracellular DUSP11, an RNA modifying enzyme associated with control of the sensitivity of the antiviral response

Presenter(s): Karina Tacconi Collaborator(s): Kayla Szymanik, Chris Sullivan Department(s): Department of Molecular Biosciences

Dual-specificity phosphatase 11 (DUSP11) is an RNA phosphatase that acts on host and viral RNAs and is involved in modulating the sensitivity of the antiviral response. DUSP11 cleaves the gamma and beta phosphates from immunogenic 5’ triphosphorylated RNA to convert the RNA into a less immunogenic monophosphate RNA. Although all host-generated RNAs contain a triphosphate before processing, the presence of 5’ triphosphate on RNA indicates to the cell that viral RNA may be present, and launches an immune response. DUSP11’s functional activity plays a role in immunomodulation and thus has potential to be used as a therapeutic agent to decrease immune response for autoimmune diseases, cancers, or various types of viral infection. However, the mechanism of DUSP11 and its interaction with its RNA substrates has not been well elucidated thus far. Although DUSP11 typically resides in the nucleus, unpublished data from the Sullivan Lab (Stephens, 2021) demonstrates that DUSP11 shifts to the cytosol in response to various cellular stressors. It has recently been discovered that antibodies against DUSP11 are a leading biomarker for the early detection of Rheumatoid Arthritis, suggesting that DUSP11 must be exiting the cell to elicit such a strong antibody response. In our current research, we aim to test the hypothesis that cellular stress causes DUSP11 to relocalize from the nucleus to the extracellular environment. To do so, we are creating a highly sensitive enzymatic reporter of DUSP11 using firefly luciferase - preliminary data has already demonstrated the feasibility of using luciferase activity to quantify the amount of extracellular protein. Using this reporter will allow us to analyze DUSP11 localization among various cellular stimuli, such as pathogen associated or housekeeping stimuli. Long term goals include targeting DUSP11 as a means of regulating immune response for use as a therapeutic agent.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 49

Virtual screening of asapartate-semialdehyde dehydrogenase in

salmonella typhi

Presenter(s): Tatum Tran Collaborator(s): Josh Beckham Department(s): Department of Molecular Biosciences

Aspartate-semialdehyde dehydrogenase in Salmonella typhi (StAsd) is the protein responsible for catalyzing L-aspartate-semialdehyde by dephosphorylating L-aspartyl-4-phosphate, which is a crucial step in metabolism that gives nutrients to the bacteria. The objective of this research was to virtually screen potential inhibitors of StAsd and to compare the different binding abilities of each inhibitor. A homology model of the protein structure was made using aspartate-beta-semialdehyde dehydrogenase from Escherichia coli (1BRM). The binding site of the protein structure was defined using a docked ligand from the complex crystal structure of sp-aspartate-semialdehyde-dehydrogenase with 3-carboxy-ethyl-phthalic acid (4R54). A small library was made by selecting positive and negative control ligands to be screened. After preparing the control ligands and the protein structure, GOLD and ICM were used to virtual screen the control library, and the docking score results were analyzed. Following the screening of the control library, GOLD and ICM were used to screen several existing ligand libraries for their binding abilities with StAsd. The top five scoring ligands from each library were observed in PyMol, and their physicochemical properties were recorded as well. The highest scoring ligands in GOLD came from the ZINC library, but more research is still currently being conducted on using different docking programs to find more conclusive results.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 50

Effect of saccharin on the gut microbiota

Sathvik Vemparala, Sara Ansari, Mindy Fu, Alexi Richardson, Joshua Louie, Madison Metzger, Reagan Presenter(s): Davenport, Erica Salazar Collaborator(s): Katie Hansen Department(s): FRI Nutrigenomics Stream

The microbiome of the human gastrointestinal tract is composed of many microorganisms that play an extensive role in host health and important metabolic processes. Saccharin is a synthetic, non-nutritive sweetener that is used as a sugar substitute since it is 200-700 times sweeter and contributes no calories. Previous studies have shown that when saccharin is ingested, disruptions in microbiota biodiversity can occur, inducing glucose intolerance and insulin resistance, and that non-nutritive sweeteners may play a role in the development of metabolic disorders such as type II diabetes and obesity. Our study examines the effect of saccharin on Lactobacillus casei, a common gut bacteria and probiotic, by analyzing its response to various concentrations of saccharin in comparison to sucrose. 1mM and 4mM saccharin were analyzed for bacteriostatic effects using a microplate with OD set to 600nm to test the absorbance of each well, determining the bacteriostatic effects on each well. The average absorbance of the 1mM experimental group was 0.128983333 and the percent change of absorbance from the positive control was -48.048%. The average absorbance of the 4mM group was 0.115355833 and the percent change of absorbance from the positive control was -53.537%. An ANOVA with post-hoc Tukey test revealed that the data is considered statistically significant, so the samples in our experiment are unlikely to have occurred by chance and are effective in our examination that the non-nutritive sweetener saccharin has an inhibitory effect on Lactobacillus casei. This research indicates that saccharin can cause a decrease in growth of beneficial bacteria in the gut microbiome, which may be a possible mechanism for saccharine’s association with metabolic disorders. In the second phase of our research, we design primers to investigate short-chain fatty acid pathways and determine differences in gene expression using saccharin in comparison to our controls.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 51

Effects of phosphate starvation on root hair growth of Arabidopsis

wild-type and apyrase loss-of-function transgenic seedlings

Presenter(s): Grace Zhou Collaborator(s): Stanley Roux, Gregory Clark Department(s): Department of Molecular Biosciences

When considering the overall growth of plants, it is useful to study root growth and development. Roots function to anchor the plant in the soil and absorb water and nutrients needed for plant growth. Root hairs are cells differentiated from epidermal cells of primary roots and their growth can be assayed easily due to their tendency to grow in a rapid and polar manner. Primary root and root hair growth may be affected by a variety of factors, such as phosphate, which is a critical nutrient found in the soil in which plants grow in, and extracellular ATP (eATP), which plants themselves secrete during growth and acts as a hormone-like signal. Phosphate is an important nutrient needed for growth, and eATP is an important signaling molecule regulating plant growth. Ectoapyrases are important players in eATP signaling because these enzymes hydrolyze and limit the levels of eATP and eADP. In our experiments, we used the model plant, Arabidopsis thaliana. One reason Arabidopsis is a good model system is that loss-of-function mutants are readily available. In our experiments, we utilized wild-type and knockout seedlings for two Arabidopsis ectoapyrases, APY1 and APY2. These two ectoapyrases are strongly associated with plant growth. Because high phosphate levels have been shown to impede root hair growth rate, while low levels of phosphate have been shown to promote root hair growth rate, we expected to see the same trend in our experiments. Meanwhile, regarding the apyrases, we expected that knocking them out would result in decreased root hair growth. In our preliminary results, we found our hypotheses generally were confirmed: phosphate starvation increased root hair growth and knocking out APY1 and APY2 inhibited root hair growth. Preliminary data was also obtained on primary root growth in the most recent experiments.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 52

Bacteriostatic effects of xylitol on enterobacter cloacae bacteria

Alicia Zitouni, Andrew Guo, Himadri Gunarathna, Iman Shah, Isabelle King, Lauren Briones, Rithvik Asani, Presenter(s): Zach Nozick Collaborator(s): Katie Hansen, Kara Rogers, Ashley Kim Department(s): FRI Nutrigenomics Stream

Our gut microbiome plays a fundamental role in moderating our health and consists of various microorganisms which function mutualistically with our bodies to regulate homeostasis. Diet is one of the biggest factors in determining the composition of the microbiota. Studies have shown that non-nutritive sweeteners (NNS) and low-calorie sweeteners (LCS) are independent risk factors for metabolic disorders like type II diabetes and obesity. This can lead to gut dysbiosis, creating a glucose intolerance in healthy individuals to result in the development of type II diabetes mellitus, as well as an overall unhealthy gut microbiota. As NNSs and LCS become increasingly popular, there is still limited information analyzing the impact of these sweeteners on our health. Consequently, we are especially interested in investigating the bacteriostatic effects Xylitol, a non-nutritive sweetener, has on Enterobacter cloacae. E. cloacae is a gram-negative bacterium that has been associated with an unhealthy gut microbiota. Utilizing 96 well microplates, we incubated E. cloacae with four different Xylitol concentration solutions (10mM, 30mM, 40mM, 60mM) and compared its optical density (600nm) with a control group. By performing an ANOVA with post-hoc Tukey Test, we discovered that the difference between bacterial growth in the 10mM (0.898975 mean), 30mM (0.5501 mean), and 40mM (0.8882375 mean) solutions were statistically significant from the control growth (p 0.05). These results indicate the Xylitol inhibited the growth of E. cloacae compared to the bacteria with no NNS, demonstrating how consumption of Xylitol could have a similar effect on the human microbiome. Further analysis will be conducted to analyze gene expression through primer designing for short chain fatty acid pathways and PCR testing.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 53

Urbanization and Waller Creek: Effects on stream energy and

biodiversity

Presenter(s): Ellianni Rodriguez, Edwin Paul, Alicia Rusthoven, Navya Cheruku, Mason Gosslee Collaborator(s): Ruth Shear, Mary Poteet Department of Molecular Biosciences,;Department of Integrative Biology; School of Human Ecology; Department(s): Department of Geological Sciences; Plan II Honors Program and Department of Neuroscience; Urban Ecosystems FRI research stream

An important source of nutrients in small stream ecosystems is derived from the breakdown and decomposition of leaf litter. Urbanization alters rates of leaf litter decomposition in complex ways through altered hydrology, nutrient availability, macroinvertebrate diversity, and thermal regimes. The goal of this study is to test what drivers control leaf litter decomposition rates in urban, restored, and rural streams. This study focuses on Waller Creek, which has undergone a controversial flood control and restoration project in the most urban watershed in Austin. To measure the differences in decomposition rates across the three different environments, mesh bags containing five grams of dry leaf matter from two leaf species, Texas Oak (Quercus buckleyi) and Common Hackberry (Celtis occidentalis), were placed at two sites in upstream, urban Waller Creek, two sites in the downstream, restored Waller Creek, and two sites in rural Bear Creek. The leaf-litter mesh bags were collected over the span of seven weeks and the percent change in leaf mass was measured and analyzed. Hackberry leaves decomposed more quickly than oak leaves at all sites. Rates of leaf litter decomposition appeared to be the highest in the restored and rural stream sites. Follow-up studies further investigate this result by assessing the biological and physical drivers of leaf litter decomposition, which include measuring macroinvertebrate richness and abundance, fungal biomass on leaf litter, and total leaf litter quantity going into the streams.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 54

Disruption and restoration: What metabolic regime can tell us about

the impact of urbanization on creek ecosystems

Presenter(s): Charles Yang, Joji Sherman, Andrea Pantoja, Hanqi Qian, Irfan Eshan Collaborator(s): Mary Poteet Department(s): Freshman Research Initiative Urban Ecosystems stream; University of Texas at Austin

Quantifying the seasonal variability in productivity of an urban stream ecosystem is essential to understanding how urban stressors shift the relative importance of production vs respiration in the stream metabolic regime. This metabolic regime is comprised of gross primary productivity (GPP), mainly through photosynthesis, and ecosystem respiration (ER), mainly through aerobic respiration. The development of affordable, long-term sensors has enabled improved examination of metabolic regimes in stream ecosystems, and recent studies suggest urbanization leads to increased ER relative to GPP. However, many of these studies are across only one season and are not located in hydrologically complex areas like Central Texas. In this study, environmental sensors are deployed to continuously measure dissolved oxygen, depth, water temperature, and relative light intensity at five minute intervals from 2019-2020. Sensors were installed in multiple locations of the greater Austin area along Waller Creek upstream and downstream of the flood control diversion tunnel, and in the less urbanized Bear Creek. From these data, a Bayesian analysis was used to model the GPP and ER at each location. The models suggest that the metabolic regime in Waller Creek is driven primarily by ER and minimally by GPP. Bear Creek also leans towards higher ER, though it is much closer to a 1:1 relationship with productivity than Waller Creek. This shift in ER/GPP is driven by seasonal increases in GPP in Bear Creek relative to Waller Creek. The differences between Waller Creek upstream of the diversion tunnel and downstream of it are less clear. These preliminary results suggest that the restoration dam does not have a significant effect on metabolic regime, that urbanization does lead to higher dependence of creek ecosystems on ER, and that seasonal variability needs to be further examined to understand how urbanization shifts productivity in creek ecosystems.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 55

Investigating source and quantity of dissolved organic matter in waller

creek, an urbanized stream iin Austin, Texas.

Presenter(s): Nathan Vu, Ariel Wang, Austin Lu, Rebekah Garza Collaborator(s): Dr. Mary Poteet Department(s): Freshman Research Initiative; College of Natural Sciences; Waller Creek; Austin, Texas.

Dissolved organic matter (DOM) acts as an essential energy source for heterotrophic organisms in all aquatic ecosystems. In urban streams, DOM is typically found in abnormally high concentrations and is usually microbially-derived. This study will attempt to determine the source and quantity of DOM in Waller Creek, an urbanized stream in Austin, Texas. The city of Austin recently implemented a flood diversion tunnel in the lower regions of Waller Creek that significantly alters the source water. The tunnel is designed to divert lake water into the creek during low flow and surface runoff underground and into the lake during high flow. We have two primary hypotheses: first, alterations of source water will cause a decrease in DOM concentrations in lower Waller Creek relative to the upstream concentrations; second, the source of DOM in lower Waller Creek will shift toward more microbially-derived content. We will use a combination of discrete and continuous measurements of dissolved organic carbons and nitrates, pH, turbidity, and temperature across seven different sites. Samples will be analyzed using fluorescence spectroscopy, a combustion TOC analyzer, and UV-VIS methods. The data will then be used to determine DOM quantity and source within the stream at different locations. The results of this study have several major impacts. It will evaluate the effects of restoration efforts on DOM quantity and source in urban streams. The results will also add to communal knowledge of the effects of restoration projects on stream function. In addition, the findings will contribute to our understanding of the drivers of energy production in urban streams. Finally, the results will be communicated with the City of Austin planners to allow them to make informed restoration decisions specifically regarding the flood diversion tunnel.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 56

Colonization and recovery of algal assemblages in response to floods

in urban creeks

Presenter(s): Ashlee Hernandez, Katherine Myers, Elaine Finney Collaborator(s): Mary Poteet Freshman Research Initiative Urban Ecosystems Stream; College of Natural Sciences; University of Texas at Department(s): Austin

Creeks in metropolitan areas are highly altered by urban inputs, creating various stressors on stream ecosystems known as the “Urban Stream Syndrome.” Urbanization influences include decreased canopy cover and higher nutrient levels, which cause significant impacts on algal assemblages within creeks. Increased impervious cover and degradation of riparian areas in urbanized watersheds lead to flashier hydrologic regimes and more frequent scour events, disrupting algal assemblages. Austin is naturally susceptible to severe flash flooding, which is exacerbated by the rapidly expanding urban core. Therefore, it is crucial to understand how these factors, along with a changing climate, will impact stream productivity. Studying how algal assemblages respond to more frequent and intense floods in urban, compared to less developed watersheds, will provide a better understanding of the impact of urbanization on stream energetics. Waller Creek is the urbanized study site for this project, as it has a highly urbanized watershed. Bear Creek is used as a less urban reference stream. To study how algal assemblages in these streams respond to flood events, algae samples are being collected before and after rainfall to assess whether a scour has occurred. If the algae is visibly scoured, subsequent algae sample collections will occur to monitor rates of recolonization. These samples will be used to measure algal biomass by Ash-Free Dry Mass and Chlorophyll A extraction methods. Algal biomass and dissolved oxygen data will provide a better understanding of how productivity recovers following flooding in different levels of urbanization. It is expected that Waller Creek will experience more scouring events than Bear Creek. It is also expected that after a scour event for both creeks, the algae will recolonize faster in Waller Creek. The results from this study will further understanding of how increased urbanization and climate change will impact local stream ecosystem health.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 57

Development of Isothermal Fitting Models to load ions into

dendrimers.

Presenter(s): Jesus Balderas Collaborator(s): Anthony Dylla Department(s): Department of Chemistry

Nanoparticles can be used in a variety of application such as catalyzing pollutants into neutral substances. Dendrimers are organic molecules that are used to synthesize metal nanoparticles that are about 40-50 atoms. These nanoparticles have increased catalytic effects and are stabilized by being encapsulated in the dendrimer. A dendrimer’s loading capacity determines how many ions it can hold. Typically, the loading capacity of a dendrimer is determined through experimental means, but it is an outdated approach. Thus, we decided to do an isothermal fit on the dendrimer that calculated the thermodynamic stability of the binding sites. This project entails using machine learning in python to create an isothermal fit curve to our dendrimer, so that each experiment involving loading nanoparticles in dendrimers can swiftly be evaluated through this method. Our approach has two parts. First, a set of code was created to determine the peaks of absorbance in the dendrimer spectroscopy data. Then, the isothermal fitting model was applied to the data now knowing where the peaks are located. These two components can thus predict the ion loading size of a dendrimer and be used to produce stable dendrimer encapsulated nanoparticles.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 58

Repurposing old pharmaceuticals: Investigating the therapeutic

effects of bupropion analogs

Presenter(s): Olivia Conway, Rachel Lee Collaborator(s): Elizabeth Ilardi Department(s): Department of Chemistry; Freshman Research Initiative

Antimicrobial resistance poses a growing problem to the medical field and traditional methods of drug development are neither fast nor efficient enough to meet the demands for new antibiotic drugs. However, drug repurposing techniques provide a better way for the development of new antibiotics through the modification of existing, FDA approved compounds. With this in mind, we aim to design a potential antibiotic compound derived from bupropion, a widely prescribed antidepressant drug. This project expands on existing research related to the antimicrobial potential of bupropion and seeks to explore new structural modifications that may enhance bupropion’s antimicrobial properties. Our goals include optimizing synthesis procedures for our proposed drug analogs and utilizing bioassays to test the antimicrobial implications of the compounds.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 59

Metabolomic profiling of Texas grapevines using mass spectrometry

Presenter(s): Soham Datar, River Tomlinson Collaborator(s): David Sarabia, Taylor Masters, Diana Zamora-Olivares, Eric Anslyn Department(s): Department of Chemistry

Metabolomics aims to detect and measure small molecules involved in the metabolism of biological systems. Recently, it has been applied to study the wine-making process, as metabolites affect the aging, aroma, and flavor of wine. Metabolomics is also used in the wine industry to understand the effects of growing conditions and geography. Herein, we aim to determine the metabolomic composition of different Central Texas vineyards and corresponding grapevines using mass spectrometry in combination with chemometric analysis. The following metabolomic workflow stages have been completed: 1) harvesting of sixteen grapevine samples from five vineyards in Central Texas, 2) extraction of metabolites using a liquid-liquid extraction method 3) experimental analysis using high-resolution mass spectrometry for untargeted metabolomic profiling, and 4) identification of 63 metabolites using chemometric analysis. This study mainly focuses on stages 3 and 4, which involve data processing of mass spectrometry metabolite data using XCMS, and multivariate data analysis using chemometric tools (MetaboAnalyst). Chemometric metabolomic analysis of six varietals (SL-SAN, SL-M, SL-T, SW-T, SL-SYR, and FC-CS) was accomplished. Principle Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), heatmaps, and dendrograms were utilized to simplify visualization of the data while elucidating important patterns and relationships between varietals and metabolites.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 60

Analyzing the additive effects of organic pesticides in California

streams

Presenter(s): Jade Ealy Collaborator(s): Cole Maguire, Simone Ritchey, Barbara Mahler, Ruth Shear Department(s): Department of Molecular Biosciences; Department of Chemistry

A chemical pollutant in a stream can have toxic effects on biology in that ecosystem. Additive effects are the combined effects of two or more chemical pollutants on biological systems, and can be overlooked unless specifically considered. In this study, the additive effects of chemical mixtures in California streams were analyzed in an effort to examine factors that contribute to toxicity in these streams. Concentrations of organic pesticides were measured in surface water at a variety of sampling sites across three California counties (Napa, Monterey, and Santa Barbara) as part of the USGS’s Regional Stream Quality Assessment (RSQA). The R toxEval package was then used to evaluate additive effects of chemical mixtures on regional stream health. ToxEval uses endpoints, which are defined as the concentration for specific chemicals at which point the chemical becomes biologically active and has discernible effects on one or more biological processes. ToxEval calculates an exposure-activity ratio (EAR) metric representing the toxicity of each particular sampling site, given the chemical levels detected at that site. EAR is a ratio of the chemical concentration measured at that site and the endpoint for that chemical (i.e - the concentration at which it has biological effect). Visualizations were created to showcase the EAR values that were determined for each chemical at each sample site. These plots allowed us to investigate the biological effects, if any, that mixtures of these chemicals induce in aquatic organisms present within the various contaminated streams. The results of this study were also compared to California land use data to explain their presence within these streams. Failure to study these interactions and their potentially toxic effects can lead to inaccurate assessment of the water quality of these streams. Assessing the water quality of streams can provide crucial information about the health of their surrounding environments.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 61

Collection of ruthenium salophen Schiff Base complexes – A

supplementary anticancer drug

Presenter(s): Nada Elessawy Collaborator(s): Elizabeth Ilardi Department(s): Department of Chemistry

Cancer has claimed many lives, and much research has been conducted in efforts to find potential cures. Unfortunately, while there has been a lot of progress, current treatments are often not selective and produce dreadful side effects, such as the reduction of white blood cells in patients. Drug resistance has also been a major obstacle to treating cancer. Thus, there is a need for the generation of new medicines that, in combination with chemotherapy, can prove to be more effective treatments. It is known that Schiff-base complexes possess many anti-cancer properties. With this in mind, a new class of ruthenium salophen compounds was designed in order to potentially target guanine-quadruplex DNA (G4), which is known to have antitumor and antiproliferative activity when stabilized through binding with metal complexes.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 62

Copper(II) thiazole Schiff base complexes as a novel anticancer and

antimicrobial agent

Presenter(s): Sanica Mehta Collaborator(s): Elizabeth Ilardi Department(s): Department of Chemistry

According to the World Health Organization, one in six deaths in 2018 was due to cancer. Therefore, it is necessary to create a new class of drugs that, in combination with chemotherapy, prove to be a more effective treatment. Schiff bases are versatile and have the potential to model new anticancer drugs. Specifically, Schiff base transition metal complexes have been found to be effective anti-cancer agents due to their chelating ability and redox properties. Chelating agents remove metal ions required in metabolic pathways and inhibit proteins involved in DNA synthesis, preventing the proliferation of cells. Furthermore, strong redox agents create reactive oxygen species (ROS). ROS causes damage to macromolecules (including proteins and DNA), leading to cell apoptosis by increasing oxidative stress. Currently, a major obstacle in the field is the selectivity of the medication as the cytotoxicity of current anticancer drugs is not selective enough. Therefore, they also target healthy cells in the body, leading to debilitating side-effects including the reduction of white blood cells. However, chelating agents have been found to inhibit microbial growth in immunocompromised cancer patients. This results in an increased risk of infection in cancer patients. The widespread occurrence of multidrug resistance in both cancer and microbial infections warrants the development of new molecules with properties that could circumvent the multidrug resistance problem. In response, the goal of this project is to synthesize two classes of anticancer drugs. The drugs will be selective, cytotoxic, chelating agents, possess exceptional redox properties, and fastacting. Schiff bases will be used as the backbone of these two drugs. Prior experiments indicate that Schiff bases have great potential as anticancer agents because of their chelating ability and versatility. The remainder of the structure and the type of Schiff base will be informed by previous research. These experiments will be compiled to determine which characteristics of compounds will yield these desired traits in anticancer drugs. There are two aims of this project. The first aim is to develop a combination of specific moieties and metals with a Schiff Base to construct a highly selective and lethal anticancer, antimicrobial agent. The second aim is to create a drug that decreases the mortality rates of cancer patients by addressing the harmful side effects of cytotoxic drugs, including immunosuppression.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 63

Investigating correlation between heavy Metals and ecological factors

in Pacific Northwestern U.S. streams

Presenter(s): Dina Orozco Collaborator(s): Ruth Shear Department(s): FRI Urban Ecosystems Stream

Heavy metals are essential for life in low trace quantities, due to their role in oxidation-reduction reactions. However, they are extremely toxic in large quantities and some are even toxic at low concentrations. Using data from the Regional Stream Quality Assessment (RSQA) study performed by the USGS, the relationship between heavy metal concentration and ecological factors in streams in the US Pacific Northwest (PNSQA) was investigated. The hypothesis for this study was that as heavy metal concentration increased, the abundance and richness of algae, macroinvertebrates and fish species would decrease. There are eight heavy metals that are routinely checked by environmental scientists due to their high toxicity to ecosystems: lead, arsenic, mercury, chromium, cadmium, silver, copper, and zinc. Initial R analysis used Principal Component Analysis (PCA) and hierarchical clustering, along with a heat map correlating heavy metal concentrations and ecological metrics. The PCAs revealed that heavy metals in the PNSQA region correlate very differently by state. Secondly, the heatmap showed that the heavy metals which were hypothesized to have a negative correlation with the ecological factors had almost no correlation. However, a separate group of unexpected heavy metals were positively correlated with the health of some species of benthic invertebrates but negatively correlated with the health of some other benthic invertebrates. Further investigation is in progress to find the cause for these trends, but it is theorized that these ecological factors might be interacting with each other in addition to their interaction with the metals.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 64

In situ photofabrication of RB/BSA conjugated gelatin for single-cell

trapping

Presenter(s): Sojin Park Collaborator(s): Jason Shear, Swayamdipta Bhaduri Department(s): Department of Chemistry

Single-cell behavior diverges with phenotypic variation for different biological processes such as homeostasis, development, adaptation, and disease. Studying single-cell effects requires techniques that provide cell isolation, spatial resolution, and compatible flexibility. Various microfluidic fabrication techniques have been developed for the manipulation of cell. However, previously developed techniques are limited to pre-loaded cells which hinders the true 3D isolation of a single cell. In the Shear Lab, we overcame these limitations through in situ multiphoton fabrication of 3D gelatin microstructures. Currently, we are developing a synthesis of covalent bond between photosensitizer and protein to improve cell compatibility. The synthesis involves conjugation between bovine serum albumin (BSA) and rose-bengal (RB) bio ink. The addition of the conjugate to the gelatin microstructure is expected to offer greater stability for single-cell study and therefore enhanced applications for drug discovery.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 65

Synthesis of coumarin derivatives to be used as photocatalysts to create thiol-acrylate polymers using orthogonal thiol Michael addition reaction

Presenter(s): Kaihong Sun Collaborator(s): Pengtao Lu, Kun-You Chung, Zachariah Page Department(s): Department of Chemistry

Thiol-acrylate polymer with tunable material properties via orthogonal thiol Michael addition reaction can be create by using two different wavelengths of light to activate two different reactions making either a stiff or soft elastic material. In this project, a series of coumarin derivatives (coumarin alcohol, coumarin aldehyde derivative, and coumarine enamine derivative) are synthesized, these coumarin derivatives can be used as photocatalysts for performing thiol Michael addition polymerization to make the thio-acrylate polymers.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 66

Repurposing tamoxifen to a renowned antifungal drug

Presenter(s): Khuong Tran Collaborator(s): Elizabeth Ilardi, Stephen Martin Department(s): FRI Bioactive Molecules Stream

Tamoxifen is an inhibition drug that targets breast cancer in estrogen positive cancer patients. It competitively inhibits the estrogen receptors of breast cells, which in turn inhibits its growth. Tamoxifen displays extracurricular activities by fighting off fungal infections in. Knowing this fact, we can repurpose Tamoxifen into a new refurbished antifungal drug, specifically for Candida a type of fungus. New antifungal drugs are welcomed in the market because antibiotic resistant fungi are becoming more common. More importantly, fungal infections can take from a few weeks to months to clear up, so designing a stronger drug could be advantageous. We ended up choosing the alkoxy amino group to be our target structure since it displays such an essential role in Tamoxifen’s antifungal character and by changing its length, we believe it can enhance its antifungal strength. Synthesizing the drug is predicted to be an easy process since only one structure is modified, and the changing structure’s length should not affect the synthesis very much. To test the strength of the new repurposed drug, the IC50 biological assay will be used to quantitatively measure the effectiveness. Various different incubation periods for the IC50 will be used to determine the most effective periods. A more effective antifungal drug could lead to better care for more patients suffering from long-term infections and better yet increase knowledge on antifungal medicine.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 67

Investigating biofilms to improve detection of anthropogenic

chemicals in Waller Creek

Presenter(s): Mindy Vu, Justin Tran, Catherine Lu Collaborator(s): Allison Rutherford, Nate Fredricks, Barbara Mahler, Ruth Shear Department(s): FRI Urban Ecosystems Stream

The Urban Ecosystems research stream is interested in detecting and quantifying pollutants in Waller Creek. Anthropogenic (a result of human activity) chemicals used in industry, agriculture, and medicine, can pollute and remain in the ecosystem for long periods of time, where they act as carcinogens, endocrine disruptors, and cause other adverse effects. However, many of these chemicals are difficult to detect due to their low concentrations in the creek. A recent study using biofilms as sample material detected pesticides in higher concentrations than measurable using sediment or water samples, and detected some pesticides not seen using either of the standard sampling methods. Biofilms, which are collectives of microorganisms including bacteria and algae, accumulate and retain these anthropogenic chemicals in their extracellular matrix, increasing the concentration of pollutants relative to that found in the water. Not only does this bioaccumulation lead to biofilms providing a more sensitive way to detect stream pollutants, but pollutants absorbed at higher levels within biofilms also lead to stronger effects on the food chain, than may be predicted from the pollutant levels measured in the stream itself. Samples of biofilm will be collected at various locations in Waller Creek, and our lab’s standard procedures will be used to extract, detect, and quantify various pollutants such as polycyclic aromatic hydrocarbons, antibiotics, heavy metals, and pesticides using such detection methods as HPLC, GCMS, and ICPMS. If any of our chemicals of interest do bioaccumulate in biofilms, increasing our limits of detection, we will perform a number of control experiments. We will grow biofilms on artificial substrates in Waller Creek for controlled periods of time to fully characterize the biofilm sampling technique, before using it in our lab’s research on quantifying and tracing the origins of various anthropogenic chemicals in Waller Creek.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 68

Modeling algal populations: Determining the relationship between

periphyton biomass and stream nutrients

Presenter(s): Noel Asmann Collaborator(s): Simone Ritchey, Peter Van Metre, Ruth Shear Department(s): Department of Molecular Biosciences; Department of Chemistry

Our long-term goal is to develop a model that will allow researchers to predict algal populations from a number of current stream conditions. This model could save time, money, and resources that would otherwise be spent in measuring the population of algae in a stream or determining stream health. By first exploring the relationship between algal population and stream nutrients (e.g., nitrates, phosphates, etc.) using USGS Regional Stream Quality Assessment (RSQA) data, we can determine which nutrients are significant predictors of algal population using General Additive Modeling (GAM). We will then expand the number of predictor variables considered to include more ecological and biological variables, followed by a range of urban environmental factors including anthropogenic pollutants, such as pesticides and PAHs. Finally, we will use the variables we have found to be significant predictors to determine not only the relationships, but the interactions that exist between these variables using Structural Equation Modelling (SEM). This will, therefore, create a complex predictor model that not only is aware of the existent relationships in current stream environments but the interactions that exist between them as well.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 69

Virtual screening of S-adenosylhomocysteine/methylthioadenosine

nucleosidase in Salmonella enterica

Presenter(s): Megan Crawford, Hoang Dao Collaborator(s): Josh Beckham, Walt Fast Department(s): Department of Integrative Biology; Virtual Cures ARI Stream

The goal of this virtual screening study was to identify potential inhibitors of the S-adenosylhomocysteine/methylthioadenosine nucleosidase (SeSAN) enzyme in the bacterium Salmonella enterica. This causes the disease typhoid fever, which has symptoms of hepatosplenomegaly, diarrhea and fever. SeSAN was chosen as it is necessary in the MTA and SAH metabolic pathways, therefore disrupting its function would result in the death of the bacteria. PDB structure 41FW was prepped in Molprobity and ICM for virtual docking in GOLD and ICM, with the active site identified by the ADE substrate in the PDB. 11 different ligand libraries were docked into the prepared active site using GOLD and ICM, including the ZINC and HF9 libraries. 2 rounds of docking were performed in order to accurately identify the ligands with the strongest affinity to the active site. 10 positive controls and 5 negative controls were docked to create a reference for the scores of the screened ligands. The highest scores of the screened ligands were 116.35 for salmeterol and 116.31 for N-{[4-(2,3-dihydro-1H-inden-2-yloxy)-3-methoxyphenyl]methyl}-N-[(oxolan-2-yl)methyl]-4-(1H-pyrazol-1-yl)benzamide (100=good ligand score). These scores indicate that the ligand is likely to bind to the docking site and block the natural substrate. The top 10 ligands from each library were evaluated for adherence to Lipinski’s rules, which determine whether a substance would be a suitable candidate for medicinal purposes. The successful ligands were then recognized as strong candidates for the next step in the medicinal drug formulation process: analyzing the real-world inhibition of this protein by the ligand in the wet lab. The virtual screening of these compounds has reduced the number of ligands to be compared in wet lab from over 100,000 to 20 which saves time and resources to increase efficiency in drug discovery.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 70

Using the Regional Stream Quality Assessment Data to Investigate the Relationship of Organic Pollutants to Environmental Land Use Factors

Presenter(s): Mohanad Elchouemi Collaborator(s): Cole Maguire, Dr.Barbara Mahler,Dr.Ruth Shear, Simone Ritchey Department(s): Biology

Urbanization, a phenomenon of migration of humans to dense city population, has dramatically increased in recent decades. With the advent of increased urbanization, there has also been a significant rise in chemical pollutants that have adversely affected the environment. The relationship of organic pollutants to various environmental land use factors will be investigated, using data from the United States Geological Survey’s Regional Stream Quality Assessment project. We are looking for correlations between different land use factors, such as urban density, urban age, total development, water percentage, and the types and quantities of chemical pollutants detected in the stream samples.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 71

Effects of annual precipitation on United States regional stream

qualities

Presenter(s): Lauren Lillie Collaborator(s): Cole Maguire, Ruth Shear, Barbara Mahler, Peter Van Metre Department(s): Department of Biochemistry; Department of Chemistry

The U.S. Geological Survey (USGS) conducted the Regional Stream Quality Assessment (RSQA) from 2013 to 2017, sampling streams and recording chemical, biological, and ecological factors in one of five regions of the United States each year in the following order: the Midwest (MSQA), Southeast (SESQA), Pacific Northwest (PNSQA), Northeast (NESQA), and California (CSQA). The Parameter-elevation Regressions on Independent Slopes Model (PRISM) Climate Group of Oregon State University tracks average rainfall and average temperature values for stream watersheds across the United States. This study used PRISM data to visualize rainfall across the RSQA sites to determine whether there were any patterns of significance. Three different ratios – the sampling year to thirty years, five years, and one year prior - were computed to display how the rainfall received by a stream’s watershed during the active RSQA sampling months compared to the site’s historical rainfall data. The ratios were divided into three bins to classify the sampling year of each site as wet, normal, or dry. The sum of rainfall received by each site three days before every individual chemical’s sampling day was calculated to begin an analysis of rainfall’s effects on organic chemical concentrations in streams; each three-day rain sum was classified as wet (characterized predominately by runoff) or dry (characterized predominately by baseflow). The study will continue to investigate the effects of rainfall on the concentration of anthropogenic organic chemical pollutants in streams.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 72

Discovering a potential drug-like inhibitor of the D-alanine D-alanine

ligase enzyme in Yersinia pestis

Presenter(s): Ezequiel A. Lozano Collaborator(s): Josh Beckham, Michelle Lee, and Izabella Hilmi Department(s): Freshman Research Initiative

Plague (also known as the bubonic plague or black death) is a disease that is caused by Yersinia pestis: a facultative, gram negative, rod-shaped coccobacillus type bacterium. As more strains of Yersinia pestis become more resistant to antibiotics, newer and more efficient methods will have to be considered in combating unforeseen outbreaks that cannot be treated with traditional antibiotic treatments.There have been findings in relation to the importance of the D-alanine: D-alanine (Ddl) ligase, an essential structural enzyme that participates in the processes of peptidoglycan biosynthesis, cell wall biogenesis, and d-alanine metabolism. The research conducted aims to increase the level of understanding concerning the between selected drug-like compounds and protein target (Ddl ligase) through virtual and wet lab applications. This comprehension of the aforementioned interactions could potentially identify a novel inhibitor of the target protein.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 73

Investigating the effects of urbanization on volatile organic

compounds found in regional streams

Presenter(s): Ashley Nguyen Collaborator(s): Cole Maguire, Simone Ritchey, Ruth Shear Department(s): FRI Urban Ecosystems Stream

As environmental health remains an important topic of scientific research, understanding all of the contributing factors to the degradation of atmospheric ozone is vital to the longevity of this planet. Volatile Organic Compounds (VOCs) have both biogenic and anthropogenic sources, and with their potential detrimental effects on atmospheric ozone and respiratory health, identifying anthropogenic sources is crucial to conserving the global ecosystem. Protecting atmospheric ozone is of utmost importance to the sustainability of human existence. VOC levels were collected by the United States Geological Survey’s (USGS) Regional Stream Quality Assessment (RSQA). Land Use data was obtained from the Natural Water Quality Assessment database. These data were combined and analyzed using Principal Component Analysis (PCA) with the intention of viewing correlations between land use types and VOC emissions. Despite urban areas showing the greatest variability in VOC emissions, ultimately, not enough data was available to indicate significant trends. The detrimental effects of long-term anthropogenic VOC exposure include thinning of atmospheric ozone and carcinogenic effects. It is crucial to collect more data on VOC emissions and monitor their effects on the environment. Retroactive filtering of VOCs are currently being studied; however, knowledge of release levels is key to comprehending the source and scale of contaminants that must be handled.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 74

Structural equation modeling of physical and chemical stressors upon

biological systems in southeastern US streams

Presenter(s): Kathy Nguyen Collaborator(s): Cole Maguire, Ruth Shear Department(s): FRI Urban Ecosystems Stream

Agricultural and urban factors have large effects on the health of an urban ecosystem, especially stream health. Through the U.S. Geological Survey Regional Stream Quality Assessment (RSQA) project, streams in the Midwest were sampled and chemical, biological, and ecological factors were measured. In a previous study, data collected from the Midwestern region (MSQA) was used to develop a Structural Equation Model (SEM), or “stressor network” including sixteen variables important to stream health and determined how environmental stressors affect stream health through analyzing their effects on invertebrates, fish, and algae. However, the majority of the sampling sites used in that study were located in agricultural areas. Another region sampled by RSQA, the Southeastern area of the United States, is much more urbanized. This study aims to use Structural Modeling techniques from the MSQA study, applied to data from the Southeast Steam Quality Assessment (SESQA), to compare how different degrees of urbanization affect biological communities in streams. The SESQA data is used in three different smaller structural equation models: fish community health model, invertebrate community health model, and algae community health model. Common trends were found amongst the three models. Urban land use tends to have fewer negative influences on each communities’ biological health than agricultural land use. It was also confirmed that Chloride and Sodium, in high amounts, have a negative influence towards the fish community health. Extreme temperatures also correlate negatively with the fish community health, although low temperatures showed a more significant effect. These results suggest that in order to measure a stream’s biological health, a number of diverse metrics need to be used in order to obtain the most accurate results.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 75

Detecting structural variants in multiple myeloma cell lines using

whole exome sequencing

Presenter(s): Lokesh Pugalenthi, Rahul Nanduri, Raymond Hong Collaborator(s): Rohit Prasad, Dhivya Arasappan, Jeanne Kowalski-Muegge Department(s): Livestrong Cancer Institute, Dell Medical School

Whole exome sequencing (WES) is a targeted sequencing technique that sequences only the protein-coding regions of the genome. As WES has superior cost- effectiveness when compared to whole genome sequencing (WGS), WES has become a respected tool in identifying small genetic variants underlying diseases. However, it is less commonly used to identify large-scale structural variants (SVs) which because of their size and complexity, are more difficult to detect using short-read sequencing data. SVs are genome alterations spanning 50 or more base pairs and have been linked to the onset or progression of certain diseases, such as Multiple Myeloma (MM). Multiple bioinformatics tools are available for the identification of structural variants from genomic data; however, it is important to benchmark their accuracies and efficiencies, particularly in the context of WES data. Using WES data from 71 Human Multiple Myeloma Cell Lines (HMCLs), we benchmarked five established SV identification tools (Delly, Pindel, Smoove, BreakDancer, SvABA) by comparing their results to the known structural variants in each cell line. We used SV visualization tools to examine output features, such as the distribution of base-pair length, types of structural variants detected, and performance metrics, such as run-time. We identified key structural variants in these Multiple Myeloma cell lines by using a combination of these tools. These SV identification tools each possess unique strengths and weaknesses, so they will be combined (along with filtering and visualization of SVs) to create a robust workflow that will be utilized to identify novel structural variants in HMCLs which can then be extended to patient tumors.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 76

Multivariate analysis and visualization of environmental data in U.S.

streams

Presenter(s): Simone Ritchey Collaborator(s): Barbara Mahler, Peter Van Metre, Ruth Shear Department(s): FRI Urban Ecosystems Stream

The chemical, biological, and ecological signatures that can be investigated with data mining methods have the potential to reveal insights into environmental phenomena such as climate change. Each analysis provides a deeper understanding of the data that can be used for further development of multiple lines of inquiry. First, hierarchical clustering heatmaps and principle component analysis (PCA) are used to visualize relationships between variables. From this, further visualization can be conducted, an investigation into different explanations for the signatures observed, or the development of models using GAM and SEM can be done.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 77

Gene expression profiling in mood disorders in the dorsal anterior

cingulate cortex

Presenter(s): Abby Spears, Ericka Salas, Simran Shah Collaborator(s): Dhivya Arasappan, Mbemba Jabbi, Vishy Iyer, Hans Hoffman Department(s): FRI Big Data in Biology stream

The National Institute of Mental Health (NIMH) has estimated that 1 out of 5 adults in the US experience a mood disorder at some time in their lives. Mood disorders include bipolar disorder (BD) and major depression disorder (MDD) and account for a majority of completed suicides. Furthermore, suicidal behaviors are associated with many factors, including mental health disorder diagnosis but the molecular mechanism behind this relationship is unknown. Understanding differences in gene expression regarding mood disorders and suicide lethality could be an important step in understanding these disorders. A postmortem RNA-Seq dataset of the dorsal anterior cingulate cortex (dACC), a brain region involved in reward-based decisions, was used to identify transcriptomic markers relating to mood disorders. The RNA-Seq dataset consisted of 308 samples, 73 of which overlapped in previous studies of other brain regions. From these 73 overlapping samples, 31 samples were diagnosed with BD, 16 samples with MDD, and 26 controls. Differential gene expression analysis was performed on the dACC dataset to identify differentially expressed genes that relate to various metadata factors and demographic information. Weighted gene co-expression network analysis (WGCNA) was explored within the brain regional dataset to identify groups of co-expressed genes. As a result of these analyses, pathways related to immune system regulation were identified, including toll-like-receptor regulation, signal transduction, and cytokine-related pathways. These results show that brain abnormalities in basic immune and cellular machinery dysfunctions may further characterize mood disorders. These results, combined with previous studies of other brain regions, have identified common and unique patterns of gene expression related to mood disorders and suicide across multiple brain regions. Identifying differentially expressed genes and pathways across brain regions can aid in further understanding mood disorders, their risk factors, and linkage to suicide.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 78

Power and temptation: computational analyses of transcriptome

evolution in cooperative cleaner fish

Presenter(s): Yiheng Su Collaborator(s): Chelsea A. Weitekamp, Zegni Triki, Redouan Bshary, Hans A. Hofmann, Rebecca L. Young Department(s): Department of Computer Science

Mutualistic relationships, in which individuals of different species both benefit from close interactions, are common in nature. One fascinating example includes the cooperative behavior exhibited by some coral reef fish, where they remove ectoparasites, mucus, and damaged tissues from larger, often predatory clients in exchange for sustenance. Member of the Labridae family (wrasses) demonstrate three distinct foraging behaviors: those who never clean (non-cleaners), those who clean in conjunction with other feeding strategies (facultative cleaners), and those who exclusively rely on cleaning (obligate cleaners). Here, we analyze the neural transcriptomes of six wrasse species with different feeding strategies to identify the genes associated with cleaning behavior. However, more closely related species are expected to exhibit more similar patterns of gene expression due to phylogenetic non-independence. To control for this phylogenetic signal, we integrate phylogenetic comparative methods with standard transcriptomic analyses. By correcting for phylogeny, we can pinpoint molecular pathways associated with convergent evolution of cleaning phenotypes across the six species in our analysis. Specifically, we find that expression diversification is mainly driven by evolutionary history. Nevertheless, we discover genes and gene co-expression networks robustly associated with cleaning behavior across species. In conclusion, our research leverages computational power and demonstrates the effectiveness of comparative neural transcriptomics in providing insights into the evolutionary basis of complex traits, such as cooperative behavior.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 79

Watch Where You’re Going! Gaze and Head Orientation as

Predictors for Social Robot Navigation

Presenter(s): Blake Holman, Abrar Anwar, and Akash Singh Collaborator(s): Mauricio Tec, Justin Hart, and Peter Stone Department(s): Department of Computer Science

Mobile robots deployed in human-populated environments must be able to safely and comfortably navigate in close proximity to people. Head orientation and gaze are both mechanisms which help people to interpret where other people intend to walk, which in turn enables them to coordinate their movement. Head orientation has previously been leveraged to develop classifiers which are able to predict the goal of a person's walking motion. Gaze is believed to generally precede head orientation, with a person quickly moving their eyes to a target and then following it with a turn of their head. This study leverages state-of-the-art virtual reality technology to place participants into a simulated environment in which their gaze and motion can be observed. The results of this study indicate that position, velocity, head orientation, and gaze can all be used as predictive features of the goal of a person's walking motion. The results also indicate that gaze both precedes head orientation and can be used to predict the goal of a person's walking motion at a higher level of accuracy earlier in their walking trajectory. These findings can be leveraged in the design of social navigation systems for mobile robots.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 80

Assessing the Importance of Vergence in Gaze Cues

Presenter(s): Mrityunjay Mishra, Max Svetlik, Tate Song, Justin Hart Collaborator(s): Justin W. Hart Department(s): Department of Computer Science

Gaze is an important form of nonverbal communication. People use gaze in a variety of interactions, such as when coordinating their movement to hand objects to each other or to pass each other in the hallway. The human visual system features ocular vergence; when both eyes turn to focus on a single point in space. Historically, many robots were designed to provide vergence cues. Many current-generation robots such as MAKI, HSR, and PR2, however, do not. This is a study of whether a robot must ocular vergence impacts an onlooker’s ability to accurately interpret the target of a robot’s gaze. The study uses three conditions in which the robot uses different methods to compute its gaze: vergence - in which the robot properly verges its eyes; no vergence - in which both eyes remain parallel, with the object in the center of the focused area; and right vergence - in which both eyes remain parallel, but the right eye verges upon the target. All three criteria are tested in a virtual reality environment, and the latter two are additionally tested on a 3D-printed robot head. The results of this study suggest that people determine the target of the robot’s gaze even when vergence is absent.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 81

Utilizing feature selection and novel visualization in order to

maximize cumulative oil [roduction

Presenter(s): Samira Ravilisetty, Sanya Srivastava, Jerry Villalobos, Jesse Pisel, Victor Favela Collaborator(s): Jesse Pisel Department(s): FRI Energy Analytics Stream

The focus of our research was to apply interdisciplinary concepts to geostatistical data to gain novel insights. By creating a review process that scouted, tested, and rated models from various fields, we were able to test their effectiveness on our set well log data. By focusing on these models' interrelatedness, we were able to combine ideas from the various models then and use that to inform the creation of new novel applications for said models. Examples include using the Edgeworth Box economic model and applying it to oil well production by equating groups who seek to maximize profits to wells that seek to maximize efficiency and production. Similarly, the Solow model is an economic model applied to oil well production by connecting technological growth, population growth, and production saving rates to optimize cumulative production. Likewise, the Pareto Chart is an economic model that calculates how each feature contributes to the cumulative percentage of production, highlighting its most impactful features. Throughout this process, what has become clear is that the integration of interdisciplinary models and concepts into the geoscience field can only be beneficial and should be incorporated into future research.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 82

Gaze understanding in people, 3D-rendered robot heads, and virtual

reality

Presenter(s): Akash Singh, Abrar Anwar Collaborator(s): Justin Hart Department(s): Department of Computer Science

Implicit communication is communication which takes place regardless of the intention to communicate. For instance, people can look to each other’s eyes to see where other people are looking. Gaze direction is a powerful cue for implicit communication which synchronizes turn talking, reveals information about the looker's object of interest and attracts attention. There exists a phenomenon in which virtual agents appear to look at observers regardless of their location with respect to the agent. This is known as the Mona Lisa effect, which posits that this loss of information when moving from 3D to 2D is to blame for this phenomenon. We developed a gaze computation system based on calibrating a 3D-rendered virtual agent as if it were a physical robot, and computing gaze as if physically orienting an object in the center of that robot’s camera by turning the eye. We hypothesize that many virtual agent heads lose accuracy due to inaccuracies in the way that they compute the robot’s gaze direction, rather than the transfer from 3D to 2D. We designed an experiment to compare study participants’ interpretations of gaze direction when observing a 3D virtual agent rendered in Unity, but on a regular computer monitor; a human head in the real world; or a 3D virtual agent rendered in Unity in virtual reality. Results of this study show that participants are able to understand the gaze of the virtual agent on the computer monitor on par with the other agents. This questions the result of several studies which have concluded that the Mona Lisa effect contributes substantially to the low gaze interpretability of other agents. This work opens the door to further exploration into differences in interactions with virtual agents and physical robots, while possibly also providing a mechanism for better interaction with social virtual agents.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 83

Rod Pump Failures Analyzed through Machine Learning Algorithms

Presenter(s): Sanya Srivastava Collaborator(s): Joshua Spaeth, Ian Artz, Timothy Riedel, Jesse Pisel Department(s): Department of Mathematics; Department of Computer Science; Department of Chemistry; Inventors Program

Machine Learning is a concept that allows an algorithm to analyze data for the ability to make predictions. In this situation, rod pumps often fail in three different cases, whether Tubing, Sucker, or Rod failure. Additionally, the rod pump lasts a specific lifetime with these failures. Many instances can cause these failures based on multiple features. To emphasize which elements impact Rod pumps' failure, there was a use of the feature selection process to see which features are impacting the target variables. Then, there was a use of the random forest, decision tree classification, K-Nearest Neighbor, and neural network algorithms to find the impact of the failing of Rods, particularly the Tubing failure from the selected features. Furthermore, there is a use of random forest and decision tree regression with the lifespan selected features. By understanding which features cause failures, it can be understood how oil companies can avoid building certain elements that cause failure. The k-nearest neighbor under-performed while the neural network was overfitting. The best models were decision trees for classification and random forest regression for the two target variables.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 84

Reasoning about human behavior in ad hoc teamwork

Presenter(s): Jennifer Suriadinata Collaborator(s): William Macke, Reuth Mirsky, Peter Stone Department(s): Department of Computer Science

Ad hoc teamwork is a decentralized multi-agent problem in which agents must collaborate online without pre-coordination. An interesting challenge in ad hoc teammate design is working efficiently with human agents, which may require a model of how these agents behave in a team. In this study, we investigate a scenario in which one of the teammates is a human, as part of a work in progress to construct an ad hoc teammate that can collaborate in mixed human-agent environments. This poster presents an experiment that evaluates human behavior in ad hoc teamwork under three different conditions: A control group which is given a basic set of instructions and two groups which are given varying levels of additional information about the collaborative nature of the task. We measure the users' performance in terms of optimality and legibility. We show that these values are significantly different between the conditions, thus highlighting the importance of acquiring a model that encompasses different human behaviors.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 85

Development of creativity and association with memory tasks

Presenter(s): Zuha Alam, Alexandra Bailey Collaborator(s): Alison Preston, Christine Coughlin Department(s): Department of Biomedical Engineering; Department of Psychology

One form of creativity is divergent thinking, which is the ability to combine diverse types of information in new ways to generate creative ideas. Dimensions of divergent thinking that are commonly assessed include flexibility, elaboration, appropriateness, fluency, and originality. Previous studies have found a positive correlation between divergent thinking, flexibility, and episodic memory in adults, possibly due to a joint reliance on retrieval processes. If true, this dimension of divergent thinking should exhibit age-related improvements during middle- to late-childhood, a period during which retrieval processes develop, and it should also relate to other cognitive abilities that rely on retrieval processes. This study examined these predictions in 7- to 12-year-olds and adults (N=111). Participants were administered the Alternative Uses Task which assessed the aforementioned aspects of divergent thinking. They also completed tasks that assessed three cognitive abilities known to place demands on retrieval processes: autobiographical memory, future event imagination, and memory guided-inference. Analyses examined age-related differences in dimensions of divergent thinking, as well as the association between these dimensions and autobiographical memory, future event imagination, and memory guided-inference. Age-related increases in the flexibility, elaboration, and appropriateness dimensions of divergent thinking were observed. In addition, the flexibility dimension was positively associated with all three cognitive abilities thought to tap retrieval processes, while other dimensions showed a differential relation across these abilities. Findings inform our understanding of the development of creativity while providing additional support for a reliance on retrieval processes.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 86

Child maltreatment and psychosomatic symptoms: A meta-analysis

Presenter(s): Sophia Betar, Morgan McGinnis, Hannah Odell Collaborator(s): Ashleigh I. Aviles, Nancy Hazen, & Deborah Jacobvitz Department(s): Development of Human Development and Family Sciences; School of Social Work

The field of developmental psychology has abundant research on the effects of physical and sexual abuse on children, but is lacking a full understanding and comprehensive research of psychological maltreatment. A potential effect of psychological maltreatment is psychosomatic symptoms, or somatization, which is the presence of physical symptoms with no apparent medical cause. This can lead to misdiagnosis, incorrect treatment, or dismissal and thus, lack of treatment. The purpose of this meta-analysis is to discover the connection between psychological maltreatment and the presence of psychosomatic symptoms in children. This meta-analysis seeks to observe if there is an association between emotional maltreatment in children and the development of psychosomatic symptoms among those cases. To do this, search terms are used to find all existing psychological maltreatment areas that looked at psychosomatic symptoms. The abstract of each identified paper will be coded by at least two members of the research team. Finally, a series of statistics is compiled combining the effect sizes of the individual studies. Through this analytic process, we are seeking to better understand and discover which types of maltreatment are consistently related to the presence of psychosomatic symptoms in children. The further study of psychological maltreatment is essential to expanding our definition and understanding of childhood maltreatment and its effects. Through analyzing the connection between psychosomatic symptoms and psychological maltreatment in children, we can deepen our understanding of the link between trauma and many psychosomatic issues. This information will further the knowledge within the field of child development on how different types of maltreatment are related to and result in the many different outcomes that we observe in children.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 87

Role of empowerment in building successful community-based health

interventions for adolescent obesity in the United States

Presenter(s): Mithilesh Bhaskaruni Collaborator(s): Phillip Schnarrs Department(s): Department of Molecular Sciences; Health Science Scholars

Adolescent obesity is a significant health issue in the United States, especially among minorities. Interventions designed to target these populations often involve components of community empowerment, the complex process which enables communities to increase control over their lives as members improve and work together for the community. However, there has been little research on how community empowerment specifically relates to the outcomes of these health interventions. The purpose of this thesis was to investigate how different domains of community empowerment considered during the planning and execution of community-based health interventions for adolescent obesity are associated with the health outcomes of those interventions. Considering community empowerment as the collection of nine interrelated domains allowed for a more nuanced study of the subject and clearer connections between intervention design and outcomes. Three particular interventions for adolescent obesity were identified through a literature review process and included in a case study analysis that focused on empowerment domains and health outcomes. An analysis of the results indicated the three most relevant domains of community empowerment associated with successful interventions. The results were also used to propose recommendations for designing future health programs for adolescents, as well as to suggest further research studying community empowerment in other populations. This study marks a preliminary step towards understanding how empowerment can be used to bridge health disparities in minority communities. Key Terms: community empowerment, interventions, adolescent health, obesity, health disparities, domains approach

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 88

Exposure to deportation and worry about deportation of close friends

or family members in relation to Latino/a adolescents’ adjustment

Presenter(s): Devin Davis Collaborator(s): Farin Bakhtiari, Aprile Benner Department(s): Department of Human Development and Family Sciences

Exposure to and worrying about deportation are two major stressors in the lives of some Latino/a adolescents. A sample of 266 Latino/a adolescents were used in the study to observe the effect of deportation and worrying about deportation of close friends and family members on adolescents’ adjustment (i.e., health, depressive symptoms, self-efficacy). The comparison between exposure to and worrying about deportation was also studied. No statistically significant associations were found between exposure to deportation and adolescent health (? = -.064, p = .331 ), depressive symptoms, (? = .065, p = .208 ), and self-efficacy (? = -.047, p = .394). Also, no associations between worrying about deportation of close friend and family members and adolescent health (? = -.076, p = .249), depressive symptoms, (? = .053, p = .357), and self-efficacy (? = -.042, p = .487 ) were found. Figure 2 can be viewed to see the comparison between exposure to and worrying about deportation. The study helps to establish research on the effect of deportation and worrying about deportation of close friends and family members as previous research has largely been focused on the association between parental deportation and adolescent adjustment.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 89

Mental health benefits of gender-related family support among

transgender and gender expansive youth

Presenter(s): Brett Dolotina Collaborator(s): Meg Bishop, Stephen Russell Department(s): Department of Public Health; Department of Human Development and Family Sciences

Transgender and gender expansive youth (TGEY) show higher rates of suicidality, self-harm, and major depressive episodes compared to their cisgender peers, denoting a marked need for intervention among this population. These mental health outcomes are mediated by coping and social support, which includes gender-related family support (GRFS). No prior literature has investigated the relationship between GRFS and mental health among TGEY, nor have there been studies on how race and ethnicity affects these relationships. The current study utilized a diverse sample of TGEY to investigate the associations between GRFS, mental health outcomes (depression, self-harm, suicidal ideation, and self-esteem), and race and ethnicity. We hypothesized that TGEY with higher levels of GRFS will report lower levels of depression, self-harm, and suicidal ideation, as well as higher levels of self-esteem. Given limited research on racial group differences in the influence of family support on mental health among TGEY, our research question regarding the effect of race on these relationships is exploratory in nature. Our sample includes 92 adolescents who self-identified as transgender or gender expansive. Depression, suicidal ideation, self-harm, and self-esteem were measured using peer-reviewed survey instruments. GRFS was measured with a one-item survey measure. Race/ethnicity, sexual identity, age, and recruitment site were covariates in this study. Racial minority TGEY faced lower levels of depression, lower levels of self-harm, and higher levels of self-esteem than that of White TGEY. Additionally, increases in GRFS are associated with lower levels of depression and self-harm, as well as higher levels of self-esteem. Lastly, the relationship between GRFS and suicidal ideation is mediated by race, such that White TGEY had a more pronounced relationship than racial minority TGEY. Implications for understanding the importance of the relationship between GRFS and mental health outcomes, as well as how these relationships may differ by race, are discussed.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 90

Racism and children's health

Presenter(s): Nabeeha Engineer Collaborator(s): Fatima Varner Department(s): School of Human Ecology; Department of Human Development and Family Sciences

Racism is a social determinant of health that has a profound impact on the health status of children, adolescents, emerging adults, and their families. Racism may be a factor contributing to poor health and health care disparities in minority children through multiple mechanisms, including effects on psychological and physical wellbeing. The purpose of this study was to examine the relationship between racial discrimination and child health for children. Using the 2018 National Survey of Children’s Health (N= 7123), I conducted logistic regression analyses to examine the associations between anxiety and depression (dependent variables) with experiencing racial discrimination on children aged 5-17 who identified as an ethnic minority . Linear regression analyses were conducted to examine the associations between experiencing racial discrimination and general health outcomes. Among minority children, children who experienced racial discrimination experienced a greater likelihood of having depression (b= .915, p

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 91

The moderating effects of resilience on the relationship between

childhood trauma and PTSD symptoms

Presenter(s): William Graber Collaborator(s): Jacqueline Evan Department(s): Psychology

Resilience is a skill that allows for people to overcome life challenges. Research on resilience has suggested that it is capable of deterring the development of negative mental health outcomes in individuals exposed to traumatizing events, and that this effect is present in an adolescent population. However, research also suggests that the strength of this effect varies depending on the trauma experienced. One traumatic event in which this effect is particularly under-researched is chronic illness. Chronic illnesses, like other traumas, often result in negative mental health outcomes, and it is likely that resilience is capable of protecting against these negative mental health outcomes within the chronically ill population. To determine if this is true, a full review of the current state of resilience research is conducted, justifying the choice of conceptualizing resilience as a process. Studies relating resilience, negative mental health outcomes, and childhood trauma to each other are collected and compared, and the overall relationship of all three is inferred from the collected articles. These articles studying general childhood trauma are then related to childhood illness. The results indicate that resilience is likely to mediate the relationship between chronic childhood illness and negative mental health outcomes. If this is the case, then the promotion of resilience within chronically ill children may benefit their long-term mental health. Suggestions for future research exploring this relationship in further detail are provided, and a model clinical study for its investigation is proposed.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 92

An ecosystem health approach to the gut microbiota and sustainable

diet strategies

Presenter(s): Carolyn Henein Collaborator(s): Timothy Beach Department(s): The University of Texas at Austin, Department of Geography and the Environment

Microbes live everywhere, both in and outside of us. The microbes in our gut are a reflection of our overall health and of the environment we live in. Environmental changes and loss of biodiversity have negative health impacts such as increased exposure to harmful pollutants, reduced in food security, and changed gut microbial composition. Between 1990 and 2016, countries that experienced higher levels of environmental degradation had lowered life expectancies and higher infant mortality rates within their populations. Population health and the environment is at its current state because of how society approaches health and diet; healthcare systems and food systems do not account for the environment or each other. The “One Health” initiative hopes to achieve good health within “people, animals, plants, and their shared environment” through an ecosystem approach to health, or “eco-health.” As opposed to previous contemporary approaches, the systems thinking of the eco-health approach provides solutions to public health issues such as food security, nutrition levels, and premature mortality levels. Implementing sustainable diet strategies has shown to promote this concept by improving gut composition while reducing carbon footprints by up to 25%. Improving our gut health through dietary changes directly affects the chances of acquiring chronic diseases such as inflammatory bowel disease (IBD), obesity, type 2 diabetes, cardiovascular disease, and cancer. This thesis explores the connection between the human gut microbiota and the environment, assesses the ecological determinants of health, and provides solutions for sustainable diet systems through a systematic literature review format. Improving eco-health literacy empowers the public to take control of their health through dietary choices, and demand more from their healthcare and food systems.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 93

Impact of saccharin on L. Casei growth: Is diet culture dangerous?

Presenter(s): Manya Iyer, Ashley Kim Collaborator(s): Katie Hansen, Kara Rodgers Department of Integrative Biology; Department of Nutritional Sciences; Department of Chemistry; Department Department(s): of Neuroscience; Department of Human Development and Family Studies; Freshman Research Initiative Nutrigenomics stream

The human gut microbiome is made up of trillions of microorganisms including bacteria, fungi, and other microbes. Many studies demonstrate its importance to human health by supporting food digestion, fat metabolism, epithelial homeostasis, promoting angiogenesis, and producing short-chain fatty acids (SCFAs) that enhance satiety and have anti-carcinogenic and anti-inflammatory effects. Lactobacillus casei is a probiotic bacterium that is ubiquitous in the human GI tract and has been shown to beneficially influence the gut mucosal immune system and alleviate diseases, especially digestive, immunological and respiratory disorders. Thus, disruptions to L. casei can lead to dysbiosis within the gut microbiome and a myriad of health issues. Although synthetic and natural nonnutritive sweeteners (NNS) have been approved by the FDA, scientists have yet to definitively determine if they have any serious consequences for those who consume them on a regular basis. They provide an attractive alternative to those who are looking to reduce their sugar and caloric intake, but saccharin, a synthetic NNS, has been associated with altering metabolic pathways, inhibiting bacterial growth, and inducing glucose intolerance and dysbiosis. Therefore, this experiment aims to elaborate on the potential relationship between saccharin and L. casei growth. A bacterial assay was performed with L. casei grown in the presence of 0.5mM, 5mM, and 10 mM concentrations of saccharin, and growth was measured using a spectrophotometer set at 600 OD. Preliminary data indicates that there is a positive correlation between saccharin concentration and L. casei growth, with one-way ANOVA and post-hoc tests for 5 mM and 10 mM concentrations showing significantly higher growth rates for L. casei than the controls. While this data deviates from the expected trend based on other experiments, further research must be performed to determine if saccharin has a significant impact on gene expression in SCFA pathways.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 94

Meeting the spiritual concerns of patients during advance care

planning in the COVID-19 era

Presenter(s): Neha Dronamraju, Camelia Esmaili Collaborator(s): Neha Dronamraju, Camelia Esmaili, Shilpa Rajagopal, Jung Kwak College of Natural Sciences; Department of Neuroscience Neha Dronamraju - College of Natural Sciences, Department(s): Public Health Camelia Esmaili - College of Education, Health Promotion and Behavioral Science/Allied Health Professions Location of Research: School of Nursing, Gerontology Lab

Purpose: Advance care planning (ACP) allows patients to define their wishes for medical treatment should they be unable to voice them later. COVID-19 can deteriorate health unexpectedly, highlighting the importance of ACP, yet social distancing guidelines pose new barriers. Given the importance and challenges of facilitating ACP in the COVID-19 era, this study explores healthcare chaplains’ perspectives on patients’ concerns expressed during ACP, and how chaplains address them. Methods: Data were collected through an online survey of 585 board-certified chaplains from three major professional chaplains’ organizations in the U.S. Both quantitative and qualitative data were collected, including six open-ended questions on how COVID-19 impacted their practice, what fears, worries, and hopes patients express during ACP conversations, and how chaplains address them. Data from 68 respondents who discussed how their ACP practice was impacted by COVID-19 were used in this study. Findings: Most participants worked at a community hospital (60%) and academic medical center (20%), and over 90% saw ACP as an important part of their job. Chaplains reported the main patient hopes for ACP were 1) wishes being honored, 2) dying a good/comfortable death, 3) minimizing suffering, and 4) not burdening loved ones. However, main patient fears regarding ACP were 1) wishes not being honored and 2) ACP meaning dying/giving up. Chaplains addressed these by 1) reflective listening, 2) educating, 3) reassuring, 4) validating feelings, and 5) eliciting and including family in discussion. However, COVID-19 has limited the time and opportunity to engage in ACP. Conclusions: The added stressors of COVID-19 on patients and health professionals have increased the barriers to successful ACP facilitation. Nevertheless, gaining a better understanding of patient concerns as well as how chaplains overcome these challenges can pave the way for effective person-centered goals of care conversation facilitation and promote shared decision-making among patients, families, and healthcare providers.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 95

Receiving advice and daily well-being in late lIfe

Presenter(s): Chloe Juanico Collaborator(s): Crystal Yee To Ng Department(s): Human Development and Family Sciences

Advice is a common form of social support in late life. If advice is perceived positively, older recipients may be more likely to cope or resolve their daily life problems effectively. However, not all advice is necessarily helpful to older recipients. The normative theory of supportive communication suggests that unwanted/inappropriate advice could potentially threaten the recipient’s face or identity, along with their independence or competence. Therefore, this study examined whether unwanted advice may affect older adults’ daily life satisfaction. We hypothesized that while receiving general advice would not have any negative effect on life satisfaction, however, receiving unwanted advice would decrease daily life satisfaction among older adults. This study used data from the Daily Experiences and Wellbeing Study (DEWS) collected in 2016-2017. The sample consists of 293 participants aged 65 who resided in the greater Austin, Texas area. In the initial interview, participants provided their demographic information such as age, gender, ethnic/race minority status, general health and marital status. They also participated in daily surveys across 5 to 6 days. At the end of each day, they reported their daily life satisfaction, and reported whether or not they received advice and if they did, if it was unwanted advice from their close social networks. Linear regression models revealed that received advice that day was not associated with life satisfaction. However, receiving unwanted advice was significantly associated with a decrease in daily life satisfaction. In other words, receiving advice may or may not boost daily-well being among older adults, since it is critically dependent on whether the advice received was perceived as wanted or unwanted. Future directions can focus on how advisor-recipient relationships and advice content can positively or negatively influence the recipient's well-being.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 96

A literature review of mindfulness-based interventions in early

childhood education.

Presenter(s): Prachi Khanna Collaborator(s): Amy E. Bryan Department of Neuroscience; Priscilla Pond Flawn Child and Family Laboratory affiliated with the Human Department(s): Development and Family Sciences

Mindfulness-based interventions (MBIs) have become increasingly popular in k-12 settings. Many early childhood education programs incorporate components of mindfulness in their curriculum; however, to date, there is no meta-analysis that compiles and analyzes the existing research studies on MBIs in early childhood education. This thesis analyzes the available literature on mindfulness-based interventions in early childhood education to determine if MBIs are acceptable, feasible, and effective in early childhood education; this information was used to inform an original, brief mindfulness intervention at the UT Austin Laboratory School. A preliminary review of the literature indicates that teachers and students find MBIs to be acceptable and feasible, which was gauged through surveys and short interviews. It is predicted that MBIs have a positive effect on executive functioning, such as working memory, inhibitory control, and cognitive flexibility. Specifically, this literature review will highlight characteristics of ‘successful’ mindfulness interventions, such as intervention length and participant demographics, that can be used in the development of MBIs in school programs.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 97

Discrimination and perceived physical health: The moderating role of

resiliency

Presenter(s): Julia Kramer Collaborator(s): Aprile Benner Department(s): Department of Human Development and Family Sciences

Experiencing racial discrimination can lead to adverse health outcomes. The current study examined whether internal and external resiliency buffer the negative effects of peer-perpetrated discrimination on adolescents’ perceived physical health and quality of sleep. Survey data were collected from 1,010 ninth graders (33% Latinx, 52% female). The results showed that adolescents who were exposed to at least one racial discrimination event from peers tended to perceive their physical health to be lower, and experienced more difficulty falling and staying asleep. This study provides deeper clarity on the relationship between discrimination, physical health, and quality of sleep, and the potential buffering roles of internal and external resiliency, as measured by psychological resiliency and friend support. In addition, the current study has implications for potential interventions aimed at mitigating the negative outcomes of discrimination experiences.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 98

Polio in the news: A sentiment analysis of polio-related news articles

from 1940 to 1965

Presenter(s): Landry J. Luker Collaborator(s): Nathaniel Woodward, Phillip Barrish Department(s): Department of Molecular Biosciences; Department of Statistics and Data Sciences

Before Dr. Jonas Salk’s vaccine became available to the public in 1955, seasonal outbreaks of Polio, a disease well-known for causing paralysis in its victims, repeatedly ravaged American communities. Information concerning these and other Polio-related events were recorded in newspaper articles, providing primary source data that can now be computationally analyzed. Taking advantage of this resource, this thesis conducts a sentiment analysis on 3,074 newspaper articles with the sentimentr R package and the Tesseract optical character recognition engine (OCR) to better understand how individuals’ perceptions of Polio changed over time. In this thesis, the Extended Parallel Processing Model (EPPM) is used to hypothesize that the emotions expressed in newspapers would become more negative after 1955. This change in emotion would be because, after the vaccine was introduced, individuals could theoretically avoid the danger Polio caused them directly instead of only having the ability to avoid the fear that Polio caused. However, no statistically significant differences exist in the positivity portrayed in Polio-related newspaper articles from 1940 - 1965, with the exception of articles published in 1955, which were more positive. The three primary emotions portrayed in these articles are sadness, fear, and surprisingly trust, with the latter two emotions tracking similarly over time. These findings suggest the EPPM may not stress enough the role trust plays in counteracting fear, but more research needs to be conducted to determine trust’s relevance to the EPPM. Whether or not this latter hypothesis is correct, the application of sentiment analysis in this thesis shows the importance of quantitative analyses in the field of media studies. Key Terms: Polio, sentiment analysis, optical character recognition, Extended Parallel Processing Model, R, media studies

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 99

Age-related differences in event memory organization

Presenter(s): Gabriela Mata, Emily McDonald Collaborator(s): Christine Coughlin, Athula Pudhiyidath, Alison R. Preston Department(s): Department of Psychology, College of Liberal Arts

Though life unfolds in a continuous stream, we remember the experience as a collection of discrete events. This study examined developmental differences in event memory organization. Prior work has shown that adults use contextual information to organize events within memory, often integrating elements with shared contextual features into the same event, and differentiating elements that span a context shift into different events. This organization is reflected in temporal memory biases, such that adults perceive elements with different contexts as “far apart” in time (event differentiation) and elements with shared contexts as “close together” in time (event integration), despite equal spacing between elements. We examined whether there are age-related differences in these temporal biases in children (5-12 years) and adults (N=133). Participants studied picture pairs made up of a scene and a trial-unique item (object or face). Unbeknownst to participants, these pairs belonged to either a same-context quartet (in which the same scene was used in four consecutive pairs) or a different-context quartet (in which a switch in scene occurred between four consecutive pairs). Once studied, they rated how far apart in time two items from a quartet occurred relative to one another. Results affirmed that adults adhere to temporal memory biases based on contextual features. Temporal memory biases consistent with event integration were present in even the youngest age group, but continued to increase across childhood. However, temporal memory biases consistent with event differentiation did not emerge until early adolescence, suggesting an earlier development of within-event integration compared to across-event differentiation. We will discuss these results while also introducing a new study designed to better understand the processes underlying the observed differences in event memory organization. This project will leverage eye-tracking methods in order to examine whether attention at encoding contributes to developmental differences in event memory organization. Keywords: episodic memory, event segmentation, memory integration, memory differentiation, temporal cognition, cognitive development

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 100

Age-related differences in event memory organization

Presenter(s): Emily McDonald, Gabriela Mata Collaborator(s): Christine Coughlin, Athula Pudhiyidath, Alison R. Preston Department(s): Department of Neuroscience

Though life unfolds in a continuous stream, we remember the experience as a collection of discrete events. This study examined developmental differences in event memory organization. Prior work has shown that adults use contextual information to organize events within memory, often integrating elements with shared contextual features into the same event, and differentiating elements that span a context shift into different events. This organization is reflected in temporal memory biases, such that adults perceive elements with different contexts as “far apart” in time (event differentiation) and elements with shared contexts as “close together” in time (event integration), despite equal spacing between elements. We examined whether there are age-related differences in these temporal biases in children (5-12 years) and adults (N=133). Participants studied picture pairs made up of a scene and a trial-unique item (object or face). Unbeknownst to participants, these pairs belonged to either a same-context quartet (in which the same scene was used in four consecutive pairs) or a different-context quartet (in which a switch in scene occurred between four consecutive pairs). Once studied, they rated how far apart in time two items from a quartet occurred relative to one another. Results affirmed that adults adhere to temporal memory biases based on contextual features. Temporal memory biases consistent with event integration were present in even the youngest age group, but continued to increase across childhood. However, temporal memory biases consistent with event differentiation did not emerge until early adolescence, suggesting an earlier development of within-event integration compared to across-event differentiation. We will discuss these results while also introducing a new study designed to better understand the processes underlying the observed differences in event memory organization. This project will leverage eye-tracking methods in order to examine whether attention at encoding contributes to developmental differences in event memory organization. Keywords: episodic memory, event segmentation, memory integration, memory differentiation, temporal cognition, cognitive development

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 101

Burden of mental health diagnoses in adults with congenital heart

disease hospitalizations in the state of Texas: a 10-year review

Presenter(s): Amelia Mercado Andrew Well, Gregory Johnson, Hanoch Patt, Ziv Beckerman, Charles D. Fraser Jr., Alexandra Lamari-Fisher, Collaborator(s): Carlos M. Mery Department(s): Department of Molecular Biosciences; Department of Surgery and Perioperative Care, Dell Medical School

Increased incidence of mental health diagnoses (MHD) has been reported in the adults with congenital heart disease (ACHD) population. This study aims to evaluate the prevalence of MHD in a hospitalized ACHD population and determine the impact MHD have on hospitalization characteristics and outcomes. The Texas Inpatient Discharge Dataset was queried for 2009-2018. Discharges of patients ?18 years from acute care hospitals with ICD-9/10 diagnosis codes consistent with ACHD were included. MHD were identified by ICD-9/10 diagnosis codes. MHD was evaluated both as a presence of any MHD as well as presence of each of the MHD included. ACHD diagnoses were categorized by the ACC/AHA lesion severity score (LSS); a score of 1 representing the least and 3 representing the most complex lesions. A total of 10,515 eligible ACHD discharges were identified. Of which 1,642 (15.6%) had a MHD, 924 (8.8%) anxiety, 470 (4.5%) depression, and 371 (22.6%) having ?2 MHD. Compared to non-MHD, MHD discharges were more likely to be female, white, non-Hispanic, and insured (p

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 102

The impact of monk fruit sweetener on Lactobacillus casei bacterial

growth

Presenter(s): Shikha Annem, Nathan Cano, Niharika Pakala, Richa Patel, Sohni Patel, Ali Saleem Collaborator(s): Katie Hansen Department(s): FRI Nutrigenomics Stream

The consumption of low calorie sweeteners has shown to have effects on the gut microbiome and the body’s ability to use glucose as a source of energy. One such low calorie sweetener, Monk fruit, is a fruit native to southeastern China which is commonly used to naturally sweeten foods and beverages. Despite their accessibility and popularity, low calorie sweeteners like Monk fruit have been found to have strong correlations with the development of insulin resistance as a result of gut microbiome disruption. To better understand the impact of low calorie sweetener consumption on gut microbiota, we conducted an experiment to determine the effects of Monk fruit sweetener on the growth of Lactobacillus casei bacteria, a strain known to adhere to human intestinal mucosa. Our results show that the presence of Monk fruit has a significant effect on the growth of Lactobacillus casei bacteria. Monk fruit negatively impacts bacterial growth, since control plates with no sweetener had the most bacterial growth, while plates with high concentrations of sweetener had the least bacterial growth. These results suggest that the consumption of low calorie sweeteners does disrupt the balance of a healthy gut and has significant effects on the growth of bacteria native to the gut microbiome.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 103

Policy reform to lower rates of addiction in America

Presenter(s): Mac Phillips Collaborator(s): Nina Palmo Department(s): Department of Sociology, College of Liberal Arts

America is currently facing the large-scale problems of high addiction and overdose rates as well as high incarceration rates among the population. More Americans are currently addicted to narcotics than ever before, and many of those same individuals are arrested and imprisoned for oftentimes nonviolent drug-related crimes. The present system fails to provide a prison environment conducive to treating addiction and often perpetuates addictions, causing released prisoners to remain addicted and prone to the same risks as they were before imprisonment. This leads to high rates of recidivism, or reincarceration, among addicted individuals and makes it more difficult for those who are addicted to fully rejoin society upon release. However, after reviewing some 30 different peer-reviewed articles and books, it has become evident that reducing the negative impacts of addiction and overincarceration is possible through policy reform. Certain countries in Western Europe including Spain, Portugal, Sweden, and the Netherlands have employed unique policy reforms that have been largely effective at lowering rates of addiction and overdose as well as recidivism. Policies such as integrating group rehabilitation into prisons, post-prison programs, minimum-security prisons, and the decriminalization of all drugs have all shown extreme promise in the nations where they have been implemented. The main criticism of most of these policies is that reform is generally expensive in the short-term, but findings suggest that successful prison reform ultimately saves money for taxpayers and the government in the long-term by keeping the prison population lower. By implementing some of these European policies on the federal level in the United States, we may be able to effectively reduce the magnitude of the negative effects of addiction and overincarceration on American society. Key terms: Addiction, Policy reform, Recidivism, Mental Health, Overincarceration

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 104

Leaving home and stress among older adults during COVID-19

Presenter(s): Suhani Ravani, Julia Shell, Mallika Khurana Collaborator(s): Yee To Ng, Shiyang Zhang, Karen Fingerman Department(s): Department of Human Development and Family Sciences

The COVID-19 pandemic has resulted in many people, regardless of age, remaining in their homes and physically isolated from others for longer periods of time. Studies have shown an association between older adults who go on more frequent outings and slower functional decline. Research also suggests older adults who engage in physical exercise during the COVID-19 pandemic show less functional decline. Yet, we know little about how older adults’ outings (e.g. leaving home for exercise or chores) during the COVID-19 pandemic may impact their daily stress levels. This study was conducted with 226 older adults during the COVID-19 pandemic (May to July 2020) through either phone, internet, or pencil and paper surveys. Using the Day Reconstruction Method, participants reported whether they left their house prior in the day (morning, afternoon, and evening respectively). If they reported leaving their house, follow up questions asked what activities they engaged in outdoors. In addition, they reported how they felt in terms of stress during different times throughout the day. Linear regression models revealed that leaving home itself was not associated with daily stress. However, with regard to specific types of outdoor activities, findings showed that leaving their home for medical and grocery purposes was associated with increased stress. In other words, when older adults left their home for medical and grocery purposes, they reported higher levels of stress. On the contrary, no significant association was found between older adults leaving their home for exercise and chores. When older adults left their home for exercise and chores, stress levels were not increased. Together, this study suggests that participants feel more stressed when they engage in activities that involve more potential exposure to COVID-19.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 106

The impact of aspartame on Lactobacillus casei and gut dysbiosis

Caitlin Richardson, Nabil Asrar, Karime Puga, Iman Ahmed, Zoya Ahmed, Jahnabi Deka, Brian Flores, and Presenter(s): Neha Farooqi Collaborator(s): Toyin Banjo, Katie Hansen, and Kara Rogers Department(s): FRI Nutrigenomics Stream

The gut microbiome is crucial to human health and acts as a health indicator; low levels of bacterial diversity are indicative of dysbiosis and are commonly found in patients with metabolic disorders. In America, where metabolic disorders are common, people often turn to non-nutritive sweeteners (NNS) as a healthy alternative to sugar, but recent research suggests that this may have adverse effects on gut bacteria. Lactobacillus casei is a popular probiotic and is characteristic of a healthy gut microbiome. While aspartame (an NNS commonly found in diet sodas) has been shown to be safe and unlikely to be metabolized in the gut, its consumption has been associated with dysbiosis. To understand whether aspartame is impacting the microbiome, this experiment examined the impact on the growth of two different concentrations of aspartame: 13.6mM and 27.2 mM. L. casei was grown in a 96 well microplate for 16 hours at 37 degrees Celsius and the OD read at 600 nm. An ANOVA with post-hoc Tukey test comparing L. casei grown in aspartame and L. casei grown in sucrose showed that there was a significant impact of aspartame on the growth of L. casei. Overall, preliminary data indicates that aspartame negatively affects the growth of L. casei. To confirm this result, more experiments will be conducted and primers designed for short-chain fatty acid pathways will be designed to look at differences in gene expression to further understanding of the relationship between aspartame and the human gut.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 107

What can we learn from diet and physical activity interventions? Parenting and teaching methods supportive of adolescent nutrition autonomy & self-efficacy

Presenter(s): Mariana Rios Collaborator(s): Ana Avalos, Darla Castelli, Sheri Burson Department(s): Department of Nutritional Sciences

Over the four past decades, the prevalence of childhood and adolescent obesity and overweight status has increased tenfold, according to the World Health Organization. In addition to increasing the risk of negative psychosocial consequences, these weight conditions are associated with various adverse outcomes including diabetes, cardiovascular disease, and certain types of cancer. As adolescents naturally gain more independence and autonomy, they should be well-equipped to handle their food environment and choose health behaviors that protect against potential overweight or obese status. Various studies show that providing adolescents autonomy-support can help increase their self-efficacy and motivation for healthy behaviors. As important figures in adolescents’ lives, parents and teachers can help increase adolescent’s autonomy over healthy diet and physical activity behaviors. However, most parents and educators do not have the time or resources to sift through all the literature on this topic to understand how to be autonomy-supportive. This thesis will review autonomy-supportive parenting and teaching practices done in previous adolescent health interventions focused on diet or physical activity. Important findings will be presented in an accessible table format. The tables will include information on the types of activities done with adolescents and provide simpler adaptations of theory-based practices that parents and teachers can use at home or school . The interventions included in this thesis will be informed by Self-Efficacy Theory and Self Determination Theory, as the constructs of these theories complement one another, overlap with other popular health behavior theories, and center around fundamentals of behavior change including motivation, knowledge, skills, and experience. Keywords: adolescents, autonomy, diet, nutrition, exercise, physical activity, parent, teacher, school, Self Determination, Self-Efficacy

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 108

Impact of sucralose on Lactobacillus casei, a common probiotic

Ritika Bhalla, Haytham El-Zaim, Kishore Botla, Jessica Liu, Jung Eun Koo, Madison Babb, Lisa Kadira, Presenter(s): Mohammad Rizvi Collaborator(s): Katie Hansen, Kara Rogers, Tyler Nguyen Department(s): FRI Nutrigenomics Stream

Research related to the effect of sweeteners on the diversity of the gut microbiome has increased in recent years as scientists have discovered correlations between non-nutritive sweetener consumption and changes in the gut microbiome diversity. The current obesity epidemic has also led to attempts at reducing caloric intake by way of substituting sucrose for sucralose and other non-nutritive sweeteners. Lactobacillus casei, a common gut probiotic, is a foundational species in a healthy microbiome. However, the consumption of sucralose, a non-nutritive sweetener that is commonly used in sugar alternatives such as Splenda or diet drinks, has been tied to both alterations of microbiome diversity and host inflammation. This experiment examined bacteriostatic interactions between sucralose and L. casei by growing L. casei in 4 different concentrations (0.5mM, 5mM, 0.7mM, and 7mM) with a 96-well plate and used a plate reader at 600nm to quantify bacterial growth. An ANOVA with post-hoc Tukey test found that increasing concentrations of sucralose had a statistically significantly lower growth rate of L. casei when compared with the traditional sugar source (sucrose). Sucralose on its own, however, had a significantly increased growth rate. These results held true for concentrations 0.5mM (mean OD = 0.191) and 5 mM (mean OD = 0.201). Interestingly, the 7mM (mean OD = 0.230) showed the opposite, leading to a bimodal impact on the growth rate. This bimodal impact of sucralose concentration has been seen in other systems; confirming this hypothesis is a goal of this experiment, and we will expand sampling to confirm this result. In the next stage of this research, primers will be designed for Short-Chain Fatty Acid Pathways to examine if sucralose impacts gene expression.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 109

Structural anti-gay stigma and incidence of HIV diagnoses in 2014

Presenter(s): Prachi Shah Collaborator(s): Allen Mallory Department(s): Department of Human Development and Family Sciences

The LGBTQ+ community faces significant health disparities, which vary in size based on social/demographic conditions and geographic location [1]. Specifically, the LGBTQ+ community consistently has higher rates of HIV diagnoses compared to the general population [2]. Recently, scientists have begun studying the impacts of demographic factors on health, politics, and the economy using data on the rates at which derogatory terms are Google-searched as a proxy measurement of negative social attitudes towards marginalized groups [3,4]. While these measures have been used as a measure of attitudes against racial/ethnic minorities4, it has never been used to study the impacts of anti-gay attitudes on health. However, studies have shown that structural stigma against sexual minorities compromises their mental and physical health [5-8]. This study hypothesized that the rate at which anti-gay slurs were searched would be positively associated with the number of new diagnoses of HIV in a given Designated Market Area. In order to avoid confounds due to the legalization of same-sex marriage in 2015, this analysis was limited to the year 2014. Three datasets were merged--search rates for the terms “f*g” and “f*gg*t” across 210 Designated Market Areas, the number of new HIV diagnoses per county, and the number of same-sex households per county (the latter two datasets were merged after aggregating to the DMA level). Based on the distribution of diagnoses, a zero-inflation negative binomial regression model was applied to examine the association between search rates and the number of diagnoses, while accounting for the number of same-sex households. Significant relationships were found between both search terms and the number of new HIV diagnoses. Contrary to our expectations based on previous literature, an increased search rate for pejorative terms was associated with fewer diagnoses. Further analyses are needed to elucidate the mechanisms that underlie this surprising finding. References: [1] Brawner, B. M., Guthrie, B., Stevens, R., Taylor, L., Eberhart, M., & Schensul, J. J. (2017, September 6). Place Still Matters: Racial/Ethnic and Geographic Disparities in HIV Transmission and Disease Burden. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5610132/. [2] HIV and Gay and Bisexual Men. (2020, September 16). Retrieved January 28, 2021, from https://www.cdc.gov/hiv/group/msm/index.html [3] Chae DH, Clouston S, Hatzenbuehler ML, Kramer MR, Cooper HLF, Wilson SM, et al. (2015) Association between an Internet-Based Measure of Area Racism and Black Mortality. PLoS ONE 10(4): e0122963. doi:10.1371/journal.pone.0122963 [4] Stephens-Davidowitz, S. (2014, June 2). The cost of racial animus on a black candidate: Evidence using Google search data. Journal of Public Economics. https://www.sciencedirect.com/science/article/pii/S0047272714000929?via%3Dihub. [5] Hatzenbuehler, M. L. (2011). The Social Environment and Suicide Attempts in Lesbian,Gay, and Bisexual Youth. Pediatrics, 127(5), 896–903. https://doi.org/10.1542/peds.2010-3020 [6] Hatzenbuehler, M. L., Bellatorre, A., & Muennig, P. (2013). Anti-Gay Prejudice and All-Cause Mortality Among Heterosexuals in the United States. American Journal of Public Health, 104(2), 332–337. https://doi.org/10.2105/AJPH.2013.301678 [7] Hatzenbuehler, M. L., Jun, H.-J., Corliss, H. L., & Austin, S. B. (2014). Structural Stigma and Cigarette Smoking in a Prospective Cohort Study of Sexual Minority and Heterosexual Youth. Annals of Behavioral Medicine, 47(1), 48–56. https://doi.org/10.1007/s12160-013-9548-9 [8] Hatzenbuehler, M. L., McLaughlin, K. A., Keyes, K. M., & Hasin, D. S. (2010). The impact of institutional discrimination on psychiatric disorders in lesbian, gay, and bisexual populations: A prospective study. American Journal of Public Health, 100(3), 452–459. https://doi.org/10.2105/AJPH.2009.168815

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 110

The impact of loneliness in late life: subjectively and objectively

measured blood pressure

Presenter(s): Ninette Siby, Noura Daryani, Willa Scanlon Collaborator(s): Karen Fingerman Department(s): Department Human Development and Family Sciences

Psychosocial well-being has been associated with physical health outcomes among older people. Specifically, depression and isolation reflects older adults’ well-being, and can predict individuals’ physical health over time. Previous studies have mainly focused on the role of loneliness on self-report health conditions or general health conditions (e.g., number of chronic diseases). With a specific focus on the associations between loneliness and blood pressure, the current study examined both self-reported history of high blood pressure as well as objective measures of blood pressure. The study used data from the Daily Experiences and Well-being Study collected in 2016 and 2017 with adults older than 65 (N = 321, M = 74.15) Participants reported their level of loneliness, history of high blood pressure, and also completed objective blood pressure measures of pulse pressure, diastolic pressures, and systolic pressures. On average, 64% of participants reported a history of high blood pressure. The average numbers for pulse pressure, diastolic pressure, and systolic pressure were 68.29 (SD =11.23), 79.67 (SD = 10.23), and 136.94 (SD = 21.23) respectively. Linear regressions showed that loneliness was not significantly associated with either subjective or objective blood pressure. The results were not independent from other background variables (e.g., gender, age, education). Overall, results suggested that loneliness was not a significant predictor of blood pressure among the current sample. Discussions will focus on other factors that may influence older adults’ blood pressure, the possibilities of using objective blood pressure measures in studies, and the broad effects of loneliness on health outcomes in late life.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 111

At-Home Test for Anemia: Improving Racial and Social Disparities in

the Detection of Anemia

Presenter(s): Erisa Stokes, Christy Nguyen, Sierra Yoshida Collaborator(s): Erisa Stokes, Christy Nguyen, Sierra Yoshida, Dr. Timothy Riedel Department(s): College of Natural Sciences. DIY Diagnostics Lab in Painter Hall.

Anemia is a condition that impacts nearly one-third of the world’s population and is one of the most prevalent global health issues (Chaparro et al., 2019). It occurs when the body has an inadequate supply of red blood cells, preventing proper oxygen transport to the body’s tissues. The goal of this project is to create an inexpensive and non-invasive diagnostic for anemia that is more accessible to underprivileged communities. With this technology, a non-invasive method to diagnose anemia will be available without having to visit the doctor, which is more accessible to people with limited access to hospitals. To address this condition, a Circuit Playground Express (CPE) microcontroller with LEDs and a light sensor was used to produce photoplethysmography (PPG) signals. These signals were used to predict hemoglobin levels in the body by using the patient’s fingertip. The circuit board is currently programmed to flash red and green LED lights and simultaneously takes the blood absorption data for the two wavelengths, resembling heartbeat graphs. The signals produced from these two wavelengths are normalized to produce a hemoglobin concentration estimate, which is then compared to established values of normal hemoglobin concentration to assess the user’s anemia status. Once hemoglobin concentration is found, a non-invasive method to diagnose anemia will be available without the need for a smartphone, which is more accessible to communities that have limited access to modern technology.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 112

Provider-targeted Interventions to Mitigate Latinx Health Disparities

in Primary Care

Presenter(s): Yiije Zhang Collaborator(s): Heather Cuevas Department(s): School of Nursing

In the United States, despite rapidly rising Latinx populations, health disparities between this population and non-Hispanic whites still prevail. To mitigate these health disparities, provider-targeted interventions have been studied to better treat this population. Provider-targeted interventions educate healthcare professionals or direct them on using specific strategies with their patients. However, current research on provider-targeted interventions is severely lacking, largely varied, and often inconclusive. Provider-targeted interventions include general quality improvement strategies, cultural competency training or culturally- tailored interventions, and motivational interviewing techniques. This study reviews the effect of these three types of interventions on primary care and preventive health issues to examine the current findings on these interventions. In this systematic literature review, evidence from original studies on racial minorities is synthesized to determine the impact of these interventions on health disparities experienced by Latinx communities. This review suggests that with certain limitations all three types of provider-targeted interventions are promising avenues of research in mitigating health disparities for Latinx and potentially other racial minorities. Since this field is relatively recent and still limited, more original studies on these interventions are essential to better demonstrate their effects on Latinx health disparities. Key words: health disparities, motivational interviewing, provider-targeted interventions, cultural competency

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 113

Analysis of logistic curves

Presenter(s): Jacob Alberts, Xzavier Chikurunhe, Chitra Rajasekaran Collaborator(s): Mark Daniels Department(s): Mathematics

The logistic curve is derived from exponential decay and translates to the hyperbolic tangent as shown in David M. Bradley’s analysis of Pierre F. Verhulst’s logistic model. This presentation reviews this analysis to corroborate its veracity. Bradley analyzes through comparisons of populations to niches of ecosystems to prove the model in respect to exponential decay. This process returns the model with exponential decay and then proved through a few cases of how this model translates to a hyperbolic tangent. Further visualizations of this model in this form confirm the famous “S” shape seen in logistic curves.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 114

The spiral of theodorus and sums of zeta-values at the half-integers

Presenter(s): Kaitlyn Conlin, Joshua Thompson, Daniela Salazar Collaborator(s): Mark Daniels Department(s): Department of mathematics; Department of physics; Freshman Research Initiative discrete math stream.

This project explores the spiral of Theodorus in coordination with the Schneckenkonstante, K, introduced by Hlawka. This constant serves as a tool for calculating the angular distance traversed by the spiral for each n value such that P_n circulates counter-clockwise about P_0. Though the only published estimate of this constant states that K is less than or equal to 0.75, we use multiple formulas involving series and summations to compute a precise value ok K.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 115

High-pressure synthesis of rare-earth nickel oxides RNiO3

(R=La1-xYx)

Presenter(s): Sara J Irvine, Holland Fielding Collaborator(s): Quinn D. B. Timmers, Gregorio Ponti, and John T Markert Department(s): Department of Physics; University of Texas at Austin

We are interested in the rare-earth nickel oxides and investigating their electronic properties by using a hot press synthesis. Materials are first prepared by an ambient solid-state reaction (950°C), creating mixed-phase RNiOx materials. A hot piston-cylinder press, which can range from 5-25kbar at high temperatures (950C-1000C), is then used to search for new phases using either an oxidizer (KClO4) or pure, as it is naturally reducing [1][2]. We are studying nickelate phases, specifically RNiO3 (R=La1-xNdx), for the metal-insulator transition. We are also looking into how the size of the rare-earth metal could affect when this transition occurs. Currently, we are still working to get a pure phase sample, but have recently seen some success. [1]Luke G. Marshall, Ph. D. Thesis, The University of Texas at Austin, pp. 80--104 (2003). [2] G. Démazeau et al., J. Solid State Chem. 3, 582 (1971)

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 116

Detecting and classifying strokes using electrical impedance

tomography

Presenter(s): Hannah Lee Collaborator(s): Jared Culpepper; Barry McDermott; Emily Porter Department(s): Department of Electrical and Computer Engineering; Cockrell School of Engineering

Strokes are one of the leading causes of disability, with the severity of the disease dependent on the timeliness of the treatment. Treatment, however, varies depending on the type of the stroke – ischemic strokes are treated differently than hemorrhagic strokes, and the result of one being treated as the other can have potentially deadly effects. To prevent this, current imaging technology such as magnetic resonance imaging (MRI) and computed tomography (CT) scans are used to detect the presence and the type of the stroke, but such technology can take a long time, preventing early treatment of the stroke. One technology that has shown promise in quickly diagnosing a stroke is electrical impedance tomography (EIT). This study seeks to investigate the effectiveness of EIT in detecting the location and the type of the stroke. The EIT simulations are performed with different head models, signal to noise ratios (SNRs), lesion locations, and lesion sizes. The data of the head models without a lesion is then compared with that of head models with a bleed and that of head models with a clot. Based on the results of the study, given a SNR of approximately 60 dB or above, EIT can accurately determine the location of the lesion and differentiate between its type regardless of the head model and lesion size. The results demonstrate that EIT shows promise in the quick detection of stroke and stroke type differentiation, allowing for quick treatment based on the stroke type and thus reducing the severity of the stroke.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 117

Proof of uniqueness for Gross-Pitaevskii hierarchy via board games

Presenter(s): Samuel Perales Collaborator(s): Joseph Miller, Natasa Pavlovic Department(s): Department of Mathematics

The Gross-Pitaevskii hierarchy of equations describes the state of quantum systems with large numbers of identical particles. In particular, we care about Bose-Einstein Condensates, which are gases consisting of infinitely many bosons which undergo two-body interactions. In this literature review of 'On the Uniqueness of Solutions to the Gross-Pitaevskii Hierarchy' by Klainerman and Machedon, we will explore the proof of the central theorem which is done by organizing interaction terms in matrices and manipulating them via a 'board game argument'.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 118

Understanding the transition from dispersion dominance to

rotational support in the FIRE-2 simulations

Presenter(s): Thomas Seive Collaborator(s): Mike Boylan-Kolchin and Andrew Graus Department(s): Department of Astronomy

My project centers around using data from the FIRE-2 simulations to measure how galaxies acquire angular momentum. This question is pertinent because we have robust measurements for simulated galaxies at low mass ranges (masses similar to the Milky Way's classical dwarf satellites) and at Milky Way masses, but we lack data at the transition point from low mass, "dispersion" dominated systems to rotationally supported, Milky Way mass systems. These measurements will be used to augment current datasets and fill gaps in the current theoretical datasets.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 119

Synthesis and characterization of selected inter-metallic alloys for

magnetic cooling

Presenter(s): Kyra Stillwell Collaborator(s): Mahmud Khan Department(s): Department of Physics, Miami University, Oxford, Ohio

A magnetic refrigerator exploits the magnetocaloric effect, which is generally defined as the tendency of certain magnetic materials to change their temperature when placed in a magnetic field. There is a great interest in the commercialization of magnetic refrigerators due to the fact that they are significantly more environmental friendly and energy efficient when compared to the currently used vapor-compression based refrigerators. However, before the magnetic refrigerators can be commercialized, application friendly magnetic materials must be developed. In this presentation, a series of four alloys belonging to the Mn0.5+xFe0.5Ni1?xSi0.94Al0.06 family will be discussed. The alloys were prepared by performing stoichiometric calculations and weighing the constituent elements, followed by vacuum arc melting and annealing. The structural properties of the resultant alloys were investigated by powder x-ray diffraction. The results of the structural analysis and the potential of these materials for application in magnetic refrigeration will be presented.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 120

An alternative approach to the denumerability of sets

Presenter(s): Omar Muniz, Kaushal Patel, Abigail Perryman, John Teague, Luke Timmerman Collaborator(s): Mark L. Daniels Department(s): Department of Mathematics

The classical way denumerable, or countably infinite, sets are presented is through Cantor’s diagonal argument; however, in this presentation, an alternative method is investigated. We utilize properties of functions and the uniqueness of prime factorization to prove that certain sets are denumerable. Lastly, we explore connections to topics in other areas in mathematics, such as linear and algebraic independence. The publication “Prime Factorization and Denumerability: A Function Approach” by Armendariz and Daniels acts as motivation and is referenced throughout.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 121

Investigating the T?0 metal-insulator transition for La0.5Nd0.5NiO3

Presenter(s): Jonathan D. K. Tebo Collaborator(s): Gregorio Ponti, John T. Markert Department(s): Department of Physics

Nickelate thin films have been known since 2019 to have a superconducting phase transition. Substituting in differently sized central atoms into the crystal structure will change the metal-insulator transition and Tc. Under the assumption that only small central atoms cause bonds in the crystal structure to break, it is hypothesized that for all La1-xRxNiO3 there is a universal T ? 0 metal-insulator transition. Using pulsed laser deposition to create thin films and van der Pauw’s method to take transport data, we seek to verify the hypothesis for the case of R = Nd, x = 0.5. I report efforts in cleaning the substrates upon which we deposit nickelate thin films. This aspect is crucial in the final films as epitaxial growth depends heavily on the surface of deposition.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 122

Construction of solutions to Euler equations using Yudovich's theorem

Presenter(s): Zerrin Vural Collaborator(s): Francesco Maggi Department(s): Department of Mathematics

This poster surveys a study of fluid dynamics in analysis. We covered the mathematics of incomprehensible non-viscous fluids by studying ideas such as incompressibility, divergence theorem, and mass conservation to motivate Euler equations. The existence and uniqueness of 2D solutions to Euler equations with bounded vorticity were studied using an iterative method within Yudovich’s theorem. This was guided by Dr. Francesco Maggi and supported by the RTG Undergraduate Fellowship in Analysis at UT Austin.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 123

Discovering new inhibitors of papain-like protease (PLpro) structure

of SARS-CoV-2 using high-throughput virtual screening

Presenter(s): Sandy Bakheet Collaborator(s): Avery Darilek, Madison Tran, Josh Beckham, Walter Fast Department of Molecular Biosciences; Department of Chemistry; College of Natural Sciences; The University Department(s): of Texas at Austin

Severe Acute Respiratory Syndrome is a respiratory illness. The SARS-CoV-2 virus is the causative agent of the most recent SARS outbreak: coronavirus disease 2019 (COVID-19). Its symptoms range from mild to severe illnesses including fever, cough, and shortness of breath. There are some known drugs being test at the moment for a COVID-19 vaccine, however, long term or side effects are unknown. Therefore, alternatives are needed to reduce the risk of contracting dangerous side effects. One of the coronaviral proteases, the papain-like protease (PLpro), is an essential protein for viral replication. Inhibiting this protease will inhibit the replication of the genomic RNA, and it is therefore an attractive target for therapeutic intervention. In this project, Virtual Screening programs such as, GOLD was used to identify potential inhibitors for the papain-like protease. Overall, the scores generated from the virtual screening programs were not as good as expected. The GOLD scores of a ligand originally placed in the active site of the protein structure generated a score of 69.19 which is lower than the optimum number which is 100. However, some ligands may be potential inhibitors with further testing in vitro.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 124

The role of HMGB1 in the repair of DNA interstrand crosslinks

Presenter(s): Lorraine-Rana Benhamou Collaborator(s): Jill Gerberich, Karen Vasquez Department(s): Department of Molecular Biosciences; Pharmacology and Toxicology

DNA Interstrand crosslinks (ICLs) are lesions caused by the formation of covalent bonds between DNA strands. ICLs can block transcription and replication, and are cytotoxic if left unrepaired, which makes them useful in cancer chemotherapy. However, some cancers can become resistant to chemotherapy through enhanced DNA damage repair. Nucleotide excision repair (NER) is one DNA repair pathway involved in the repair of ICLs. We have found that a protein called High Mobility Group Box Protein 1 (HMGB1) is involved in NER-mediated DNA ICL repair. Previous research from our lab has shown that HMGB1 can interact with NER protein, XPA, at ICLs and that mammalian cells lacking HMGB1 exhibit increased sensitivity to ICLs. However, the mechanism(s) by which HMGB1 facilitates NER-mediated ICL repair is not clear. One of the two subpathways of NER, global genome NER (GG-NER), recognizes DNA damage through the distortion of DNA structure by the XPC protein. Since GG-NER recognizes lesions from the distortion of DNA, and HMGB1 can bind to distorted DNA and is involved in NER-mediated ICL repair, we hypothesize that HMGB1 plays a role in GG-NER. To study this hypothesis, we transfected ICL-containing mutation-reporter plasmids (or an undamaged control plasmid) into XPC-deficient and XPC-proficient human (U2OS) cells, that were either siRNA depleted or not depleted for HMGB1. We used blue-white screening to determine the mutation frequencies, and Sanger sequencing to determine the mutation spectra that resulted from ICL repair that occurred in the human cells. From the preliminary results of the experiment it appears HMGB1 could be involved in GG-NER. We are now pursuing the use of CRISPR-Cas 9 knockout U2OS cell lines for future experiments to siRNA deplete HMGB1, and have successfully obtained XPC knockout clones. This will allow us to determine the extent to which HMGB1 plays a role in GG-NER-mediated ICL repair.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 125

Breaking is bad: Evolutionary stability of genetic devices

Presenter(s): Luciano Cantu, Alvin Ta, Jorge Ramirez Collaborator(s): Hannah Do, Alex Macaskill, Dennis Mishler Department(s): Neuroscience; FRI Synthetic Biology Stream

In nature, the accumulation of mutations in an organism's genome may serve as a powerful tool that can promote genetic diversity and adaptations via natural selection. However, in synthetic biology, it is crucial to avoid genetic instability within a genetic device to prevent the accumulation of mutations capable of altering its novel function. Fortunately, ways of analyzing genetic devices for unstable sequences have become available, notably the Evolutionary Failure Mode Calculator, a computational device responsible for alerting the user of genetic instability sources found within an input DNA sequence. However, these calculators have largely failed to detect short repeat sequences (SRSs), which are characterized to mediate deletion of varying lengths of DNA. The continuous inclusion of such sequences within genetic devices may lead to the unfortunate death of novel or promising genetic devices. To optimize the EFM calculator by including SRSs within its registry, we sought to determine the mutational rate of a series of short repeat sequences. To do so, we used a series of modified Kanamycin resistance genes whose function was altered by the presence of a SRSs, we then measured the mutation rate using a modified Luria-Delbruck fluctuation test. The expression of these genes in bacteria and within a kanamycin-rich environment allowed for the isolation of reverse mutants that had undergone the characterized SRSs mediated deletion and restored kanamycin functionality. These mutants were then used to derive a mutational rate via the R script "Fluxxer" on the Barrick Website. We have found repeats as low as 8 base pairs in length can cause upwards of a 10 fold increase in mutation rate.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 126

Improving plant-based vaccines through increasing protein

production in the seeds of Arabidopsis thaliana

Presenter(s): Tam Do Collaborator(s): Tony Gonzalez Department(s): FRI Plant Pathways Stream

Plant-based vaccines are a recent upcoming alternative to the typical vaccine production methods, but currently, only one FDA-approved plant-based vaccine exists. The benefits of using plants to produce vaccines are numerous, such as efficient storage, cost effective manufacturing, needle-free delivery due to being edible, and no physical damage to the body. Protein production is a significant factor in plant-based vaccines since the plants need to produce the desired antigens at high enough levels. One con of plant-based vaccines is that plants are relatively not high sources of protein. To possibly solve this problem, previously discovered protein production genes in other plants will be used in an effort to increase the amount of protein in the seeds of Arabidopsis thaliana. Arabidopsis will be used due to its inexpensiveness, ease of genetic manipulation, and previous use in plant-based vaccine research. Responsible for the protein storage in its seeds, the arcelin 5-1 (arc5-1) gene of the bean Phaseolus vulgaris is one potential gene that could be altered and implemented into Arabidopsis’ genome. Alternatively, known Arabidopsis seed protein genes, such as the AT4G25140 gene, can be modified to increase expression and consequently increase protein synthesis. The results of this investigation can lead to more diverse methods of increasing protein production as there are a variety of protein genes from countless different plants. Besides Arabidopsis, common crops such as tobacco and corn can be tested as well. Improving antigen production can also be experimented on in conjunction with the increased protein production.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 127

Plant-based vaccine for canine parvovirus

Presenter(s): Hayden Flume Collaborator(s): Tony Gonzalez Department(s): Freshman Research Initiative Plant Pathways stream

Vaccines are substances that provide antigens which produce antibodies in animals that cause immunity against a specific virus. Similar to how vaccines are made synthetically, plants have the ability to produce antigens to fight off foreign diseases. The source of mass antigen proliferation would be from plants and the antibodies could then be uptaken by animals. Instead of a shot, a plant-based vaccine could be administered through ingestion of an edible seed. Making a transgenic plant overproduce antigens would lead to future generations of plants producing antigens. If the necessary antibodies can be made in plants naturally and the immunization can be edible, then accessibility of the vaccine will increase. The aim of this research is to modify the genome of a plant to mass produce the antigen 2L21 which can cure an infectious disease in dogs called Canine Parvovirus (CPV). The first objective to achieve this is to develop an expression gene fusion with the seed specific promoter bound to the 2L21 antigen and the CTB gene sequence in order to have the plant produce the antigen in the seeds. The second objective to achieve the goal of this proposal is to create stable transgenic Arabidopsis plant lines containing the seed-specific antigen expression fusion gene. The plasmid containing the CTB protein and 2L21 antigen would be integrated into the plant genome using agrobacterium Ti plasmid vectors in order to accomplish plant transgenesis. The seeds would then be used as a vaccine in dogs for Canine Parvovirus (CPV).

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 128

Development of an aptamer database for the preservation of sequence

information

Presenter(s): Kayla Goodman Hailey Ferrell, Sumedha Kota, Ali Askari, Brandon Ta, Issac Weislow, Pearlyn Ang Yi Hui, Daniela Hernandez Collaborator(s): Taylor Oliphant, Sina Saberi Department(s): Department of Molecular Biosciences

Aptamers are oligonucleotide sequences that bind to a specific target. Aptamers are commonly generated through the in vitro selection process termed Systematic Evolution of Ligands by Exponential enrichment (SELEX). Natural sequence databases, such as GenBank, do not include aptamer sequences which are considered non-natural (Benson et al., 2013). With the exponential growth of the use of SELEX, there is a large need for an aptamer database. The purpose of the aptamer database is to compile, store, preserve, and make accessible an accurate list of information about aptamers that have been generated through SELEX. This project can be broken down into two broad steps which involve (1) collecting and peer reviewing information from journals and (2) creating a website that is accessible to the public. The research methods of this project are heavily influenced by those of Andrew Ellington’s previous database that has since been abandoned (Lee et al., 2004). For example, the same search term of “Aptamer SELEX” is being used to maintain consistency of data. There are 877 entries to the dataset so far with various applications that include therapeutic, diagnostic, and detection. Creating this database will not only centralize information for current aptamer researchers, it will lower the barrier of entry for new researchers by providing basic information they will need to get started. Additionally, it will improve the understanding of the distribution of functional nucleic acids and further the understanding of aptamers and their purposes overall.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 129

Anti-HRP RNA aptamer utilized in an ELONA diagnostic for

Alzheimer's Disease

Presenter(s): Doru Gucer Collaborator(s): Gwen Stovall Department(s): Freshman Research Initiative

Alzheimer’s Disease is a neurodegenerative condition impacting millions of people and is characterized by the deterioration of cortical structures leading to a loss of function in several cognitive processes, most notably memory. Despite the debilitating effects of the illness and its widespread prevalence, a definitive diagnosis prior to an autopsy has remained elusive to the medical community. One of the primary pathological hallmarks of the disease is an overproduction of ?-amyloid peptides and their subsequent deposits in the brain as senile plaques. Thus, a complex utilizing a reporter molecule designed to signal an increase in the precursor elements of these plaques could potentially serve to indicate the onset of the disease. A notable example of such a reporter molecule is horseradish peroxidase (HRP), a fluorescent enzyme found in the roots of the horseradish plant. A novel solution to test for Alzheimer’s may be found utilizing aptamers: short sequences of oligonucleotides that are highly specific to their targets. The degree of specialization that aptamers have to their targets and the inexpensive in-vitro nature of their manufacture (as opposed to antibodies created through in-vivo methods) make them ideal candidates in diagnostic applications. Therefore, the objective of this study is to select for an aptamer that binds to the HRP reporter molecule to subsequently create an enzymelinked oligonucleotide (aptamer) assay (ELONA) designed to detect increased ?-amyloid peptide prevalence in the brain. This aptamer will be isolated through iterative in-vitro SELEX (Sequential Evolution of Ligands by Exponential Enrichment) selection processes. Currently, the third round of aptamer selection is underway. Once 6-8 rounds of selection have been completed, the resulting product will be sequenced, and binding assays will be conducted to determine the selectivity of this detection aptamer towards HRP so that it may be incorporated into the diagnostic ELONA downstream.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 130

A hot-start RT Xenopolymerase: A novel RNA aptamer based

reversible inhibitor to improve performance of single-enzyme RT-PCR

Presenter(s): James Guerra Collaborator(s): Gwendolyn Stovall Department(s): University of Texas at Austin

The discovery of once novel enzymes such as those of Taq DNA polymerase and reverse transcriptases have resulted in fundamental techniques of molecular biology that allow for the amplification and manipulation of desired nucleic acid templates. Improving upon these enzymes through synthetic enzyme evolution techniques has resulted in the recent development of an evolutionarily distinct enzyme known as reverse transcription xenopolymerase (RTX). RTX, derived from DNA polymerase lineage, allows for single enzyme reverse transcription-polymerase chain reactions with proofreading domains for both DNA and RNA templates. To further increase the fidelity and capabilities of this novel enzyme, an RNA aptamer against RTX is being selected to develop a hot-start RTX technique. The RNA-based aptamer inhibitor will reversibly bind to RTX at temperatures below 60°C but will dissociate at higher temperature PCR cycling conditions in order to prevent non-specific DNA amplification. The RNA aptamer against RTX is being selected using a technique known as the Select Evolution of Ligands by EXponential enrichment (SELEX). Development of this aptamer is ongoing, two successive rounds of the SELEX method need to be performed as well as Sanger sequencing in order to begin performing enzyme assays assessing aptamer effectiveness on RTX fidelity.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 131

The expression and function of 6 putative aPKC phosphorylation

targets during asymmetric cell division of C. elegans zygotes.

Presenter(s): George Huang, Carrie Meng, Sara Blanco, Ella DeMott, Aubrie Rettmann, Melynda Sylvester Collaborator(s): Ryan Doonan, Daniel Dickinson Department(s): Department of Molecular Biosciences; University of Texas at Austin

Cell polarity is when certain proteins are localized to one side of the cell and not the other (e.g. anterior vs. posterior) prior to mitosis, resulting in asymmetric cell division. Understanding how cell polarity is established is important because asymmetric cell division is essential to cell differentiation and thus, development of multicellular organisms. The microscopic worm, Caenorhabditis elegans, is ideal for studying cell polarity because of stereotyped development, the vast quantity of embryos they produce, and because they are easily amenable to genome engineering. Prior to division of the C. elegans zygote, two kinases asymmetrically localize: atypical protein kinase C (aPKC) to the anterior and PAR-1 kinase to the posterior. In both aPKC and par-1 mutants, the zygote divides symmetrically, derailing subsequent stereotyped development, ultimately resulting in embryonic lethality. Although roles for aPKC and PAR-1 in cell polarity have been known for decades, the proteins phosphorylated by these kinases are mostly unknown. Thus, the Dickinson laboratory at UT used co-immunoprecipitation and proteomics to screen for potential aPKC interactors. That screen identified 46 putative aPKC targets and the Glow Worms FRI stream was tasked with using CRISPR/Cas9 genome engineering to knockout gene function and knock-in fluorescent protein tags for all of these proteins. Here we examine the zygotic expression and function of 6 of these targets that we successfully tagged: ATTF-2, EEL-1, GYF-1, NPP-10, SPT-16, and W08E12.7. All of these proteins have human orthologs, some had completely unknown cellular functions, and our studies have revealed that some are required for normal embryonic development.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 132

A Review of the propagation of unexplained mutations to

the IgE aptamer

Presenter(s): Leslie Imafidon Collaborator(s): Gwendolyn Stovall Department(s): Freshman Research Initiative, Aptamer Stream

Aptamers are oligonucleotides that are found to have a strong binding affinity for a target molecule. Due to the short length of many aptamers, modifications to the oligonucleotide sequence can have pronounced effects on an aptamer’s binding affinity to its target molecule. Previous research has shown that the propagation of mutated aptamer sequences throughout literature is a result of inconsistent sequence reporting practices. These sequence mutations can be categorized as publication-induced mutations, which result from vague reporting of aptamer sequences in such a way that key information (e.g. nucleic acid type) is excluded from the publication, and unexplained mutations, which are published aptamer sequences with unexplained deviations from the original aptamer sequence. To determine the degree to which these modified sequences persist in literature, this research aims to provide a comprehensive phylogeny showcasing the evolution of the immunoglobulin E (IgE) aptamer sequence. This is accomplished by reviewing publications that cite mutated aptamer sequences and collecting data on reported sequence information, nucleic acid type, selection conditions, and binding affinity. This research will further highlight the need for standardized publication guidelines in the aptamer field, with the goal of influencing aptamer researchers to adopt protocols that mitigate the propagation of mutations to aptamer sequences.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 133

Examining the biochemical activity of the Anti-CRISPR protein,

AcrIIA7

Presenter(s): Negar Koupaei Collaborator(s): Soo Hyun Yang Department(s): Department of Integrative Biology; Freshman Research Initiative Biobricks Stream

Bacteria are constantly exposed to microbes and bacteriophages. The race between bacteria and phages resulted in the development of evolutionary mechanisms to prevent infections in bacteria including the CRISPR-Cas system. In return, phages have developed anti-CRISPR activities to reduce CRISPR-Cas proteins’ effects. The CRISPR technology can be used to edit DNA/RNA sequences. However, this editing might cause accidental changes in the genome as a result of off-targeting. Therefore, developing a method to allow precise editing of DNA/RNA sequences is critical. ACRs are used as a method to precisely control the DNA/RNA editing of CRISPR enzymes that can minimize the side-effects of off-targeting. There are several genes that have anti-CRISPR proteins (ACRs) activity. Among those, AcrillA7 was shown to exhibit a strong inhibitory effect on Cas9 in vitro. The overall goal of this project was to examine the biochemical activity of the AcrIIA7 on inhibiting the DNA or RNA processing activities of the CRISPR Cas nucleases. The experimental aims of this project are: 1. To clone the genes coding for the Acrll7 anti-CRISPR proteins into the 6XHis-TwinStrep-SUMO-pET19b E.coli expression vector via Gibson Assembly, 2. To optimize the expression and purification condition of the recombinant AcrIIA7 protein, 3. To examine the inhibitory effect of AcrIIA7 on the DNA/RNA processing activities of Cas nucleases. The results of this project could be used to study the effect of anti-CRISPR in inhibiting/removing off-targeting Cas nuclease and potentially become an applicable method to treat genetic disorders.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 134

Molecular mapping of Austin's dirtiest water

Presenter(s): Vincent Pham Collaborator(s): Stuart Reichler Department(s): FRI Urban Ecosystems Stream

Measuring fecal indicator bacteria (FIB) is a major component of water quality monitoring. FIB levels provide a useful index for the health of the aquatic system and potential harmful impacts for humans and other organisms. High FIB levels can signal defective infrastructure and provide data for city officials to identify the specific problem and create possible solutions to protect public health. This study intends to apply the novel Filter Heat Spin (FHS) method to perform a high throughput Molecular Source Tracking (MST) of urban waterways across Austin. Preliminary results suggest that aging infrastructure and other inputs near Waller Creek are contributing to increased levels of human associated FIB and causing levels of bacterial contamination in the creek to rise significantly above the EPA’s maximum amount for contact recreation. This study plans to expand these results to other urban water systems along with looking at levels of dog-associated FIB to form a complete picture of the levels of biological pollutants. This will also allow for the detection of infrastructure issues before serious environmental and/or public health damage is done.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 135

Amino acid mutations in the genes that code for the H4 histone in

cancer vs. non-cancer patients

Presenter(s): Rachel Lopes, Faiza Quadri, Sneha Rajendran, Hailey Allen, Kalei Ragland Collaborator(s): Dia Bagchi, Vishy Iyer Department(s): FRI Functional Genomics Stream

Post-translational modification of histones has been associated with various forms of cancer. Since this type of modification of histones can change the expression levels of genes, our question examines the relationship between amino acid mutations in genes and identifiable patterns of change within their corresponding histones. After looking at this relationship, further research could be conducted to examine any post-translational modifications in the histones that promote cancer. First, we sought to analyze whether we can discernibly ascertain whether certain amino acid mutations were found more commonly in tumor samples versus samples of healthy tissue and whether any mutation patterns could be seen across various cancers. This was done in Python 3 and R, using data from the gnomAD and cBioPortal databases, to visualize differences in amino acid mutations present across samples from both databases. To thoroughly investigate this question, access to a wet laboratory would be necessary to test whether any mutation seen multiple times in cancer tissue and not seen in healthy tissue could be a driver gene in the onset of cancer, and this would be the next step after computational methods of analysis are completed. Of the genes visualized in Python so far, none of the genes that code for the H4 histone have any significant amino acid mutation differences between healthy and tumor samples of tissue.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 136

Discovery of novel compounds and current antivirals for possible inhibition of SARS-CoV-2 RNA Dependent RNA Polymerase through virtual screening methods

Presenter(s): Alia Segura Collaborator(s): Josh Beckham, Walter Fast Department(s): FRI Virtual Drug Screening Stream

The rapid advancement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in numerous efforts on multiple fronts to reduce virulence and lethality. Current therapies against SARS-CoV-2 range from vaccinations to convalescent plasma to drugs that have shown success in targeting aspects of the virus that decreases the severity of infection. The essentiality of RNA Dependent RNA Polymerase (RdRp) in SARS viral replication makes for a significant protein to target for inhibition. In this study, the Zinc ChemBridge and MicroFormat libraries (307,466 ligands total) were screened against RdRp using the Genetic Optimization for Ligand Docking (GOLD) program to identify novel compounds that can bind to the active site. In addition, drugs used in therapies to inhibit polymerases from a variety of viruses were selected and covalently docked onto the polymerizing RNA strand in the active site of RdRp. The Zinc ChemBridge and MicroFormat libraries resulted in two high scoring ligands, ZINC02831197 with a GOLD fitness score of 99.64 and compound 7777452 with a GOLD fitness score of 97.98, respectively. The novel compounds and antivirals with favorable GOLD scores may provide guidance for in vitro studies in their ligand selection. The high scoring ligands may also be used in the identification of pharmacophores for further drug discoveries.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 137

Engineering cyanobacteria biosensors for detection of copper, zinc,

and lead in waterways

Presenter(s): Jennifer Tang, Sophia Hoefner, Maanasa Cherukuvada Collaborator(s): Jaden Ju, Olivia Tang, Dennis Mishler, Jeffrey Barrick Department(s): FRI Microbe Hacking Stream

As conventional methods of detecting heavy metal pollutants in waterways remain complicated and costly, a need for a more convenient and cost-effective alternative arises. Cyanobacteria, natural photosynthetic inhabitants of waterways, are a candidate for heavy metal biosensors. Previous research revealed that cyanobacteria Oscillatoria sp. exists as consortia of symbiotic bacteria. Studies have shown that engineering a consortium, as opposed to just one species, allows division of labor and increases robustness of the engineered system. Therefore, we aim to genetically engineer cyanobacteria symbionts to detect various heavy metals in the environment. Through literature review, we found three biosensors that had previously been engineered with cyanobacteria, including a copper biosensor, a zinc and copper biosensor, and a lead biosensor. We designed three different plasmids containing these biosensors and constructed the vectors using BioBrick Assembly. We are currently troubleshooting transformations of chemically competent E. coli with these constructed plasmids. After transformation, we will conjugate with Oscillatoria symbionts and test the conjugants in samples of copper, zinc, and lead.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 138

Effects of 8-Bromo cGMP and 8-Nitro-cGMP on arabidopsis root hair

growth

Presenter(s): Rustin Tourgoly Collaborator(s): Abigail Tyree, Gregory Clark Department(s): FRI Discovering Signals Stream

Extracellular ATP (eATP) is an important hormone-like signaling molecule in both animal and plant cells. However, the role of extracellular ATP in plants is a relatively new area of research. Arabidopsis thaliana is a model plant used for basic research by plant biologist because it was the first plant to have its genome fully sequenced. Previous research in my FRI stream using Arabidopsis seedlings found that low levels of applied ATP promote root hair growth while high levels of applied ATP inhibit root hair growth. In Arabidopsis seedlings one of the early signaling steps induced by applied ATP is an increase in the level of the nitric oxide. Nitric oxide can have different effects in plant cells but it is known to be a co-factor for guanylate cyclase which produces the second messenger, cGMP. Recent research indicates that cGMP can also be post-translationally nitrated to become 8-Nitro-cGMP which may mediate different cellular responses. This potential role for nitric oxide of promoting the production of cGMP leads to the question of whether cGMP or 8-Nitro-cGMP is a required step in eATP-induced root hair growth changes in Arabidopsis seedlings. 8-Bromo-cGMP is a stable analog of cGMP which scientists use to determine the effects of cGMP on the cell signaling pathways. In my preliminary experiments, I tested the effects of varying concentrations of 8-Bromo-cGMP and 8-Nitro-cGMP on root hair growth of Arabidopsis seedlings. This is the first step toward addressing the potential role of cGMP in eATP-mediated effects on root hair growth in plants.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 139

Examining the effect of ethanol on transcription of Wnt/PCP pathway

members.

Presenter(s): Thy H. Vu Collaborator(s): Desiré M. Buckley, Johann K. Eberhart Department(s): Department of Molecular Biosciences

Fetal alcohol exposure is the cause of many birth defects and developmental disabilities that are collectively referred to as Fetal Alcohol Spectrum Disorders (FASDs). The Wnt Planar Cell Polarity (Wnt/PCP) signaling member, Vangl2, is critical for regulating convergent/extension in developing vertebrate embryos which is important for body axis elongation and eye field separation. In addition, Vangl2 is essential for directed cell migration in the hindbrain. Previous studies have shown that embryonic alcohol exposure induces cyclopia and disrupts cranial motor neuron migration in zebrafish with reduced Vangl2 function, indicating that alcohol interacts with the Vangl2 allele. However, the mechanisms underlying this interaction have not been elucidated. It is possible that alcohol interacts with the Wnt/PCP pathway at the level of transcription, translation, and/or protein localization. Using zebrafish, we will examine the effects of alcohol (i.e. ethanol) on transcription of the Wnt/PCP pathway. We will quantify mRNA expression levels of core Wnt/PCP genes (vangl2, celsr2, fzd3a, pk1b and dvl) in control and ethanol-exposed wildtype embryos by quantitative RT-PCR. We will expose groups of embryos during early and late stages of neurogenesis, from 6-24 hours post-fertilization (hpf) and 6-48 hpf to 0%, 1.0% or 1.5% (volume/volume) ethanol. Total RNA will be obtained from embryos at 18 hpf, 24 hpf and 48 hpf. I predict that ethanol disrupts transcription of Wnt/PCP pathway members which has downstream effects on the amount of protein produced and cellular localization of the protein in the developing organism.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 140

Analyzing the role of mitochondria in synaptic transmission within

the dentate gyrus using reconstruct, a 3DEM visualization software

Presenter(s): Soummitra Anand Collaborator(s): Kristen M. Harris, Dusten Hubbard, and Pritakshi Das Department(s): Department of Neuroscience at the Center for Learning and Memory; University of Texas at Austin

Because long-term potentiation (LTP) is thought to be involved in learning and memory, it is important to study factors that modulate its induction and persistence, especially as studied in freely moving animals. In the following paper, we will investigate the role of mitochondria in supporting synaptic transmission. Mitochondria serve many vital functions in neurons such as helping with the production of ATP, sequestration of calcium, and synthesis of glutamate. However, not all hippocampal CA1 presynaptic axonal boutons contain mitochondria, raising the question of whether synapses without mitochondria can sustain changes from LTP. To address this question, we will compare the cross-sectioned postsynaptic density (PSD) areas and docked vesicle counts associated with presynaptic boutons that contain mitochondria with presynaptic boutons that do not contain mitochondria. We will also compare the sizes of presynaptic mitochondria with the docked vesicle counts and PSD areas associated with the presynaptic boutons. The Long-Evans rat tissue being studied is from 2 hours after LTP was induced in the middle molecular layer (MML) of the dentate gyrus as well as from a control animal. In order to derive the quantitative data we are seeking, we will utilize Reconstruct, a 3D electron microscopy software. Based on previous literature, we suspect that the presence of mitochondria in presynaptic boutons will reflect enhanced vesicle mobilization and larger PSD sizes 2 hours after LTP was induced in the MML. We also predict that the size of the presynaptic mitochondria will correlate with vesicle counts and PSD sizes in this tissue. Ultimately, we hope to learn more about the role of mitochondria in supporting synaptic transmission within the dentate gyrus.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 141

Drosophila demonstrates acquisition of tolerance to ethanol in

ethanol-induced aggression

Presenter(s): Madeleine Cope Collaborator(s): Jed Golman, Julia Pena, Thilini Wijesekera, Nigel Atkinson Freshman Research Initiative Behavioral Neuroscience stream; Department of Neuroscience; University of Department(s): Texas at Austin

Drosophila demonstrates acquisition of Tolerance to Ethanol in Ethanol-induced Aggression by Madeleine Cope of the Behavioral Neuroscience FRI Stream, UT Department of Neuroscience Acts of aggression are typically associated with the use of alcohol in humans, prompting this study of the response in Drosophila melanogaster. This research has gathered that male flies typically respond to low dosages of alcohol with an increase of male: male fighting in the presence of a female fly as if they are competing to court the female. This type of aggression is typically measured through the number of lunges, wing threats, and fencing seen in these males. However, knowing these flies are under the influence of ethanol then raises the question if over time these male flies develop a tolerance to alcohol. Moreover, this study tries to determine whether the acquisition of tolerance to alcohol will remove the effect of alcohol on aggression. To determine whether flies acquire tolerance to the aggression-promoting effects of alcohol we exposed the flies to alcohol twice and asked whether the second treatment produces the same increase in aggression as the first treatment. This was accomplished by separating male flies into groups where they are exhibited to either ethanol vapor on two consecutive days, to ethanol vapor on day one and water vapor on day two, water vapor on day one and ethanol vapor on day two, or water vapor on two consecutive days. Following these treatments, two male flies from each group are put into a chamber with a decapitated female placed on a bed of food in order to induce aggressive behavior. After filming, the video is then watched and the latency (number of seconds before the first lunge) and number of lunges over a thirty-minute period are counted (representing our metrics of aggression). With this series of experiments, we hope to determine whether aggressive behavior subsides when alcohol tolerance is built, thus indicating a specific stimulus for aggressive behavior.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 142

The function of non-nuclear NfkB isoform DifB in mating and female

receptivity in Drosophila melanogaster

Presenter(s): Natalie Dezso Collaborator(s): Hanna Gedemu, Thilini Wijesekera, Nigel Atkinson Department(s): Freshman Research Initiative Behavioral Neuroscience stream

One of the most important defenses in fighting off disease is an individual's innate immune system. The innate immune system of Drosophila melanogaster consists of two molecular pathways, the Toll and IMD pathways. In the Toll pathway, infection by gram positive bacteria and fungi triggers the nuclear translocation of two NF-kB proteins called Dif and Dorsal, which facilitate antimicrobial peptide production. Recently, two isoforms of the Dif NF-kB, Dif A and Dif B, were discovered. Research has shown that Dif A acts directly in the nucleus while Dif B is localized outside of the nucleus and is expressed in Drosophila nervous tissue, indicating that it may influence behavior. Preliminary research supports this theory and shows that the knockout of Dif B reduces courtship behavior in male Drosophila. However, the effect of Dif B on female courtship behavior has not been studied. The goal of this study is to investigate the effect of Dif B on female receptivity to male courtship. Female receptivity to male courtship was measured through an assay in which a wild type male and either a wild type or Dif B mutant female fly are placed in a courtship chamber and the time until copulation is recorded. In order to determine the role of Dif B in female receptivity, receptivity assays were conducted on flies with the Dif B protein either knocked out, using a mutation that prevents Dif B expression, or knocked down, using a UAS-Dgrad transgene that expresses a Dgrad protein which marks a GFP-tagged DifB protein for destruction. This transgene is expressed through the Tubulin Gal4 system, which targets the UAS of the Dgrad transgene in order to express Dgrad throughout the body. Preliminary data shows that the knockdown, knockout, and wild type flies all exhibited comparable levels of receptivity to male courtship.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 143

The function of non-nuclear NfkB isoform DifB in courtship behavior

in Drosophila melanogaster

Presenter(s): Hanna Gedamu Collaborator(s): Nigel Atkinson, Thilini Wijesekera, Natalie Dezso Department(s): Department of Neuroscience; Freshman Research Initiative Behavioral Neuroscience Stream

The Toll pathway is one of the ways by which Drosophila melanogaster mediate their innate immune response. This process is analogous to processes in humans referred to as Toll-like receptor pathways. In the flies, a gene by the name of Dif is ultimately transcribed, resulting in two splice isoforms, DifA, and DifB, which are translated into their respective NF-?B proteins. When there is a mutation in the Dif gene, various behaviors of the flies are dramatically altered. Preliminary findings suggest that when male Drosophila melanogaster are mutant for the DifB isoform, they show a decrease in courtship behaviors. Courtship is quantified by the latency until the first courtship behavior (in this case, wing extension by the male fly) and the total duration of the courtship behavior. For the following assays, the effects of DifB on other reproductive behaviors of courtship are analyzed. This includes heterosexual courtship, where the female is the wild-type virgin and the male is an isolated mutant virgin. The other assay includes male to male courtship, where both flies are isolated, virgin males. For both of these assays, the appropriate flies were produced through genetic crosses. The widely known Gal4-UAS system was used to express deGradFP throughout the flies’ bodies with a tubulin promoter. The DifB proteins in these flies were tagged with GFP, which in turn allowed deGradFP to bind to the tagged protein. The deGradFP flagged the protein complex for ubiquitination, causing degradation of the DifB protein. Therefore, flies that still had completely effective DifB mRNA, but did not accumulate DifB protein because of deGradFP. Since there is preexisting data on heterosexual courtship on the DifA and DifB mutants and their parental strain, J4, male to male courtship was the only assay that needed to be performed on them.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 144

Infection and alcohol sensitivity in Drosophila melanogaster

Presenter(s): Aula Haidry Collaborator(s): Thilini Wijesekera, Nigel Atkinson Department(s): Department of Neuroscience; Painter and Patterson Laboratories

Ethanol is an addictive drug that affects a wide variety of signaling pathways. In mammals, ethanol alters the activity of the innate immune system and this change appears to contribute to the process of alcohol addiction. Research done on the effects of alcohol on the immune system have shown that acutely it suppresses the innate immune system whereas long term use activates the innate immune system to produce a state of chronic inflammation. Through the use of genetic manipulation, it is possible to invoke a modified immune system response. Suppression of the innate immune system results in an increased sensitivity towards ethanol whereas activation of the immune system produces ethanol resistance. An actual infection, which naturally activates the immune system, was performed to observe if the same result would be produced. Ethanol sedation assays were used to analyze alcohol sensitivity in two groups of wild type Drosophila melanogaster. The experimental group was infected with Beauveria bassiana (a fungal insect pathogen), while the control group was mock infected by being stabbed with an uncontaminated needle. The infection with B. bassiana invokes a greater innate immune system response than that of the mock infection group. The ethanol vapor sedation profile was determined using cameras to monitor the rate of sedation of a large population of flies. Movement of the flies was determined using Perl and R scripts that digitally subtract consecutive photographic images. Referenced as the Knock Down 50, KD50 represents the period of time taken for the movement in vials to reach 50% of the maximal observed amount of movement in each respective vial. The flies that were infected with B. bassiana were observed to have an increased resistance, expressed as a larger KD50 value, to sedation with ethanol vapor.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 145

Hippocampal microglia are vulnerable to aging-induced pro-inflammatory morphological changes that are partly alleviated by M. vaccae immunization

Presenter(s): Reha Kakkar Collaborator(s): Kevin Sanchez, Laura K Fonken College of Natural Sciences; University of Texas at Austin College of Pharmacy; Division of Pharmacology and Department(s): Toxicology

Aging is associated with increased risk for neuroinflammation, and related neurodegenerative diseases. In addition to an aging populace, developed urban societies face a rise in chronic inflammatory disorders. One potential explanation is the “hygiene hypothesis,” which attributes this rise in low-grade chronic inflammation to reduced exposure to key microbes. In particular, Mycobacterium vaccae (M. vaccae) is a common bacterium with strong immunoregulatory abilities, such as enhancing the production of anti-inflammatory cytokines. Microglia, the brain’s resident immunocompetent cell, are mediators of the neuroinflammatory process. With aging, microglia can adopt a “primed” or “pre-activated” phenotype where they react hyper-actively to inflammatory challenges. This study examines whether aging induces morphological features indicative of “primed” microglia, which brain regions are most susceptible to age-associated changes, and whether M. vaccae immunization can ameliorate the primed morphology. Adult and aged F344xBN rats were immunized with M. vaccae or vehicle every week for three weeks. Three days after the third M. vaccae immunization, rats were euthanized, paraformaldehyde perfused, and brains were extracted, sliced and stained with Iba1 to visualize microglia. Microglial soma morphological analyses reveal the CA1 and CA3 subfields of the hippocampus are most sensitive to aging: microglia exhibited an increase in soma area in the CA1 region and an increase in soma area, perimeter, and circularity in the CA3 region. These morphological features indicate a more activated microglia phenotype. In the CA3, M. vaccae treatment reduced soma perimeter, suggesting M. vaccae may partially ameliorate effects of aging. However, M. vaccae treatment also increased circularity in the CA3. In contrast to these hippocampal subfields, microglia in other brain regions including the amygdala and prefrontal cortex did not exhibit age- or M. vaccae-associated morphological changes. Elucidating the relationship between aging, microbial exposure, and neuroinflammation may contribute to understanding neurodegenerative diseases with a neuroinflammatory component in aging societies.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 146

Withdrawal from chronic alcohol exposure dysregulates the

cortical phosphoproteome in rats

Presenter(s): Janet Le Collaborator(s): Le, JY1, Yu NK2, Diedrich J2, Faull, PA1, Roberto M2, Yates JR III2, Natividad LA1,2 1The University of Texas at Austin, College of Pharmacy, Division of Pharmacology and Department(s): Toxicology, Austin, Texas USA The Scripps Research Institute, Department of Molecular Medicine, La Jolla, California, USA

Growing evidence suggests that chronic alcohol (EtOH) exposure induces proteome-wide dysregulation in the brain, and here we sought to bring consensus to potential mechanisms that may mobilize these systemic changes. In this regard, protein kinases regulate phosphorylation states, often serving as “molecular switches” that induce a variety of biological responses, such as changes in protein signaling. Here, we broadly examined the cortical phosphoproteome of male rats made dependent on EtOH using vapor inhalation procedures. A separate group of rats remained naïve to EtOH and served as non-exposed controls. We dissected the dorsal and ventral regions of the medial prefrontal cortex (mPFC) 14 days into EtOH withdrawal, coinciding with the emergence of cognitive impairments in previous work. The dual-region dissection allowed us to compare molecular processes of cognitive behaviors that are thought to be functionally distinct. The mPFC samples were digested into fragment peptides, labeled with isobaric tags for quantitation and enriched for phosphorylation. The comparison between EtOH-naïve (CON) and CIE-exposed rats (n=3 pooled samples per group) revealed 748 and 1,323 significantly changed phospho-peptides collected from the dorsal and ventral mPFC, respectively (p75%), ±1.5-fold (EtOH/CON) significant changes and prior identification in the literature (PhosphoSitePlus database), resulting in the identification of 35 (dorsal) and 110 (ventral) high-confidence phospho-peptides. A consensus analysis of these data revealed the presence of a binding motif for calcium/calmodulin-dependent protein kinase II (CaMKII; RxxS*) that was overrepresented in the dorsal mPFC and demonstrated a pattern of up-regulation for glutamate-related phosphosites (Grin2B, Grm5). The ventral mPFC aligned with a motif for casein-kinase II (CKII; S*xxE) in which decreases in phosphorylation of Gap43 (neuromodulin) and Stx1a (syntaxin 1A) may have important implications for impaired synaptic transmission. These findings suggest that the mechanisms regulating phosphorylation states are dysregulated in EtOH dependence and may contribute to hyperphosphorylated tone in the mPFC during a period of increased susceptibility to EtOH relapse.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 147

Autoimmune epilepsy patients: A role for cellular immunity?

Presenter(s): Cole Maguire Collaborator(s): Cole Maguire, Sam Bazzi, Blaine Caslin, Debb Briggs, Todd Triplett, Esther Melamed Department(s): Department of Neurology; Dell Medical School

Although autoimmunity has been implicated as an etiology in a subset of refractory epilepsies, exact mechanisms of how the immune system drives seizures are still being discovered. Current clinical evaluation of potential autoimmune epilepsy is focused on assessment of known neuronal antibodies. More auto-antibodies are being characterized yearly, but many suspected autoimmune patients remain sero-negative. As a result, it is challenging to treat these patients since they do not respond well to antiepileptic drugs, devices, or surgeries. Thus, it is critical to better understand all aspects of the immune response in seizures, including cell and cytokine immune components in order to develop more specific therapies for these patients. In this study, we recruited patients with (i) suspected autoimmune epilepsy who were seronegative for autoimmune epilepsy antibody panel, (ii) non-autoimmune epilepsy (iii) multiple sclerosis, and (iv) healthy controls. Patient sera was evaluated for a total of 65 known inflammatory and anti-inflammatory T-cell, B-cell, and macrophage cytokines. PCA on the cytokine multiplexing data revealed a distinct group of patients with suspected autoimmune epilepsy clustering separately from patients with non-autoimmune epilepsy, controls, and patients with treated autoimmune neurological conditions. From the panel of 65 inflammatory cytokines, GM-CSF, a cytokine known to affect blood brain barrier trafficking in other neuro-autoimmune diseases, was significantly increased in patients with untreated suspected-autoimmune epilepsy patients compared to other evaluated patient groups. Other cytokines, including IL-10, IL-13, IL-15, IL-20, and IL-23 were also elevated in patients with suspected-autoimmune epilepsy patients compared to other patient groups. Flow cytometry on lymphocytes revealed altered T-cell cytokine production in response to immunological treatment that correlated with clinical improvements. The results of our study suggest that a subset of epilepsy patients who are seronegative for known auto-antibodies may experience neuroinflammation due to cell-mediated immune responses. Identification of patients with distinct autoimmune epilepsy subtypes could accelerate the development of specific neuroimmune treatments and improve health outcomes in patients with refractory seizures due to autoimmunity.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 148

Valence and ruminative thoughts influence efficiency of replacement

in working memory

Presenter(s): Meghan Mallya Collaborator(s): Allison Bruning, Jarrod A. Lewis-Peacock Department(s): Department of Neuroscience; Department of Psychology

We are faced with different stimuli in our environment, which can get encoded in our working memory. Working memory is a limited capacity cognitive system that allows us to hold information in mind for a short period of time. There are mechanisms in our working memory that allow us to inhibit irrelevant information, such as negative thoughts or stimuli, from our mind. When this mechanism does not work efficiently, people may fixate on these negative thoughts in a maladaptive way. Researchers still do not understand how this inhibitory mechanism operates in people who have a tendency to ruminate or worry, such as those with depression or anxiety. In this behavioral study, we evaluated how emotional stimuli and traits of internalizing disorders play a role in the success and efficiency of manipulating information in working memory. We expect to see lower accuracy levels and greater inefficiency when participants with symptoms of internalizing disorders manipulated emotional material. With further research, we will better understand working memory processes in clinical populations and use these findings to improve cognitive therapies.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 149

M. Vaccae immunization leads to greater microglial branching in the

hippocampus of adult rats compared to aged rats

Presenter(s): Claire Harper Collaborator(s): Kevin Sanchez, Laura Fonken Department(s): Department of Neuroscience; College of Pharmacy (Division of Pharmacology and Toxicology)

The global aged population is rapidly increasing, and it is projected to double to two billion people by 2050. This rise in aging is concurrent with an increase in the prevalence of chronic neuroinflammation in industrialized societies, which puts older individuals at risk of developing neurodegenerative diseases. The hygiene hypothesis proposes that industrialized countries experience a reduced exposure to microorganisms, which may lead to increased vulnerability to immune pathology and thus increased neuroinflammation. Therefore, we examined whether aging induces regional differences in the morphology of microglia, the resident immune cells of the central nervous system (CNS). Further, we examined whether immunization with Mycobacterium vaccae, a commensal bacterium with immunoregulatory properties, ameliorates age-associated changes in morphology. For this study, we immunized aged (24 mos) and adult (3 mos) male Fischer 344 x Brown Norway rats with three injections of M. vaccae spaced one week apart. Three days after the final injection, we euthanized the rats and removed their brains to analyze microglia morphology. Our experiment focused on the CA3 region of the hippocampus because we previously found that it may be the most responsive subfield to M. vaccae treatment in a microglia soma morphology analysis. We conducted a Sholl analysis with FIJI (ImageJ) to analyze microglial complexity. We found that M. vaccae immunization results in greater and more distal microglial branching to the soma in adult rats compared to controls, indicating a more quiescent microglial phenotype. In contrast, M. vaccae immunization produced fewer and more proximal branching in aged rats compared to controls. However, aging did not have a direct effect on microglial complexity. These results suggest that M. vaccae immunization had less impact on microglia morphology in aged as compared to adult rats.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 150

Automated drosophila larval-Learning assay and its benefits

Presenter(s): Jordan W. Matkin Collaborator(s): Nigel Atkinson Department(s): Department of Neuroscience

Drosophila as a model organism is advantageous because of its low cost and ease of handling. A variety of associative-learning assays show that flies are capable of associating a stimulus with a reward or a punishment. The powerful genetics of the fly and its small nervous system makes it ideal for genetic dissection of learning and memory. The third instar larvae, which is the third larval developmental stage after larvae have molted twice, can be used for negative association learning, where a painful or unfavorable stimulus is paired with another stimulus to elicit the same response to both the stimuli. The unconditioned stimulus, in this case, is heat shock based on Drosophila having a natural and innate reaction to the shock. The conditioned stimulus, a stimulus that elicits a different response or no response, is paired with the unconditioned stimulus to obtain the unconditioned response for both stimuli. A simplistic negative reinforcement learning assay using a single reinforcement (or trial) of heat shocking allows for quick training of larvae before experimentation. Heat shocking requires fewer learning trials and more flexibility in the reinforcement window than other negative reinforcers like electroshocking. However, due to Drosophila not being mammals, larger sample sizes are necessary to conclude a relevant assumption for the mammalian system. The increased sample size would require more time and persons to complete larvae learning, if not for the ability to automate the assay. With the advancement of personalized 3D modeling through 3D printing and laser cutting, larval learning assays are a model template for automation. A semi-automatic system that will train larvae to associate a punishment (heat pulse) with a normally favorable food odor is currently being developed. This causes the food odor to become repellent to the larvae, a behavior that can be easily scored as physical avoidance.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 151

Learned hierarchical knowledge generalizes to inform adaptive

decision-making

Presenter(s): Connor McKee Collaborator(s): Alison Preston Department(s): Department of Neuroscience

Decision-making in our daily lives depends on the context in which choices are made. For example, the coat you chose to wear (i.e. a parka or raincoat) may depend on your environment (e.g. the mountains or rainforest). Prior rodent work has shown that after learning, knowledge becomes organized hierarchically in a context-dependent manner. Such that, depending on whether you are in the mountains or rainforest, a parka would be the most rewarding coat selection in one context and least in the other. Here, we aim to quantify the emergence of context-dependent hierarchical knowledge and the flexible use of that knowledge to generalize across different scenarios. Participants learned about objects with context-dependent reward values in an X-shaped virtual environment consisting of an elongated, contextually-varying hallway with decision points on either end. First, participants learned the context-dependent object-reward pairings for one set of three objects. Next, they learned the context-dependent object-reward pairings for a new set of three objects. We hypothesized that prior knowledge of the hierarchical structure would generalize to the second set of objects as evidenced by a facilitation in learning rates. Participants gradually learned the context-dependent object-reward pairings during the first three runs. When introduced to the new object set, there was no significant difference in performance, indicating generalization of the hierarchical reward structure to the new object set. To further understand how decision-making unfolded, we applied a reinforcement learning (RL) model to our behavioral data. The RL model used participants’ past selections to successfully calculate the probability of future decisions and predict reward value expectations, indicating that current decisions were guided by prior selections. Our results demonstrate that participants learned to flexibly decide which actions were the most adaptive, promoting correct decision-making in a given context. Furthermore, the structure of prior knowledge may support the generalization of learned experience.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 152

Testing for odor discrimination and habituation in a rat model of

Fragile X Syndrome.

Presenter(s): Destiny Okwubodu, Damola Ashade Collaborator(s): Sohmee Kim, Emma Robson, Uzair Saleem, and Laura Lee Colgin Department(s): Center for Learning and Memory, Department of Neuroscience

The principal neurons of the hippocampus are place cells, neurons that have receptive fields for particular locations in space. Previously published research by the Colgin lab showed that place cell firing patterns in CA2, a hippocampal subregion hypothesized to be important for social memory, change in response to social experiences. Ongoing work indicates that CA2 cells respond to the olfactory component of social stimuli. Preliminary data using a rat model of Fragile X Syndrome (Fmr1 knockout rats) suggest CA2 place cell responses to social odors are absent. Fragile X Syndrome is a genetic disorder characterized by social behavioral deficits associated with autism spectrum disorders. In our current work, we aim to determine whether the lack of CA2 place cell response to social odor in Fmr1 knockout rats is due to a dysfunctional olfactory sense. Olfactory habituation and dishabituation tests were performed to determine whether Fmr1 knockout rats can detect and discriminate odors compared to age-matched wildtype control rats. The data indicates Fmr1 knockout rats display normal detection and habituation of odors, indicative of a functioning olfactory system. This suggests deficits in CA2 place cells are likely due to factors downstream of the olfactory system, such as hippocampal abnormalities.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 153

Pheromone-binding protein LUSH plays a role in aggression in

drosophila melanogaster

Presenter(s): Julia Pena Collaborator(s): Jed Golman, Madeleine Cope, Thilini Wijesikera, Nigel Atkinson Department(s): FRI Behavioral Neuroscience Stream

LUSH is an extracellular pheromone-binding protein present in the lymph surrounding the trichoid sensilla in Drosophila melanogaster. This protein can bind with the male pheromone 11-cis-vaccenylacetate (cVA) in order to activate the Or67d receptor which is expressed by T1 neurons found on the antennae of male and female flies. These neurons are incredibly specific to the detection of cVA which is vital for intraspecies communication among Drosophila, determining everything from aggregation and aggression to the attractiveness of a female during courtship. In this study, we looked at how LUSH affects aggression by comparing a LUSH mutant, lush+ transgene, and a LUSH D118A trangene with the wild type Canton S strain. We will do this using an aggression assay to analyze the latency of the first lunge and the number of lunges of male Drosophila between the genotypes. Due to the role that the LUSH protein plays in aggression, we suspect that a LUSH null mutant would not allow the flies to sense cVA and therefore could not enact aggression. However, a direct analysis of the different types of LUSH mutants’ responses to aggression has not yet been conducted, so we will be observing the impact of each LUSH mutant on aggression in Drosophila melanogaster. These findings could help us to better understand how aggression is mediated in the fly nervous system and shed more light on the LUSH protein’s role in Drosophila intraspecies communication.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 154

Time-restricted feeding protects against inflammation induced

depressive-like behavior in female but not male mice

Presenter(s): Akshay R. Prabhakar Collaborator(s): Jeffrey S. Darling, and Laura K. Fonken Department(s): Division of Pharmacology and Toxicology, College of Pharmacy

Time-restricted feeding (TRF) protects against metabolic dysfunction and regulates inflammatory pathways. As TRF is rapidly gaining attention as a dietary strategy in humans, determining whether this feeding paradigm regulates brain function and behavior is critical. The goal of this study was to determine the impact TRF plays on cognitive and neuroimmune function in both adult males and female C57Bl6/J mice. Adult male and female mice were either administered food ad-libitum across the day or food access was limited to 10 hours during the active dark cycle (TRF) for XXX weeks. During the first five weeks of diet, body mass and caloric intake were tracked. In agreement with previous findings, males fed ad-libitum gained more weight than TRF males, despite no difference in overall caloric intake. Next, to test the impact of TRF on neuroimmune function, mice were given an intraperitoneal injection of lipopolysaccharide (LPS) to induce an immune response (validated by decreased body weight and increased spleen mass versus saline controls). Mice were tested for depressive-like behavior on a forced-swim task 24h later. Mice given LPS exhibited increased depressive-like behavior. Interestingly, TRF rescued this behavior in females but not males. We next investigated possible underlying mechanisms mediating these TRF induced metabolic and behavioral changes. PCR analysis revealed gene expression for Interleukin-1? (IL-1?), a pro-inflammatory cytokine, to be elevated in mice administered LPS and fed ad-libitum but reduced for those on TRF. Elevated IL-1? has previously been associated with increased behavioral despair in mice. Unexpectedly, TRF also led to a decrease in brain-derived neurotrophic factor as well as inflammatory cytokine IL-6 in mice that received LPS. Future experiments will investigate other gene changes that may regulate behavioral outcomes as well as examine changes in microglia morphology, cells that critically regulate neuroinflammation.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 155

Analysis of behavior-seizure correlates in a mouse epilepsy model

Presenter(s): Juan Enrique Villacres Perez, Nicholas Riveira Collaborator(s): Sohmee Kim, Uzair Saleem, Laura Corgin Department(s): Department of Neuroscience

Absence epilepsy is characterized by spike-and-wave discharges (SWD) in electroencephalographic (EEG) signals that correspond to patients' cognitive and behavioral arrest. Many studies have identified various physiological effects of absence epilepsy on human development, and pharmaceutical intervention has significantly improved the treatment of absence seizures. However, despite these advances, little understanding of mood and behavioral comorbidities is commonly present in pediatric and adult patients with childhood-onset absence epilepsy. The Ank3 gene provides a unique opportunity to study these comorbidities, as it has been linked to mood disorders in human genetics studies and, more recently, absence of epilepsy in rodents. Thus, this study aims to identify unique event-related behavioral correlates in EEG signals of Ank3 knockout (KO) mice. Data were collected during paired EEG and video recordings of Ank3 homozygous and heterozygous KO mice and littermate controls during home-cage activity overnight. EEG signals were sampled at 200 Hz from four electrodes overlying the frontal cortex and referenced to the cerebellum. SWDs were subsequently identified via a supervised learning algorithm and visually verified. The videos were manually scored by an observer who recorded how each mouse performed different behaviors (e.g., sleeping, eating, walking, and grooming). Additionally, we are in the process of training another supervised learning algorithm, DeepLabCut, to track the movements of mice in the video recordings to scale up our behavioral analyses by automating the behavioral scoring process. Raw EEG recordings were lowpass filtered at 50Hz and normalized. Then power-frequency analysis was conducted for signal frequencies between 1 and 50Hz using the Morlet wavelet transform. The results indicate that homozygous KO mice have an increase in slow gamma frequencies during grooming, eating, and walking. In contrast, heterozygous KO mice have an intermediate phenotype, with corresponding gains in slow gamma related to seizure phenotype severity.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 156

The neural transcriptomic basis of attaining social dominance status

Presenter(s): Joyce Y. Wang Collaborator(s): Lisa X. Paggeot, Caitlin N. Friesen, Tessa K. Solomon-Lane, Hans A. Hofmann, Rebecca L. Young Department(s): Department of Integrative Biology

Group-living animals nimbly respond to social challenges and opportunities by changing hormone profiles, neural activity patterns, and gene expression. How these processes are integrated into context-appropriate changes of behavior is not well understood. In vertebrates, this complex process depends on the distributed activity of a highly interconnected and evolutionarily conserved set of fore- and midbrain regions known as the social decision-making network (SDMN). Here, we use the highly social African cichlid fish Astatotilapia burtoni, a model system in social neuroscience, to characterize the neural transcriptomic response to a social opportunity. We provided subordinate males an opportunity to ascend to dominant status for up to 1 week and quantified behavior and physiology at three time points after the onset of social ascension, followed by an analysis of transcriptomic response of three critical SDMN nodes (homologs of the preoptic area, hippocampus, and extended medial amygdala). We first replicate that behavioral and physiological changes that have previously been shown to accompany social ascent. We then find that the three SDMN nodes we investigated have distinct transcriptomic profiles that change in specific ways as animals ascend in social status. Finally, we uncover genes that are associated with behavioral and physiological measures, suggesting specific molecular pathways that allow ascending males to take advantage of social opportunity. Taken together, our results provide insight into the neuromolecular changes occurring throughout the process of social ascent.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 157

Now You See It, Now You Don't...Sensory Transcriptomes Across

Variable Environments

Presenter(s): Xueling Wang, Asha Gomez Collaborator(s): Mariana Rodriguez Santiago, Janette W. Boughman, Hans A. Hofmann, Murielle Ålund, Rebecca L. Young Department(s): Department of Integrative Biology

As natural and human-induced climate change forces organisms to adapt to changing environments and colonize new habitats, survival is dependent on their ability to respond to novel ecological challenges. Here, we use the three-spined stickleback fish Gasterosteus aculeatus to ask how adaptation to novel environments is reflected in the neuromolecular processing of three sensory modalities - olfaction, vision, and mechanosensation. Originally found in marine habitats, sticklebacks exhibit an impressive capacity to adapt to widely different environments, having invaded freshwater lakes and streams across the Northern hemisphere. We collected 64 fish in 8 distinct populations from marine, lowland spring-fed, highland spring-fed, and highland glacial waters in Iceland. The habitats vary in nutrient availability and water clarity among other ecological factors. Specifically, lowland and highland spring waters are clear and low in nutrients; marine environments are clear to turbid and high in nutrients; glacial waters are very turbid and nutrient-rich. Using a common garden experiment, we find that fish from different habitats show distinct behavioral responses to predator simulation experiments. In particular, fish from turbid waters were slower to react and more likely to stay active after exposure to the predator stimuli compared to the fish in glacial light. Next, we assess variation in the transcriptomes of three sensory brain regions - olfactory bulb (OB, olfaction), optic tectum (OT, vision), and torus semicircularis (TS, mechanosensation) - across habitats and in response to a predator. We identify gene expression differences across populations and environments and gene co-expression modules associated with predator avoidance behavior. Our results reveal how variation in selective pressures and evolutionary divergence are reflected in transcriptomic changes in the brain.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 158

Estrogen does not regulate microglial soma characteristics in response

to an immune challenge

Presenter(s): Sienna L. Wu Collaborator(s): Kevin Sanchez, Laura K. Fonken Department(s): Division of Pharmacology and Toxicology, College of Pharmacy

Estrogens are a class of hormones predominantly known for regulating the female reproductive system; however, estrogens also affect the central nervous system and can regulate microglia, the brain-resident immunocompetent cell. Microglia become activated following immune challenges, modulating the brain’s immune response by proliferating and producing and releasing pro-inflammatory cytokines. Microglia activation in response to inflammatory challenges can be adaptive; however, prolonged microglial activation can lead to maladaptive chronic neuroinflammation and associated disorders. Estrogens have anti-inflammatory properties and may regulate microglial morphological changes and the synthesis of pro-inflammatory factors. This study analyzed changes in microglial morphology as an indicator of microglia activation state in response to estrogen modulation. We hypothesized that estrogen deficiency in mice results in an exacerbated microglial response following an immune challenge with lipopolysaccharide (LPS), eliciting changes in microglial morphology. Bilateral ovariectomies (i.e., removal of both ovaries) and sham operations were performed on C57BL/6 mice. Subsequently, the mice received either sesame oil or estradiol replacement, and one month later were then injected with saline or LPS. 24 hours following LPS, mice were euthanized and brains were extracted and processed for immunohistochemistry with Iba1 to visualize microglia. We analyzed microglia morphological features using a soma and Sholl analyses to examine parameters related to microglia activation state (i.e., roundness, circularity, perimeter, and area). Our preliminary analyses of the CA1 region indicate a robust increase in soma area and perimeter and decrease in soma roundness and circularity in response to LPS, changes indicative of an increased active phenotype. However, estrogen deficiency did not affect soma parameters. Future work will investigate other aspects of microglial morphology, such as microglial complexity, density, and processes length and branching. Understanding mechanisms by which estrogen deficiency modulates microglial activity may lead to the development of novel therapies targeted for estrogen-deficient women.

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Oral Presentations

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 159

Heart rate measurements using photoplethysmogram (PPG) and fast

fourier transfrom (FFT)

Presenter(s): Hadis Askari Collaborator(s): Haroon Dossani, Rhiannon Morris, Timothy Riedel Department(s): Biochemistry; Freshman Research Initiative DIY Diagnostics; University of Texas-Austin

The aim of this case study was to use Photoplethysmography (PPG) to validate the Heart Rate count at a low cost through Fast Fourier Transform (FFT). This method has the same functions as electrocardiograms but has a simpler approach. This method has only a slight deviation from the actual heart rate that can provide reliable measurements during COVID-19. To validate the accuracy of FFT heart rate count, the Circuit Playground Express was used to measure the light level absorption of blood in the tissues of the finger. Collected data was analyzed in excel and graphed through Fast Fourier Transform. The calculated heart rate was an accurate measurement of the actual heart rate, lying between 50 to 200. However, traces of noise and human error could be seen in some parts of the data. The sampling frequency in the graph obtained was calculated to be in the range of 16 to 18 data points per second. These findings helped to validate our heart rate counts at a much lower cost compared to commercial alternatives for heart rate screening tools especially for unfacilitated communities such as areas in the least developed countries.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 160

Alternative splicing in multiple Myeloma

Presenter(s): Anisha Bagaria, Anshul Modh Collaborator(s): [email protected] Department(s): Livestrong Cancer Institute; Dell Medical School; University of Texas at Austin

Alternative splicing is a process that occurs during gene expression where portions of exons or noncoding regions of mRNA are differentially joined or skipped. This can result in a multitude of protein isoforms encoded by a singular gene impacted by an alternative splicing event. While contributing to gene regulation, disruption of alternative splicing can be a driving factor in diseases such as Multiple Myeloma. To date, many bioinformatics tools exist to identify alternative splicing events using a variety of computational methods. Benchmarking these tools and developing a standardized workflow using multiple tools to identify splicing events from sequenced data would be valuable. Using next-generation sequencing data from 71 Multiple Myeloma samples, we evaluated a variety of alternative splicing tools and analyzed their computational differences, relative accuracy, as well as comparative overlap. We evaluated 5 bioinformatics tools using either event-based(PSI-Sigma, SUPPA2, JuncBASE, SplAdder) or isoform-based(StringTie) approaches to identify alternative splicing events. Given that these tools use different computational methods that contribute to differing strengths, they will be combined to create a robust workflow that will be utilized to identify alternative splicing events in Multiple Myeloma cancer samples.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 161

Modeling COVID-19 school reopening risks for teachers in Austin,

Texas

Presenter(s): Audrey Bahr Collaborator(s): Remy Pasco, Cameron Matsui Department(s): Department of Integrative Biology

Schools in Austin have begun to reopen with the goal of minimizing COVID-19 risks for students and their families while providing as much in-person support as possible. Though risks for students and families have received considerable attention from policymakers and public health officials, risks for school employees have received relatively less attention. In order to quantify COVID-19 risks for teachers in Austin, we use our Austin-Round Rock COVID-19 Pandemic Model to analyze the effects of school reopenings on school employees under various scenarios.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 162

Applications of fuzzy set theory: A fuzzy logic approach to medical

diagnostics

Presenter(s): Oswaldo Ceballos Collaborator(s): Austin Alderete Department(s): UT Mathematics Department

Given the current COVID-19 pandemic, medical experts continuously and actively provide guidelines to the general public in hopes to help stop the spread of the COVID-19 virus. In this research, a potential new method of approach on guideline suggestions to the general public via an app is provided. The mathematical algorithm used to construct the described demo app encompasses the concept of a Mamdani controller: a fuzzy logic approach. The general concept behind fuzzy logic follows quantification of ordinary boolean statements. There are seven main steps behind the implementation which include: input, fuzzification, rules, rule evaluation, aggregation, defuzzification and output. A simple yet powerful procedure that with the assistance of medical experts, could potentially serve as an alternative to clearly advise users of the app as to whether they should go outside their homes given that they have provided the app with the required input data. Types of linguistic inputs may vary over time, but can easily be adjusted by the controller creators. In the demo app demonstration created, three linguistic variables are used for sake of simplicity: temperature, exposure, and socialization.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 163

Exoplanet detection using AI: removing stellar activity signals from

radial velocity measurements using neural networks

Presenter(s): Zoe de Beurs Collaborator(s): Andrew Vanderburg, Christopher J Shallue, HARPS-N Collaboration Department of Astronomy; The University of Texas at Austin; Department of Astronomy, University of Department(s): Wisconsin-Madison; Madison, WI; Center for Astrophysics; Harvard & Smithsonian (CfA); 60 Garden St., Cambridge, MA

Future large space missions designed to search for biosignatures in the atmospheres of Earth-like exoplanets will operate more efficiently and have a higher chance of success if stars with possible Earth analogs are known before launch. One way to find these Earth-like candidates is with the radial velocity technique, but this method is currently limited by spurious signals introduced by stellar activity (i.e. faculae, starspots). Here we show that machine learning techniques such as linear regression and neural networks can effectively remove these activity signals from RV observations. Previous efforts have focused on carefully filtering out activity signals in time using Gaussian process regression (e.g. Haywood et al. 2014). Instead, we separate activity signals from true center-of-mass RV shifts using only changes to the average shape of spectral lines, and no information about when the observations were collected. We demonstrate our technique on simulated data, reducing the RV scatter from 82.0 cm/s to 3.1 cm/s , and on approximately 600 observations taken nearly daily over three years with the HARPS-N Solar Telescope, reducing the RV scatter from 1.47 m/s to 0.78 m/s (a 47% or factor of ~ 1.9 improvement). In the future, these or similar techniques could remove activity signals from observations of stars outside our solar system and eventually help detect habitable-zone Earth-mass exoplanets around Sun-like stars. In this way, improvements in RV precision could significantly accelerate the characterization of habitable zone Earth-sized exoplanets.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 164

Using machine learning to automate complex behavioral analyses

Presenter(s): Michelle Dias Collaborator(s): Ross Gillette and Andrea Gore Department(s): Department of Integrative Biology; College of Pharmacy; Division of Pharmacology and Toxicology

Endocrine-disrupting chemicals (EDCs) are man-made environmental contaminants that alter the social behavior of adult Sprague Dawley rats. An important aspect of rat sociability is familiarity recognition through “nose-touches”. Our lab previously generated a vast amount of behavioral data but could not quantify the considerable number of nose-touches. These data were obtained from the offspring of dams exposed during gestation to different types of EDC’s (vinclozolin, A1221), or vehicle. Descendent generations (F1, F3, F4, and F6) were assayed for social behavior using a sociability apparatus, where a target animal socializes with a novel or familiar stimulus animal housed at opposite ends of the apparatus. We used DeepLabCut to train a neural network to automatically identify a rat and its individual body parts by manually labeling frames from sociability videos which were split into training and test sets. The root-mean-squared error (RMSE) between the network’s predicted body position and manually labeled body parts was used to evaluate the model’s performance. We created an algorithm in R that utilized model-generated data to identify nose-touches based on the proximity of two rats’ noses and the duration spent within that proximity. Comparison of these results to manual counts of nose-touches from a smaller subset of videos allowed us to optimize the model until its performance was comparable to human analysis. The model’s performance was very accurate. The RMSE between manually labeled and machine-predicted body parts was 6.28 pixels, about half the width of a rat’s nose. The RMSE between computer-predicted nose-touches and human-scored nose-touches was 4.96 sec, which was more consistent than the RMSE between two human-scored data sets (RMSE = 5.19 sec). Currently, the model is analyzing over 1200 videos (~400 hours) of rat social behaviors. The results from this analysis will reveal how EDC exposure influences social behavior in rats.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 165

Experimental method development and analysis of pseudomonas

aeruginosa surface attachment

Presenter(s): Mara Eccles Collaborator(s): Zilei Chen, Vernita Gordon Department(s): Department of Physics; University of Texas at Austin

Approximately 75% of all hospital-acquired urinary tract infections are associated with urinary catheters. Pseudomonas aeruginosa is a biofilm-forming bacteria that is frequently responsible for these infections. P. aeruginosa attachment to a surface can be altered by varying the surface stiffness. This study focuses on the development of experimentation methods used to measure bacterial attachment to surfaces of different stiffnesses over time. The first study analyzed bacterial attachment to 0.5 to 3% concentrated agar gel at 2 and 24 hours after inoculation using a vortex mixer to prepare the attached bacteria and gel for dilution. The second study used a bead homogenizer in place of the vortex. Due to the pandemic, this study switched to a related project that analyzes previously-collected data on attachment of P. aeruginosa to PEGDA gel surfaces from 0.5 to 3 hours after inoculation. Developing a high throughput method to measure surface attachment is incredibly important for future analysis of different species of bacteria under the same growth conditions, and multiple types of bacteria competing for the same surface. This study analyzes growth patterns and collection methods to recommend methods for measuring attachment and surface conditions to minimize bacterial growth.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 166

Using old and new approaches: Determining physical properties of

brown dwarfs with empirical relations and machine learning

Presenter(s): S. Jean Feeser Collaborator(s): William Best Department(s): Department of Astronomy; University of Texas at Austin

The unique properties and atmospheric conditions of brown dwarfs are useful for studying the evolution of massive planets and low-mass stars. Absolute magnitudes of these objects are essential data used to understand and model their evolution and spectra. Furthermore, analyzing the spectra of brown dwarfs provides a crucial tool for their classification and is an important source for learning about their physical properties. Using a volume-limited sample of several hundred brown dwarfs, defined entirely by parallaxes, we provide an update to the absolute magnitudes as a function of spectral types for L0-T8 dwarfs in 14 bands spanning Pan-STARRS g to WISE W3. These include the first relations for brown dwarfs using Pan-STARRS1 photometry. We also investigate applications of machine learning models to directly infer physical properties, such as effective temperatures and luminosities, of brown dwarfs from their photometry and spectra. We present data-driven models developed by The Cannon and discuss the efficacy of extrapolating physical quantities from the low-resolution spectra of these objects, comparing the inferred parameters to those derived from our empirical relations. Our results indicate The Cannon could provide a novel method of analyzing and obtaining new information from the spectra of brown dwarfs.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 167

I spy transits and pulsations: Empirical variability in white dwarfs

using gaia and the Zwicky transient facility

Presenter(s): Joseph Guidry Zach Vanderbosch, JJ Hermes, Brad Barlow, Isaac Lopez, Thomas Boudreaux, Kyle Corcoran, Bart Dunlap, Collaborator(s): Keaton Bell, Mike Montgomery, Tyler Heintz, Don Winget, Karen Winget, John Kuehne Department(s): Department of Astronomy; The University of Texas at Austin

We present a novel method to detect variable astrophysical objects and transient phenomena using anomalous excess scatter in repeated measurements from public catalogs of Gaia DR2 and Zwicky Transient Facility (ZTF) DR3 photometry. We first provide a generalized, all-sky proxy for variability using only Gaia DR2 photometry, calibrated to white dwarf stars. To ensure more robust candidate detection, we further employ a method combining Gaia with ZTF photometry and alerts. To demonstrate the efficacy, we apply this latter technique to a sample of roughly 12,100 white dwarfs within 200 pc centered on the ZZ Ceti instability strip, where hydrogen-atmosphere white dwarfs are known to pulsate. Through inspecting the top 1% samples ranked by these methods, we demonstrate that both the Gaia-only and ZTF-informed techniques are highly effective at identifying known and new variable white dwarfs, which we verify using follow-up, high-speed photometry. We confirm variability in all 33 out of 33 (100%) observed white dwarfs within our top 1% highest-ranked candidates, both inside and outside the ZZ Ceti instability strip. In addition to dozens of new pulsating white dwarfs, we also identify five white dwarfs highly likely to show transiting planetary debris; if confirmed, these systems would more than triple the number of white dwarfs known to host transiting debris. Our results are fully presented in our manuscript which we have submitted for publication in The Astrophysical Journal and are publicly available in preprint at arXiv:2020.00035.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 168

A gRPC-driven spot simulator for autonomous navigation

Presenter(s): Geethika Hemkumar, Daksh Dua, Shikhar Gupta, Parth Chonkar Asha K. Jain, Maxwell Svetlik, Nicholas Machak, Kavan S. Sikand, Cem Karamanli, Kaiyu Zhou, Anurag Patil, Collaborator(s): William Kwon, Kent Hansen, Justin Hart, Joydeep Biswas, Luis Sentis, Junfeng Jiao Department of Computer Science; The University of Texas at Austin; Freshman Research Initiative Autonomous Department(s): Robots Stream

Simulation is an essential part of robotics development, as the process of starting up and running a test on a robot is much slower than that of other software development efforts. Additionally, with the emergence of the COVID-19 pandemic, remote development has become even more important in advancing robotics research and software development. The Short-to-Medium Range Autonomous Delivery System (SMADS) is a system developed to allow users to place orders for food delivery on the UT Austin Campus. Users place their orders using a mobile application. A robot comes to one of a set of locations, which we hope to eventually expand to anywhere on the UT campus, to deliver food to the user. One of the robots utilized for SMADS is the Boston Dynamics Spot, a quadruped robot that is capable of navigating on a wider variety of terrain than traditional wheeled robots. We have implemented a simulator for Spot using the Gazebo robotics simulator. The majority of robots built today run a system called Robot Operating System (ROS). Spot, however, implements similar functionality using a system called gRPC. We have written a gRPC server that mimics the behavior of the server on the physical robot. It can send and receive gRPC messages to communicate with Spot’s Software Development Kit and its Python client library. The gRPC server communicates with Gazebo using ROS to obtain robot state information and visualize reactions to movement commands. To communicate with the rest of the ROS-based SMADS software system, we leverage a customized version of Microsoft's Spot-ROS Wrapper. The Spot-ROS wrapper converts messages on the client side of the gRPC server. The simulator has been demonstrated to work as a replacement for Spot, and we are in the process of validating our implementation of SMADS on the real Spot this spring.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 169

Neutron star remnants from the first stars

Presenter(s): Rabia Husain Collaborator(s): Boyuan Liu, Volker Bromm Department(s): University of Texas at Austin; Department of Astronomy

Population III stars are the oldest stars in the universe and are composed of hydrogen and helium made from the Big Bang. Theory predicts that such stars were massive in size, unlike those today, which are low-mass stars like our Sun. Because of their high mass, the Population III stars were very luminous but very short-lived. Despite their intrinsic luminosity, powerful telescopes cannot directly observe the first stars because of their extreme distance. We thus need to focus on the remnants left behind when Population III stars die; they are indirect probes of the early universe, and a number of them are expected to have survived throughout cosmic history. We investigate neutron star (NS) remnants to assess the feasibility of detecting a Population III remnant in our Milky Way. First, we use the Press-Schechter formalism to calculate the number of dark matter minihalos, regions where Population III stars form, in the Milky Way. Then, we determine the amount of star forming gas per minihalo to find the number of NS remnants per minihalo. We found about 20,000 Population III NS remnants in the Milky Way. Since these remnants are more massive, they are brighter, so we can distinguish these remnants from those formed later. We calculate a timescale for binary capture of 10^10 years, implying that a Population III NS will acquire a companion every 10^10 years. Due to bright accretion from binaries, we can detect these sources. We are constructing a function that will show the number of NS at a particular luminosity as a function of luminosity. Population III remnants lie at the high luminosity end of this plot. From this, we will constrain the properties of the first stars, thus guiding searches with next-generation telescopes, such as the James Webb Space Telescope.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 170

Finding expressed mutations in multiple myeloma cell lines

Presenter(s): Wenxuan Jiang, Jensen Richardson, Jafrin Pritha Collaborator(s): Jensen Richardson, Jafrin Pritha, Dhivya Arasappan, Jeanne Kowalski-Muegge Department(s): College of Natural Sciences Locations of research: FRI Big Data in Biology stream, Livestrong Cancer Institutes

Neoantigens are newly formed peptides created from somatic mutations that are capable of inducing tumor-specific T-cell recognition. Prediction of these neoantigens can lead to personalized immunotherapies for the treatment of cancers. Identification of expressed somatic mutations (or variants) using next-generation sequencing data is a crucial step in neoantigen prediction. Because of the expansion of next-generation sequencing data, there exist a plethora of tools designed to sift through this data and return high quality Single Nucleotide Variants (SNVs) and small insertions and deletions (indels). However, it is essential to choose those tools which are flexible, efficient, and above all, accurate at detecting these mutations. Using RNA sequencing and whole exome sequencing data from 71 Multiple Myeloma cell lines, different variant calling tools were compared to develop an efficient workflow for identifying expressed mutations from cancer sequencing data. Because these were standard cancer cell lines, the known SNVs and indels in each cell line were available, allowing us to evaluate the accuracy of each variant calling tool. Four variant calling tools (VarScan, GATK, Pisces and Deepvariant) were benchmarked for accuracy and efficiency; post-filtering, annotation, and visualization of found variants were incorporated to our workflow. Approximately 20 expressed mutations were found per sample by VarScan2, the most efficient and accurate tool among our selected tools. An ongoing workflow has been designed, and the completed workflow will provide a standardized means for identifying expressed mutations using patient cancer sequencing data.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 171

Exploring the effect of video games in STEM education

Presenter(s): Lois Owolabi Collaborator(s): Shelley Payne Department(s): Department of Molecular Biosciences; Department of Arts and Entertainment Technologies, College of Fine Arts

According to Statista, video game players make up approximately 34% of the global population. Given the popularity of gaming, this thesis examines the usefulness of video games in scientific learning. 100 college freshmen with at least one semester of introductory biology were asked to independently play three levels of the video game, IRON’ed IT! on their personal computers. The game uses popular game design characteristics such as a narrative, animation, and a graphical user interface, to communicate a niche topic; the genetics behind the iron acquisition machinery of Vibrio Cholerae. Before and after gameplay, participants answered biology content questions and recorded the duration of their game play. Players also rated their emotions toward the game using the scale “Strongly Agree…Strongly Disagree” for the options “Boring, Entertaining, Educational, Exciting, and Frustrating.” The (preliminary) results show that on average the students that played the game improved their understanding of the genes associated with the iron uptake systems of Vibrio Cholerae. We also found that participants that played for longer periods demonstrated statistically significant improvement in their post-game scores and that participants that found the game enjoyable, exciting, and entertaining scored higher on the post-game survey than players that ranked the game as highly frustrating or boring.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 172

Transcriptomic signatures for mood disorders within anterior insula

cortex and anterior cingulate cortex

Presenter(s): Ericka Salas Collaborator(s): Zo-Ann Lee, Dhivya Arasappan, Mbemba Jabbi, Vishy Iyer, Hans Hoffman Department(s): FRI Big Data in Biology Stream

Mood disorders such as bipolar disorder (BD) and major depression disorder (MDD) have a lifetime prevalence of ~20% and accounts for the highest share of morbidity and disability. However, our understanding of the transcriptomic changes in the brain in relationship to these disorders is limited. Using a large-scale postmortem RNA-Seq dataset on two brain regions known to regulate mood functions, we identified transcriptomic markers related to mood disorder diagnoses. Our RNA-Seq dataset was generated from the anterior insula cortex (AIC) and anterior cingulate cortex (ACC) brain regions and consisted of 298 samples, 72 of which were sampled in both brain regions. Samples had a lifetime diagnosis of BD (n=75), MDD (n=84), as well as a non-mood disorder schizophrenia sample (n=46) and unaffected controls (n=93). Differential gene expression analysis was performed on AIC and ACC brain region dataset to identify marker genes for each diagnostic condition and the corresponding biological pathways. Weighted gene co-expression network analysis (WGCNA) was explored within each brain regional dataset to identify groups of co-expressed genes. We found that the neuroimmune system to be the most dysregulated in mood disorders across brain regions. Cell communication receptor pathways, which contribute to immune response functions, were observed to be dysregulated in mood disorders. These results show that brain abnormalities in basic immune and cellular machinery dysfunctions may underlie mood disorder symptoms. Discoveries in genetic etiology for these psychiatric disorders could be significant due to the high number of misdiagnoses that have been a result from dealing with these idiopathic psychiatric disorders which could lead to an improvement in treatments.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 173

Towards designing future fuel cell electrode materials Using machine

learning and ab-initio studies

Presenter(s): Angelo Scanio, Jesus Munoz-Castaneda Collaborator(s): Sahithi Adduri, Katherine Gianvecchio, Wenrui Chai Department(s): Department of Chemistry

Hydrogen evolution reaction (HER) and Oxygen Evolution Reaction (ORR) are two mechanisms used in hydrogen fuel cells to generate energy; however, it requires an efficient catalyst. The best current material for this purpose is the precious metal Platinum. To find more economic and better performing alternatives, The FRI Stream of Computational Materials has built a database composed of 79-atom FCC nanoparticles and slab models of binary alloys that could potentially be used as cathode (ORR) and anode (HER) materials for this purpose. A LASSO-based machine learning model with four-fold cross-validation was then built upon this data to determine the importance of several factors in predicting the functionality of electrode materials, evaluated by their respective binding energy to each substrate. We were able to create an algorithm that could identify several factors that could impact the catalytic activity, in this case measured through binding energy, of a material and evaluated their relevance. It was determined that what is dominating in influencing the binding energies is the ensemble effect, which shows the influence of local alloy composition has on binding energies. Though the ensemble effect is dominant in all cases, the magnitude of its impact varies between ORR and HER, and between nanoparticles and slabs. Interestingly enough for HER in nanoparticles, we observed that the influence of alloy composition of the surroundings is opposite to what they would produce in the ensemble. Future exploration with LASSO regression will allow for the identification of more factors that could be used to fine tune the catalytic activity of a material. Furthermore, these factors could then be integrated into our Machine Learning model to autonomously find more efficient cathode and electrode materials.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 174

Classification of Lyman-alpha emitters in HETDEX using

unsupervised machine learning

Presenter(s): Khavvia Shanmugasundararaj Collaborator(s): Benjamin Thomas, Edward Robinson, Karl Gebhardt, Erin Mentuch Cooper Department(s): Department of Astronomy

The HETDEX project will constrain the evolution of dark energy at z = 2-3 by measuring the characteristic scale-length of galaxy-galaxy separations across the cosmos (i.e. Baryon Acoustic Oscillations; BAO). Lyman-alpha emitting (LAE) galaxies are used as tracers of these oscillations. The project uses VIRUS IFU spectrographs on the 10-m Hobby-Eberly Telescope (HET) to conduct an unbiased spectroscopic survey of two large (100 square degrees) regions in the spring and fall skies, and expects to identify 5 million emission-line objects. We present a new method to classify emission line objects as either LAE galaxies or non-LAE. We identify them with a cluster analysis of the emission-line spectra using the unsupervised machine learning algorithm t-SNE. Our results show significant separation in an abstract parameter space between the spectra of LAE galaxies and non-LAEs. We develop a quantitative method to assign a likelihood that 2500 spectra were emitted by LAE galaxies. Our pipeline will ease the workload of the HETDEX BAO survey by many person-hours, and we encourage its use in other upcoming spectroscopic galaxy surveys.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 175

Evaluating the effect of COVID-19 on relationship satisfaction

Presenter(s): Yukta Sunkara Collaborator(s): Hannah Williamson, Veronica Cantu, Samantha Chow, Rachel Lin Department(s): Department of Human Development and Family Sciences

The COVID-19 pandemic has had far reaching impacts across various fields, and specifically, personal relationships have been exposed to another dimension with the implementation of stay-at-home orders and quarantine guidelines. Previous research has shown that stressors can often place strain on relationships, but understanding this impact in the context of the pandemic is novel. This study aims to identify and evaluate how the early months of the pandemic affected relationship satisfaction and affect. Data was collected using an online surveying tool in March 2020 and May 2020, and responses at these timepoints were compared to baseline responses collected in December 2019, before the pandemic hit the United States. Open-ended responses were transformed into quantitative data using a coding system. Subjective and objective data measures were compared using statistical analyses. Results suggest that generally, relationships were not heavily impacted in a positive or negative direction within the first few months of the pandemic. However, there were recurring categories of growth or distress that were reported, some of which include communication and support. Comprehending the impact that immediate, transformative crises such as the pandemic have on relationships is essential for developing more effective therapies and practices aimed at improving relationships.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 176

Extraversion and marital status on empathy in older adults

Presenter(s): Anthony Tang Collaborator(s): Yee To Ng, Shiyang Zhang, Karen Fingerman Department(s): Department of Human Development and Family Sciences

Lack of empathy has been associated with loneliness and depression, suggesting that empathy may play a key role in supporting life satisfaction in older adults. However, personality characteristics and background factors that contribute to empathy in late life are still largely unknown. It is likely that married older adults have greater empathy than their unmarried counterparts because they have a social partner to talk with about negative life events that require empathy. Additionally, as extraversion and empathy share similar caring and communicating components, extraverted older adults may practice empathy more often than less extraverted adults do and therefore are likely more empathetic. By studying the relationships empathy has with other characteristics, its influence on older adult well-being can be better understood. The current study uses data from the Daily Experiences and Well-being Study (DEWS) to examine the association between marital status, extraversion, and empathy. The sample consisted of 333 participants over the age of 65 in the greater Austin, Texas metropolitan area. Participants were asked questions regarding their demographics and personality characteristics (e.g., extraversion). Linear regression models found a main effect of extraversion on empathy. Older adults with higher extraversion were significantly more empathetic than those with lower extraversion, regardless of marital status. However, marital status was not significantly associated with empathy level. The study also tested the interaction between marital status and extraversion on empathy. For older adults of average extraversion, married individuals did not have significantly different mean empathy levels than their unmarried counterparts. Overall, by revealing the association between extraversion and empathy, the study stressed the importance of considering personality attributes when discussing empathy among older adults. Implications of these findings in the social networks and interactions of older adults are discussed.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 177

Simulation studies for the KLEVER small-angle calorimeter

Presenter(s): Emily Tsai Collaborator(s): Matthew Moulson, Tim Andeen Department(s): Department of Physics; Istituto Nazionale di Fisica Nucleare, Rome, Italy

The Standard Model of particle physics attempts to describe all observable particles, forces (excluding gravity), and their interactions. There are three lepton flavours that must be conserved: electron, muon, and tau. However, lepton flavour violation was discovered in rare decays of particles called kaons. Lepton flavour violation in rare kaon decays could lead to new physics beyond the Standard Model, and it could provide answers for big questions such as the matter-antimatter asymmetry of our universe. A branching ratio, denoted as BR, is the probability of one decay happening out of all possible decays for a specific particle. The KLEVER experiment aims to measure the branching ratio of a lepton flavour violating neutral kaon decay to a neutral pion and a neutrino-antineutrino pair. This branching ratio is predicted to be 3.4 x 10^-11. One challenge that detectors face when searching for rare decays is an excess of background noise. This project focuses on studying the effectiveness of using a lead fluoride-based small-angle calorimeter (SAC) placed at the end of the KLEVER detector to eliminate the background decay of a neutral kaon to two neutral pions, which mimics the rare decay that KLEVER is searching for. First, fast-simulation of the entire KLEVER detector was used to obtain needed efficiencies for the SAC. Then a more detailed simulation was constructed using Geant4 in order to test whether and how the needed efficiencies could be reached, in addition to assessing potential radiation damage to the SAC and differentiating between hits from different types of particles. Finally, future work focuses on physics analyses and improving experimental and simulation design.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 178

Fractals in Pollock’s paintings

Presenter(s): Naila Hajiyeva, Silverio Villanueva, Yueyuanmei Zhang Collaborator(s): Mark Daniels, Soleste Starr, Meryn Riley Zeigler Department(s): Department of Mathematics

An artist named Jackson Pollock created paintings by observing nature’s patterns and utilizing the technique of pouring a stream of paint onto canvases and allowing trajectories to be formed. When looking at the lines in the painting, you can see how they are separated in several occurrences, continuing in many directions. As an experiment used tree branches to create a large structure and attempted to create a painting similar to Pollock’s, it was discovered that Pollock’s paintings consist of fractal geometry. Fractals display similar appearance at varying magnifications and they were characterized as the complexity of paintings under the computers’ analysis of Pollock’s paintings. A scale ranging from a single line to a filled area was used to represent the paintings’ complexity. We present computer analysis data on the differences between Pollock’s fractal paintings and nature's patterns. As this research discovered the essential connection between aesthetics and the science of patterns, we welcome different perspectives and discussions from both the art and science community.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 179

A low-cost headset for epilepsy using convolutional and recurrent

neural networks to predict seizure onset

Presenter(s): Sruja Arya, Jennifer Zhou, Athulya Nagarajan, Maansi Srinivasan, Zain Moin, Nidhi Dubagunta Collaborator(s): Aditya Ojha, David Oh, Sruti Iyer, Nathan Hardham, Madhumitha Sakthi, Ahmed Tewfik Department of Biomedical Engineering, Cockrell School of Engineering; Department of Electrical and Department(s): Computer Engineering, Cockrell School of Engineering; McKetta School of Chemical Engineering, Cockrell School of Engineering

Epilepsy is a severe neurological disease that impacts 65 million people worldwide. Although the direct cause of epileptic seizures is unknown, they have been shown to result from previous head trauma, hypoxia, and bacterial meningitis. One of epilepsy’s most dangerous consequences is the possibility of sudden unexpected death in epilepsy (SUDEP). Studies have indicated that patients undergoing SUDEP were found to be prone and pulseless only 15 minutes following the onset of a SUDEP-inducing seizure. These results demonstrate that novel devices and methodologies are necessary for premature intervention to avoid potential SUDEP and other bodily injuries. A significant treatment gap also exists in developing nations -- this has highlighted the need for a low-cost solution to avoid exacerbating global inequalities. The presenters propose a seizure prediction system consisting of a neural network and a low-cost wearable alarm system to address these issues. A machine learning model consisting of a deep convolutional autoencoder (DCAE) for feature extraction and a bidirectional long short term memory (Bi-LSTM) network for classification is paired with a physical 16 channel 10-20 system EEG head cap. The head cap receives and filters raw EEG signals -- these are first transported via Bluetooth to a Raspberry Pi controller, which then stores the machine learning algorithm and classifies incoming data as preictal (immediately before a seizure event) or interictal (between seizure events). EEG signals that are recognized by the trained neural network as preictal alert the user and local pedestrians of an oncoming seizure event, allowing them to situate themselves accordingly.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 180

Using Ethovision software to profile coercion evasion abilities in

differentially reared swordtail females

Presenter(s): Elena Adams Collaborator(s): Molly Cummings Department(s): Integrative Biology; Patterson Labs; University of Texas at Austin

Coercive mating tactics have been observed in many different species, and are indicative of intense conflict between the sexes— when males and females differ in their reproductive goals, mating strategies which are beneficial to one sex may be detrimental to the other. One such species is the poeciliid fish Xiphophorus nigrensis; but the species' three distinct male genotypes differ in the level of sexual conflict they impose on their females. Each male type exhibits a different mating strategy — coercion, courting, or both — which in turn requires a different behavioral response from a female in order to maximize her fitness. Most notably, the coercive males’ frequent, forceful mating attempts can prove extremely costly, requiring female counter-strategy. Female poeciliids are able to reduce sexual harassment by shoaling with other females (Dadda, 2015); and some studies suggest that female poeciliid brains grow larger when under strong sexual conflict pressure (Buechel et. al., 2016). In this study, we tested X. nigrensis females that were raised with coercion-only, courtship-only or both male tactics in a coercion evasion assay. Using Ethovision tracking software, we quantified these differentially reared females’ abilities to evade a coercive male. To date, no previous studies have examined the effects of courtship and coercion on female cognition and behavior directly within the same species. This data reveals important information concerning the effects that experience with each distinct mating strategy may have on female cognition and behavior.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 181

Neuron morphology in the SCN1b mouse model of Dravet Syndrome

Presenter(s): Alisha A. Ahmed Collaborator(s): Jessica Hotard Chancey, MacKenzie A. Howard Department(s): Department of Neuroscience; Center for Learning and Memory; University of Texas at Austin

Dravet syndrome (DS) is a severe genetic epilepsy that leads to prolonged seizures, developmental delays, and severe cognitive deficits. Mutations in the SCN1B gene, which encodes the protein ?1, have been linked to DS. Our lab uses an Scn1b knockout mouse model, which models many aspects of DS including spontaneous seizures and early death, to study the neurophysiological changes underlying the disease. ?1 is important in regulating neuronal excitability and physiology, and has also been shown to play a role in neuron growth and development. We have found that loss of ?1 leads to abnormal intrinsic and synaptic physiology in one of the primary neuron types responsible for learning and memory: hippocampal pyramidal neurons. My research aims to examine how loss of ?1 affects both neuronal morphology and synaptic plasticity, the selective strengthening (long-term potentiation) or weakening (long-term depression) of neuronal synapses, in hippocampal neurons. Our lab has found that hippocampal neurons are hyperexcitable and long-term potentiation is lost in Scn1b knockout mice. These findings lead me to hypothesize that the changes in excitability may be linked to a change in neuronal morphology, and that long-term depression is increased in Scn1b knockout mice. To examine neuronal morphology, I used the Neurolucida tracing program to analyze dendritic branching patterns and two-photon imaging to analyze dendritic spine density in Scn1b knockout neurons, and found no overall changes in morphology. To examine long-term depression, I analyzed local field potential recordings using a low-frequency stimulus, and found no difference in long-term depression between knockouts and wildtype littermates. My findings illustrate that the links between neuronal physiology, morphology, and plasticity are altered atypically in ?1-deficient hippocampal neurons, suggesting a complex role for ?1 in this brain region.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 182

Long-Term preservation of aptamer research utilizing a comprehensive dataset consisting of over seven-hundred entries displayed via an online database

Presenter(s): Ali Askari Hailey Ferrell, Kayla Goodman, Sumedha Kota, Daniela Hernandez, Taylor Oliphant, Brandon K Ta, Isaac Collaborator(s): Weislow, Angelica R Montes, Pearlyn Ang Yi Hui Department(s): Department of Neuroscience; University of Texas at Austin

Aptamers are oligonucleotides that bind to a specific target with high affinity and specificity (Lin, 2015). Aptamers have practical applications in diagnostic, therapeutic, bioimaging, hazard detection, and they are one of the most practical research tools in today's world. From 1990 to March 2021, there are about 15,000 publications about aptamers in PubMed. A comprehensive publicly available aptamer dataset is needed to standardize aptamer sequences and pool type, aggregate data, and expand on current research in the aptamer field. An aptamer database and website will make this information more accessible and is useful for accessing the vast amount of existing data about aptamers and continuing to build upon that over previous research (Lee and Hesselberth, 2004). A dataset is where the information is stored, and a database is a coordinated set of information that offers an interactive and searchable experience to the aptamer community. Aptamer research has been growing at an unprecedented rate and has piqued the interest of many researchers around the world; therefore, a need to create an aptamer database has been formed (Wang and Tao et al, 2019). This project seeks to obtain a representative collection of aptamers from each year from 1990 to 2021. The Dataset contains 999 aptamer entries as of March 23rd, 2021. And it is expected that entries will be continuously added in the future. It is expected to create a comprehensive, user-friendly website to accompany the dataset and implement the mechanism to sustain it so that the aptamer community can refer to one platform that contains all the information. The sustaining mechanism includes submission forms for all researchers to submit their aptamer, save data in a spreadsheet, and store data in a database platform called Caspio.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 183

Unsupervised selection of optimal criterion for analysis of

single-molecule time-series

Presenter(s): Argha Bandyopadhyay Collaborator(s): Marcel Goldschen-Ohm Department(s): Department of Neuroscience; College of Natural Sciences; The University of Texas at Austin

Single-molecule (SM) approaches have provided valuable mechanistic information on many biophysical systems. As technological advances lead to ever-larger datasets, tools for rapid analysis and identification of molecules exhibiting the behavior of interest are increasingly important. In many cases the underlying mechanism is unknown, making unsupervised techniques desirable. The Divisive Segmentation and Clustering (DISC) algorithm is one such unsupervised method that idealizes noisy SM time series much faster than computationally intensive approaches without sacrificing accuracy. However, DISC relies on a user selected objective criterion (OC) to guide its estimation of the ideal time series. Here, we explore how different OCs affect DISC’s performance for data typical of SM fluorescence imaging experiments. We find that OCs differing in their penalty for model complexity each optimize DISC’s performance for time series with different properties such as signal-to-noise and number of sample points. Using a machine learning approach, we generate a decision boundary that allows unsupervised selection of OC based on the input time series to maximize performance for different types of data. This is particularly relevant for SM fluorescence datasets which often have signal-to-noise near the derived decision boundary and include time series of nonuniform length due to stochastic bleaching. Our approach allows unsupervised per-molecule optimization of DISC, which will substantially assist rapid analysis of high-throughput single-molecule datasets with noisy samples and nonuniform time windows.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 184

Insights into modular polyketide synthase loops aided by repetitive

sequences

Presenter(s): Ronak Desai Melissa Hirsch, Kaan Kumru, Brendan Fitzgerald, Takeshi Miyazawa, Katherine Ray, Nisha Saif, Samantha Collaborator(s): Spears, Adrian Keatinge-Clay Department(s): Department of Chemistry; Department of Molecular Biosciences

Modular polyketide synthases (PKSs) synthesize powerful polyketide medicines such as including the antibiotic erythromycin and the anticancer agent epothilone, but studying PKS structures and engineering these synthases remains a challenge. Repeated amino acid sequences in the loops of PKSs may aid in analyzing these molecular machines. Genetic events including slipped-strand mispairing insert these sequences into PKS loops, but the repeats seem to impact polyketide synthesis minimally and serve no apparent function. Their existence in a loop, thus, suggests that a tolerance to the insertion of amino acids exists within that loop. To assess such tolerance and aid in ultimately engineering PKSs, tandem repeats of DNA and the corresponding amino acids from 949 modules of 129 cis-acyltransferase PKSs were catalogued. The loop downstream of the ketosynthase (KS) and upstream of the acyltransferase (AT), where the updated PKS module boundary exists, was most frequently inserted with amino acid repeats, and the loops bordering the dehydratase (DH) were very rarely inserted. Bordering the acyl carrier protein (ACP), the presence of relatively short loops (14±6 residues) indicates that a functioning ACP may require AT to access a conformation similar to that observed through electron microscopy of pikromycin’s PKS, placing the active sites of ACP and AT nearer one another. Within domains, loops varied in sensitivity to alteration: no repetitive insertions were found within ACP, and only 2 exist in KS domains analyzed, but a single loop within DH contained a total of 16 insertions across the 949 modules.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 185

Developing antibodies against CDHR3 to prevent RV-C infection

Presenter(s): Mahnoor Faheem Collaborator(s): Soo Hyun-Yang Department(s): Department of Integrative Biology; University of Texas at Austin

The rhinovirus, or the RV-C species, is one of the greatest causes of the common cold and other respiratory issues in younger children. Studies have shown that RV-C binds to domains 1 and 2 of a protein called cadherin related family member 3, or CDHR3. CDHR3 is highly expressed in the airways of human cells and serves as a docking site for RV-C. This interaction leads us to the idea that RV-C infection can be prevented in human cells by developing an antibody against the two domains of CDHR3 that inhibits binding of RV-C. However, when it comes to examining the CDHR3 protein, another issue is that it is a membrane-bound protein, making it insoluble and impossible to purify and analyze the protein. Therefore, the first aim of this study is to introduce mutations in domains 1 and 2 of CDHR3 via site-directed mutagenesis and examine whether the mutation can alter its affinity to the membrane. Once the solubility of CDHR3 is increased, the next aim is to optimize the expression and the purification of the recombinant CDHR3 mutant. After isolating the recombinant CDHR3 protein, the goal is to examine its structure to develop and identify antibodies against the protein that can block the binding of RV-C effectively. This is a novel method that can be used to prevent various viral infections of human cells.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 186

Improving caffeinated coli functionality and characterizing its genome

Presenter(s): Mina Kim Collaborator(s): Dennis Mishler Department(s): Department of Neuroscience

Caffeinated Coli is an efficient, low cost alternative to current methods of measuring caffeine concentrations. The genetically engineered ?guaB E. coli functions through a pDCAF plasmid with caffeine demethylation genes that promote xanthine synthesis. A bioassay using an OD600 spectrophotometer can indirectly measure caffeine concentrations through these bacterial cell counts. To improve functionality of the bioassay, the strains were evolved to grow at E. coli's optimal temperature of 37°C from 30°C, and had GFP integrated into its genome to display fluorescence as a more reliable marker for lower caffeine concentrations. The genome was subsequently analyzed against previous generations to characterize mutations and the GFP gene location responsible for these improvements. During this process, a PurR gene mutation was also found in all strains that may contribute to the original generation's success at demethylating caffeine.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 187

Depression and alcohol use in young adults during the COVID-19

pandemic and relations with insula structure

Presenter(s): Raquel Kosted Collaborator(s): Elizabeth Lippard, Dylan Kirsch, Vanessa Le Department(s): Department of Neuroscience; Dell Medical School Department of Psychiatry

Recent studies have shown the COVID-19 pandemic has resulted in an unprecedented increase in stress and mental health issues globally. The underlying neurobiology that may contribute to differences in COVID-related stress, and associated mood and alcohol use outcomes is unclear. The current study investigated relations between COVID-related stress and change in depressed mood from pre-COVID to during-COVID in young adults with a mood disorder (major depressive disorder and bipolar disorder), compared to typically developing young adults, and how change in depression related to change in alcohol use from pre-COVID to during-COVID. We further investigated how insula structure assessed at baseline (pre-COVID) related to COVID-related stress and change in depressed mood and alcohol use at the COVID follow-up assessment. Greater COVID-related stress was associated with greater increase in depression symptoms during the pandemic, and greater increase in depression symptoms was associated with lower left insula cortical thickness in all participants. In young adults with a mood disorder, greater increase in depression symptoms was associated with greater increase in alcohol use during the pandemic, and greater increase in alcohol use was associated with lower left insula cortical thickness. Our results suggest that lower left insula cortical thickness relates to greater depression symptoms in young adults with and without a mood disorder, and greater alcohol use in young adults with a mood disorder, during the pandemic. Additionally, our results suggest greater increase in depression symptoms relates to greater increase in alcohol use in young adults with a mood disorder during the COVID-19 pandemic.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 188

Predicting rain with monkey calls: Investigating zoological predictors

of weather with bioacoustics.

Presenter(s): Anna Kurtin Collaborator(s): Silvy van Kuijk, Luciana Oklander, and Anthony Di Fiore Department(s): Department of Integrative Biology; Anthropology

Howler monkeys (Alouatta seniculus) are one of the loudest mammals in the world, famous for their long-range vocalizations, which function in intergroup communication as well as mate and resource defense. This study tests an additional widely-held belief in Central and South America: that howler monkey long-range calls (“howls”) also predict the onset of rainfall. The hypothesis is howler monkeys respond vocally to changes in ambient conditions or acoustic signals of incoming weather. If this hypothesis is true, a significantly greater number of howler monkey calls followed by rain events and a significantly greater number of rain events preceded by howler monkey calls than would be expected by chance are predicted. To address this question, 50 days of acoustic recordings collected at the Tiputini Biodiversity Station in the Ecuadorian Amazon were analyzed. Using the software Audacity, spectrograms were created from which the start time of howling and rainfall onsets were extracted, both of which yield recognizable signatures and were confirmed by independently listening to the audio recordings. There were 19 days when howling and rain occurred on the same day, 17 when rain occurred but no howling, and 6 with howling and no rain. Additionally, rain onset peaked in the midafternoon when the onset of howling was the least frequent. The relationships of rain and howling within each day are being further investigated using a permutation test to analyze whether rainfall events are preceded by howling within one hour more often than would be expected by chance, and conversely, whether howling events are followed by rainfall within one hour more often than expected by chance. If the hypothesis is supported, future studies could elucidate what aspects of incoming weather prompt the production of energetically expensive calls and what potential applications this local ecological knowledge has for community adaptability to climate change.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 189

Virtual screening of Dehydrosqualene synthase, a virulent protein in

staphylococcus aureus

Presenter(s): Sean Lau, Katherine Huang Collaborator(s): Josh Beckham Department(s): Department of Integrative Biology; ARI Virtual Drugs Stream

Staphylococcus aureus is a very common bacteria that can be found all over the body including our mouths and noses. It is also the cause of skin and tissues infections such as Staph infections. The goal of our research experiment is to find new potential drugs to treat such infections by screening a library of compounds for their ability to bind the active site of our target enzyme SaDS (Staphylococcus aureus dehydrosqualene synthase) with the GOLD and ICM docking programs. In our protein preparation, we used GOLD/Hermes to add hydrogens and assess the quality of the crystal structure. In our docking, we used several known control compounds along with libraries of novel ligands such as the Maybridge Hitfinder and the Zinc Chembridge Libraries. We used PyMOL to visualize and analyze the predicted binding modes and used scores to assess their potential as hits. Overall, we discovered 3 new ligands or new inhibitors of SaDS that we could move forward with testing in a wet lab setting.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 190

The gut microbiota associated with Texas dung beetles

Presenter(s): Meagan Mehlhop Collaborator(s): Heyji Ro, Tae-Young Uhm, Jo-Anne Holley, Nancy Moran Department(s): FRI Bugs in Bugs Stream

Dung beetles harbor distinct assemblages of symbiotic gut bacteria that contribute to their hosts’ survivability, development, and metabolism. Dung beetles can be organized into three functional groups: rollers, tunnellers, and dwellers. The beetles’ diverse feeding and reproductive strategies likely impact their gut microbial compositions and influence transmission to offspring and other beetles they may interact with. Using the 16S rRNA gene to identify the microbiome of 28 dung beetles and the corresponding 18 longhorn dung samples, it was possible to characterize the predominant bacteria present in these sources and compare their bacterial abundances and compositions. The results of this study indicate that the gut microbiota of dung beetles varies widely in abundance and diversity, but there is some level of host specificity present. The finding of clustering in roller species suggests that life history traits play an important role in bacterial colonization. However, the microbiomes of the other dung beetles sampled were intermixed and did not exemplify any significant clustering. There was also a decrease in the abundance of bacteria between beetle guts and longhorn dung, which implies that there are selective pressures reducing direct bacterial acquisition from the environment. It is unclear, however, which factors contribute most to the conservation of a consistent microbiota, although gut structure, which is related to feeding habits, may play an important role.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 191

Contribution of urban heat islands to water temperature in Austin

Presenter(s): Shobha Melukote, Emily Buell Collaborator(s): Department(s): Department of Integrative Biology

Urban heat islands are local urbanized areas that experience warmer temperatures than rural areas due to the absorption of heat by infrastructure and land surfaces. Many studies have been done to show how urban heat islands can affect the water temperatures of nearby lakes. In this study, we further assessed this association by predicting a positive association between proximity to the Austin metropolitan area and temperature of the lakes nearby. To test our hypothesis, we gathered data for the temperatures of several different bodies of water around Austin using the database Hydromet, produced and maintained by the Lower Colorado River Authority and USGS (LCRA Hydromet 2020). Our regression analysis found no association between the proximity to an urbanized area and fall temperature of nearby lakes and a negative association between summer lake temperature and proximity to downtown Austin. Our results indicate the opposite pattern than that found by previous studies, which suggests that the development of heat islands in central Texas may be influenced by other factors.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 193

Identifying the site of CDX2 responsible for inhibiting ATM-MRN

interaction in the presence of DSBs

Presenter(s): Janice Oh Collaborator(s): Soo Hyun Yang Department of Molecular Biosciences Freshman Research Initiative Biobricks for Molecular Machines, College Department(s): of Natural Sciences, University of Texas at Austin, Austin, Texas

DNA double-strand breaks (DSBs) are one of the most lethal forms of DNA damage. Improper repair of these breaks can lead to mutations and cancerous cell formation. Ataxia-Telangiectasia Mutated (ATM) serine/threonine kinase and Mre11/Rad50/Nbs1 (MRN complex) interact as key components of the DNA repair pathway. At the damaged site, MRN activates ATM, which is responsible for phosphorylating downstream proteins to initiate the DNA repair process. Caudal Type Homeobox 2, CDX2, is a homeobox transcription factor expressed in intestinal epithelial cells. As a transcription factor, its primary functions consist of aiding in embryonic development and maintaining homeostasis of the intestine. Recent studies have found a novel function of CDX2, in which its homeodomain inhibits ATM-MRN interaction, preventing proper DNA repair. While the homeodomain of CDX2 has been shown to be responsible for both transcription and inhibition of ATM-MRN interaction, the amino acid site within the homeodomain that separates the two functions remains unknown. The purpose of this study is to identify the site within the homeodomain of CDX2 that is responsible for inhibiting ATM-MRN interaction without affecting the transcriptional activity of CDX2. This study consists of performing site-directed mutagenesis on certain amino acids in the CDX2 homeodomain, expressing and purifying the CDX2 mutant, and examining the transcription activity and the ATM-inhibitory activity of the CDX2 mutant through in vitro assays. In particular, in vitro DNA binding assays and reverse transcription assays will be conducted to examine the effect that the mutation on CDX2 has on its transcriptional activity. In vitro ATM kinase assays will be conducted with the CDX2 mutant to analyze the effect that the CDX2 mutant has on ATM inhibition compared to the CDX2 wild-type. Creating a separate function mutant would further lead us to examine the physiological effect of CDX2 on ATM-MRN interaction in mammalian cells.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 194

Response to reproductive opportunity in dynamic environments in a

highly social fish

Presenter(s): Niharika Pakala Collaborator(s): Hans A. Hofmann, Isaac Miller-Crews Department(s): Department of Integrative Biology

Social animals, including humans, are responsive to changes in their environment and can alter their behavior in the presence of perceived social threats or challenges. Two fundamental social behaviors, aggressive and reproductive, utilize overlapping neural pathways and have clear tradeoffs. Here, we ask how an aggressive challenge interferes with the response to reproductive opportunity by observing individuals in dynamic social communities. As a model system we use Burton’s Mouthbrooder cichlid, Astatotilapia burtoni, a highly social African cichlid fish with complex social dominance hierarchies. Dominant males of this species exhibit high levels of aggression against subordinates and engage in courtship behavior with females. Social challenges can be simulated by placing an intruder male into the territory of dominant male, which will respond aggressively. We employed hormone assays and spatial location tracking in combination with exogenous administration of prostaglandin F2? (PGF2), a fatty acid hormone that induces reproductive behavior in females regardless of their reproductive state, to examine how such a social challenge affected subsequent male and female reproductive behavior. Female reproductive behavior changed in response to a social challenge. However, circulating levels of the sex hormone estradiol and the stress hormone cortisol did not vary across treatment groups, suggesting that the observed differences in reproductive behavior were independent of a physiological response in the stress axis.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 195

Food resources in suburban neighborhoods: is there an association between the amount of eastern cottontail rabbit (Sylvilagus floridanus) nests and increased access to residential gardens?

Presenter(s): Jyotsnaa Krishi Pradeep, Maleeha Rizvi, Ayotoluwafunmi Osunsade Collaborator(s): Laura Gonzalez Department(s): Department of Integrative Biology

Many studies have been conducted on the effects that the presence of sustenance and prey have on the abundance of small mammals. In this study, we are seeking an understanding on how the access to human-produced food resources in suburban communities affects the abundance of Sylvilagus floridanus, or eastern cottontail rabbits, in Texas. To explore this question, we estimated rabbit abundance indirectly using nest count. Neighborhood surveys were conducted in five suburbs within three of Texas’ major cities (Austin, Dallas, and Houston) to collect data. We also collected data on the effect of other variables on abundance. We found that there was a significant difference in the number of rabbit nests with the presence of a vegetable garden (Chi-Square=8.7154, 1 d.f., P = 0.003155). Our results suggest that there is a significant correlation between the presence of suburban vegetable gardens and abundance of nests. This implies that suburbanization does not have a negative effect on the abundance of rabbits.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 196

Using high-performance computing to discover potential inhibitors of

acetate kinase - an essential enzyme of mycobacterium tuberculosis

Presenter(s): Annabelle Vincent, Mackenzie Noell Collaborator(s): Josh Beckhan Department(s): FRI Virtual Cures Stream

Infecting 10 million individuals and killing 1.4 million each year, tuberculosis (TB) is the global leading cause of death from a pathogen despite having the Bacille Calmette-Guérin vaccine as well as antimicrobials. In 2018, the United Nations targeted to have $2 billion each year to lessen TB’s incidence rate by 80% before 2030 (WHO, 2020). However, strains of Mycobacterium tuberculosis, the bacterium causing TB, resistant to the antibiotics isoniazid, rifampin and fluoroquinolones have emerged, hindering doctors’ ability to treat and cure TB. These multidrug-resistant and extensively drug-resistant strains of TB indicate the severity of the epidemic, solidifying its place as a global health concern. This research analyzed one of the essential enzymes - acetate kinase - of Mycobacterium tuberculosis, the causative agent of the disease. Through high-performance computing, the researchers docked libraries of x-ray crystallography models of ligands to the active site of the enzyme. The virtual screening programs, GOLD and ICM, measured the strength of the binding interaction with higher scores reflecting a stronger interaction and a higher potential to inhibit one of the bacterium’s metabolic pathways. In order to validate GOLD and ICM, positive and negative control ligands were docked to the enzyme. Screening controls resulted in similar ranges of results for both the GOLD and ICM runs, with citrate scoring consistently in runs with a score of 45,21. After validation, over 100,000 small molecules from eleven libraries docked to the target, resulting in a consistent interquartile range of scores 38.04-58.00. Significantly departing from this range, formoterol fumarate dihydrate scored the highest overall, with a GOLD score of 95.08. The predicted top scoring ligands can be evaluated through enzymatic assays to verify their ability to inhibit acetate kinase. If confirmed, these novel ligands are strong potential drug candidates for treating tuberculosis.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 197

Evolutionary diversity of calmodulin within the fungi kingdom

Presenter(s): Muxin Wang Collaborator(s): Richard W. Aldrich Department(s): Department of Neuroscience

Calmodulin is a highly conserved, ubiquitous messenger protein that can be activated by calcium ions. It exhibits a "dumb-bell" like shape, with a flexible linker region connecting two globular domains each containing one EF-hand motif. Each of the EF-hand motifs can bind two calcium ions, causing a conformational change in the protein to the active form. Activated calmodulin can interact with a wide variety of other proteins in signal transduction pathways, such as kinases and phosphatases. This calcium sensitivity allows calmodulin to play a role in many different cellular mechanisms, including calcium regulation, intracellular signaling, and muscle contractions, making it essential for a wide range of physiological functions. Calmodulin has also been shown to play an important part in cardiac diseases, including cardiac arrhythmia and heart failure. Due to its importance in promoting healthy neuronal function and high conservation across ecological time, we are interested in understanding its function and regulation from an evolutionary perspective. More specifically, we will examine how calmodulin has evolved within the Fungi kingdom, which contains the most diverse clades of eukaryotes in the terrestrial ecosystem. We will first compile a phylogenetic tree that covers the diverse spectrum of species and subphyla within the Fungi kingdom. Then, we will analyze the genomic sequence of calmodulin for these species to highlight important events in calmodulin's evolutionary history. This approach allows us to decipher potential mutations or duplication events and place them in relation to each other using the phylogenetic tree. We will also be able to identify regions of the protein that are more conserved than others, which can imply functional necessity. By identifying organisms and protein regions of interest, our project will set the stage for many more future studies on calmodulin's function, regulation, and physiology.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 198

A review of low-copy-number plasmid positioning in relation to

chromosomal position in E. Coli

Presenter(s): Brady Wilkins Collaborator(s): Rasika Harshey, David Walker, Phan Thieu Khang Ho Department(s): Department of Molecular Biosciences

From complex multicellular organisms to the simplest of bacteria, all organisms must properly partition their DNA during cellular replication to ensure equal inheritance of genetic material. One key protein to the proper segregation of the E. coli chromosome is Structural Maintenance of Chromosomes (SMC) protein MukBEF. MukBEF condenses the chromosome along a linear, axial core that maintains the order of chromosome arms. Systems for proper plasmid partitioning are typically native to the plasmid itself. For the P1 and F plasmids, the ParABS and SopABC partitioning systems ensure equal inheritance of these low-copy-number plasmids. While vastly different, an end result of the proposed mechanisms by which MukBEF and ParABS/SopABC operate places both ori and the P1/F plasmids at the cell quarters. Therefore, these low-copy-number plasmids and ori occupy the same physical space in the cell during replication. The transposable phage Mu serves as an ideal tool to study this interaction in vivo, as Mu can only transpose to DNA it physically contacts. Transposition data from Mu lysogenized into P1/F plasmids showed increased propensity to transpose into ori, confirming that the P1/F plasmids and ori are physically close. However, do these plasmids and ori share physical space due to a coincidence of the mechanics of DNA partitioning, or is an unknown factor causing these low-copy-number plasmids to associate with ori? This literature review proposes an experiment to help answer this question while exploring the segregation of chromosomal and low-copy-number plasmid DNA.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 199

Characterization of antigen-specific T cell receptors to mediate

immune responses

Presenter(s): Amanda Xia Collaborator(s): Alexandra Schonnesen, Chad Williams, Eunise Chen, Ning Jiang Department(s): Department of Molecular Biosciences; Department of Biomedical Engineering, Cockrell School of Engineering

Modern T cell cancer immunotherapies are based on the ability of cytotoxic T cells to recognize and attack infected cells. This process is activated by the T cell receptor (TCR) recognizing a peptide-bound major histocompatibility complex on the surface of target cells. It is of particular interest to target neoantigens, antigens derived from tumor-specific DNA mutations, to create a tumor-specific immune response. One method of broadening the T cell response is to genetically engineer the patient’s T cells to express neoantigen-specific TCRs isolated from healthy donors. Here, we created a model system to characterize the functionality of effector T cells. We chose to study human T cells specific for a common cytomegalovirus (CMV) antigen due to the scarcity of human neoantigen-specific T cells. We isolated T cells specific to the CMV antigen from CMV seropositive human donors and then measured the affinities of their TCRs for the antigen. We also sequenced the TCRs of the T cells. Next, we expressed the TCRs onto T cells from healthy human donors using a stable lentiviral expression system. To survey the functionality of the transduced T cells, we measured their cytotoxic abilities in response to the CMV peptide. This model system demonstrated that the T cells could maintain high TCR expression over a sustained period and that the affinity of the TCR expressed positively correlated with cytokine production. This sets the foundation of a promising approach to study neoantigen-specific TCRs for the development of cancer immunotherapy.

• Return to table of contents Undergraduate Research Forum 2021 - Schedule of Presenters 200

Rapid high-resolution 3D-printing with visible light

Presenter(s): Kevin Zhou Collaborator(s): Dowon Ahn, Lynn M. Stevens, Zachariah A. Page Department(s): Department of Chemistry

Traditional manufacturing methods are subtractive: raw materials are subtracted from a bulk and used to make products. Techniques like machining, milling, and molding must be used—the additional machinery increases energy use and potential material waste. Additive manufacturing, also known as 3D-printing, instead builds a larger product from pieces, mitigating those intermediate techniques that lower efficiency. One promising technique is a form of light-based 3D-printing known as vat photopolymerization, where light is shined in specific patterns into a monomer resin to create a solid layer; the layers are then stacked to produce the final print. Unlike existing 3D-printing techniques, vat photopolymerization is far more precise and can create more detailed objects. An issue with current vat photopolymerization methods is that high-energy ultraviolet light is used to achieve desirable polymerization speeds to turn the monomer resin into a desired object. The high energy can degrade the final quality of the print, and also prevents usage of any biological applications. This research sought to develop novel resins were fast to print with lower energy visible light, and were able to be used to print a variety of objects to high degrees of detail and accuracy. The insight gained from this research will open up biomedical applications such as organ printing, or serve as a stepping stone for the development of new techniques such as multimaterial 3D-printing with polymers. Further research includes doping the resins with thiols to prevent oxygen from slowing down the prints, thus making the resins more accessible to the average person.

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Alphabetical Index of Authors

Lilah Adams 57 Alice Burington-Luna 2 Camelia Esmaili 94 Elena Adams 180 Nathan Cano 102 Mahnoor Faheem 185 Iqra Ahmad 27 Luciano Cantu 125 Neha Farooqi 106 Iman Ahmed 106 Oswaldo Ceballos 162 Victor Favela 81 Zoya Ahmed 106 Elizabeth Chandler 37 S. Jean Feeser 166 Alisha Ahmed 181 Navya Cheruku 53 Elaine Finney 56 Jadelynn Aki 11 Maanasa Cherukuvada 137 Shannon Fitton 3 Zuha Alam 85 Xzavier Chikurunhe 113 Brian Flores 106 Jacob Alberts 113 Nia Choi 15 Hayden Flume 127 Hailey Allen 135 Ji Min Chon 16 Mindy Fu 50 Matthew Allen 202 Parth Chonkar 168 Mia Fuentes 36 Sofia Alvarez 12 Matthew Clark 28 Erika Garcia 57 Payal Amin 13 Kailtyn Conlin 114 Rebekah Garza 55 Arya Anagol 47 Olivia Conway 58 Hanna Gedamu 143 Soummitra Anand 140 Madeleine Cope 141 Asha Gomez 157 Shikha Annem 102 Megan Crawford 69 Kayla Goodman 128 Sara Ansari 50 Ting Cui 29 Mason Gosslee 53 Abrar Anwar 79 Kayla Daly 30 William Graber 91 Abrar Anwar 82 Hoang Dao 69 Kaden Green 40 Sruja Arya 179 Noura Daryani 110 Doru Gucer 129 Rithvik Asani 52 Soham Datar 59 Nitya Gudipaty 41 Damola Ashade 152 Reagan Davenport 50 James Guerra 130 Hadis Askari 159 Nick Davila 1 Joseph Guidry 167 Ali Askari 182 Devin Davis 88 Himadri Gunarathna 52 Noel Asmann 68 Zoe de Beurs 163 Andrew Guo 52 Nabil Asrar 106 Jahnabi Deka 106 Antara Gupta 14 Madison Babb 108 Ella DeMott 131 Shikhar Gupta 168 Anisha Bagaria 160 Ronak Desai 184 Aula Haidry 144 Audrey Bahr 161 Natalie Dezso 142 Naila Hajiyeva 178 Alexandra Bailey 85 Michelle Dias 164 Shreyaa Hari 36 Sandy Bakheet 123 Brett Dolotina 89 Sarah Hatcher 32 Jesus Balderas 57 Neha Dronamraju 94 Anna Helmers 31 Argha Bandyopadhyay 183 Daksh Dua 168 Geethika Hemkumar 168 Lorraine-Rana Benhamou 124 Nidhi Dubagunta 179 Carolyn Henein 92 Sophia Betar 86 Jade Ealy 60 Ashlee Hernandez 56 Aneesa Bhakta 14 Mara Eccles 165 Cristhy Herrera 33 Ritika Bhalla 108 Cassidy Edwards 36 Abriana Joy Himantog 1 Mithilesh Bhaskaruni 87 LuLu Eisenberg 30 Sophia Hoefner 137 Sara Blanco 131 Mohanad Elchouemi 70 Sarah Hollis 34 Kishore Botla 108 Nada Elessawy 61 Blake Holman 79 Lauren Briones 52 Haytham El-Zaim 108 Raymond Hong 75 Sarah Bruce 1 Hannah Engebretson 31 George Huang 131 Emily Buell 191 Nabeeha Engineer 90 Katherine Huang 189 Alexa Burchak 14 Irfan Eshan 54 Rabia Husain 169

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Jeff Huynh 16 Landry Luker 98 Kathy Nguyen 74 Imafidon, Leslie 132 Cole Maguire 147 Christy Nguyen 111 Sara Irvine 115 Connie Mai 41 Nhu Nguyen 192 Sakif Islam 23 Thomas Maina 1 Mackenzie Noell 196 Ashley Itzep 45 Rory Malek 19 Zach Nozick 52 Manya Iyer 93 Meghan Mallya 148 Hannah Odell 86 Miriam Jaime 23 Claire Manners 149 Janice Oh 193 Aleena Jamal 94 Claire Marrone 35 Destiny Okwubodu 152 Yuyin Jiang 33 Alexia Martin 39 Taylor Oliphant 21 Wenxuan Jiang 170 Teresa Martinez 40 Dina Orozco 63 Chloe Juanico 95 Gabriela Mata 99 Ayotoluwafunmi Osunsade 195 Lisa Kadira 108 Gabriela Mata 100 Lois Owolabi 171 Reha Kakkar 145 Jordan Matkin 150 Niharika Pakala 102 Lalitha Kaligotla 23 Sarah Mayberry 20 Niharika Pakala 194 Nour Kassem 35 Emily McDonald 99 Andrea Pantoja 54 Prachi Khanna 96 Emily McDonald 100 Sojin Park 64 Mallika Khurana 104 Morgan McGinnis 86 Richa Patel 102 Ashley Kim 93 Connor McKee 151 Sohni Patel 102 Sohmee Kim 155 Aubrey Medrano 4 Kaushal Patel 120 Mina Kim 186 Aubrey Medrano 9 Edwin Paul 53 Isabelle King 52 Meagan Mehlhop 190 Marie Pearce 22 Jung Eun Koo 108 Sanica Mehta 62 Julia Pena 153 Raquel Kosted 187 Shobha Melukote 191 Samuel Perales 117 Negar Koupaei 133 Carrie Meng 131 Abigail Perryman 120 Julia Kramer 97 Poorna Menon 41 Riley Perugini 41 Anna Kurtin 188 Amelia Mercado 101 Wyatt Peters 44 Tho Lam 36 Madison Metzger 50 Anna Pham 32 Danielle Landry 17 Isaac Miller 39 Vincent Pham 134 Maanasa Lanka 23 Mrityunjay Mishra 80 Mac Phillips 103 Sean Lau 189 Daniel Mock 5 Akshay Prabhakar 154 Katherine Le 37 Anshul Modh 160 Jyotsnaa Pradeep 195 Erin Le 57 Zain Moin 179 Pranav Premnath 7 Janet Le 146 Jaycee Morales 36 Jafrin Pritha 170 Tia Leary 38 Yusuf Mufti 42 Karime Puga 106 Kaitlyn Lee 18 Leslie Mui 41 Lokesh Pugalenthi 75 Madison Lee 37 Omar Muniz 120 Ishani Purohit 45 Rachel Lee 58 Jesus Munoz-Castaneda 173 Hanqi Qian 54 Hannah Lee 116 Katherine Myers 56 Faiza Quadri 135 Lauren Lillie 71 Neel Nagarajan 6 Noor Radde 46 Albert Lin 38 Athulya Nagarajan 179 Kalei Ragland 135 Peiru Liu 38 Rahul Nanduri 75 Chitra Rajasekaran 113 Jessica Liu 108 Cate Naukam 23 Sneha Rajendran 135 Rachel Lopes 135 Kimberly Ngo 57 Jorge Ramirez Salinas 125 Joshua Louie 50 Maria Nguyen 19 Gautam Rangappa 23 Ezequiel Lozano 72 Jennifer Nguyen 35 Suhani Ravani 104 Austin Lu 55 Nhu Nguyen 43 Samira Ravilisetty 81 Catherine Lu 67 Ashley Nguyen 73 Mowna Ravipati 43

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Aubrie Rettmann 131 Brandon Ta 24 Julia Zheng 19 Lexi Richardson 50 Alvin Ta 125 Andy Zhou 26 Caitlin Richardson 106 Karina Tacconi 48 Grace Zhou 51 Jensen Richardson 170 Do Tam 126 Jennifer Zhou 179 Mariana Rios 107 Jennifer Tang 137 Kevin Zhou 200 Simone Ritchey 76 Anthony Tang 176 Alicia Zitouni 52 Mohammad Rizvi 108 Valentina Tardugno Poleo 1 Maleeha Rizvi 195 John Teague 120 Heyji Ro 190 Jonathan Tebo 121 Ellianni Rodriguez 53 Antonio Terrazas 38 Alicia Rusthoven 53 Kyahria Thomas 36 Ericka Salas 77 Joshua Thompson 114 Ericka Salas 172 Luke Timmerman 120 Daniela Salazar 114 River Tomlinson 59 Erica Salazar 50 Rustin Tourgoly 138 Ali Saleem 102 Cat Tran 36 Aniket Sanghi 8 Tatum Tran 49 Angelo Scanio 173 Khuong Tran 66 Willa Scanlon 110 Justin Tran 67 Alia Segura 136 Emily Tsai 177 Thomas Seive 118 Jessica Turk 36 Iman Shah 52 Tae-Young Uhm 190 Simran Shah 77 Sathvik Vemparala 50 Prachi Shah 109 Raghav Venkataramanan 9 Khavvia Shanmugasundararaj 174 Juan Villacres 155 Julia Shell 104 Jerry Villalobos 81 Joji Sherman 54 Silverio Villanueva 178 Mattie Sherwin 47 Annabelle Vincent 196 Ninette Siby 110 Justin Vu 25 Mahima Singeetham 12 Nathan Vu 55 Akash Singh 79 Mindy Vu 67 Akash Singh 82 Thy Vu 139 Ren Smith 33 Zerrin Vural 122 Aislinn Smith 201 Ariel Wang 55 Tate Song 80 Joyce Wang 156 Abby Spears 77 Xueling Wang 157 Maansi Srinivasan 179 Muxin Wang 197 Sanya Srivastava 81 Delaney White 10 Sanya Srivastava 83 Brady Wilkins 198 Kyra Stillwell 119 Sienna Wu 158 Erisa Stokes 111 Amanda Xia 199 Yiheng Su 78 Charles Yang 54 Kaihong Sun 65 Karen Yao 41 Yukta Sunkara 175 Donya Yazdi 41 Jennifer Suriadinata 84 Sierra Yoshida 111 Max Svetlik 80 Yijie Zhang 112 Melynda Sylvester 131 Christina Zhang 178

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