Research Projects & Mentors
Please contact faculty directly if you have specific questions about individual research projects.
The SCOPE Mentor Meet and Greet event will be Wednesday, March 8th, from 12:30-1:30pm in FJS 151. At this event you will have the chance to chat one-on-one with SCOPE faculty and get your questions answered before applications are due.
SCOPE 2017 Mentors and Research Projects
Aging, Experience, and Sexual Motivation
The period prior to menopause is fraught with many unsettling symptoms not the least of which is variable or decreased sexual desire. Although preclinical research in animals has informed our understanding of human health issues such as the neuroendocrine triggers of menopause, much less research has investigated the effects of aging on symptoms related to sexual motivation and desire. By using a comprehensive animal model of sexual motivation, we can advance our understanding of these sexual symptoms. We propose to measure sexual motivation in middle aged female rats to determine if there are consistent signs of sexual dysfunction in aged females compared to young adults. Furthermore, we will be able to determine if drugs that increase sexual motivation, such as methamphetamine or ketamine, in young adults improves sexual motivation in middle aged rats. Finally, we will measure other emotional symptoms associated with aging such as anxiety. We hope that we could inform clinical research of potential treatments for age-related sexual dissatisfaction and dysfunction.
Identifying the Inhibitory Factors of ICE391 Responsible for Attenuating RumA’2B Mutagenic Activity
In bacteria, the integrating conjugative element ICE391 codes for the error‐prone DNA polymerase RumA’2B. When cloned separately from ICE391, RumA’2B has been shown to factor in cellular levels of spontaneous and DNA damage‐induced mutagenesis, which can contribute to the establishment of antibiotic resistance. Our research looks to identify factors/genes found on ICE391 that regulate RumA’2B‐mediated mutagenesis and consequently contributes in establishment of antibiotic resistance.
Induction of apoptosis in yeast and transformed mammalian cells using small cell‐penetrating peptides
Project 1: A novel “chimeric” peptide was designed from structural analysis of two types of bioactive peptides: an antimicrobial and apoptosis‐inducing small peptide, bound to a polycationic cell‐penetrating peptide. The “chimera” contains the biologically active sequences of each type of peptide; we hypothesize that the cell‐penetrating portion of the compound will assist in cellular uptake of the peptide where the apoptosis‐inducing component can interact with intracellular targets of of the eukaryotic cells. We will test the effects of the novel peptide using methods to measure rates of cellular growth in microbes, and by detecting induction of apoptosis in eukaryotic cells by the processing and activity of caspase enzymes.
Project 2: Proteins involved in signal transduction and membrane fusion are often targeted to specific intracellular membrane structures by palmitoylation. We will compare the distributions of palmitoylated small, regulatory GTP‐binding proteins in normal and virally transformed embryonic mouse fibroblasts, using characteristic chemical properties of the palmitoylated proteins to modify them with a biotin‐containing reagent. This will allow us to identify differing amounts or cellular location of these proteins in the two cell types.
Improving the observable fluorescence time of the Cy3 and Cy5 dyes
Fluorescent techniques provide a solution to imaging systems in a manner that is high resolution with low noise. Understanding fluorophore photophysics and improving their behavior can help to increase the efficiency of techniques that utilize fluorescence. Photobleaching and photoblinking are two common phenomenon which reduce the signal from a fluorophore, working against the strengths of high signal to noise that fluorescence techniques specialize in. The cause of photobleaching and photoblinking is often the interaction of the fluorophores with other species in solution, predominantly triplet oxygen. It has been shown that through the use of photoprotection systems such as redox or antioxidant solutions the effect of photobleaching is mitigated and the fluorophores can emit for longer periods of time. In this project we aim to develop a screening method to test the effect on increasing the time to photobleaching for proposed photoprotection systems. Our initial methods will be tested against a photoprotection system that is known to increase the fluorescence on time and we will seek to optimize the ratio of the components in the photoprotection system to maximize the observable fluorescence time of two dyes, Cy3 and Cy5.
Unusual DNA Structures and DNA Damage in Yeast Cells
DNA damage is thought to play a role in many human age‐related diseases such as cancer, cardiovascular disease, and neurodegeneration and can arise from both exogenous factors and endogenous processes. The most common DNA conformation is the well‐known, double‐helical B‐form; however, DNA can adopt also non‐B form DNA structures such as such three‐stranded triplex DNA structures. We will examine how damage to intramolecular triplex structures affect mutation frequency in yeast and characterize the type of mutation that occurs.
Developing Artificial Intelligence for Video Games
Video games are a popular testbed for many Artificial Intelligence (AI) techniques because they are simulated, controlled environments, but have a level of complexity that makes optimal decision making by in‐game entities difficult. We will work to design intelligent agents for a game or other simulated environment using cutting‐edge AI techniques such as Evolutionary Computation and/or Reinforcement Learning. Available environments include simulated robot mazes, abstract predator/prey scenarios, and video games such as Ms. Pac‐Man, Super Mario, Doom, Unreal Tournament, Tetris, and more. Depending on the game chosen, there is also potential for participation in one of many international game AI competitions.
A Language for Describing Dynamic Graph Visualizations
Biochemists studying interactions between proteins, engineers detecting threats in a computer network, and sociologists studying popularity in social networks all make use of dynamic graphs‐‐‐changing collections of data points and the relationships between them. Dynamic graph visualization involves mapping all three components (points, relationships, and changes) of a dynamic graph to visual elements using a function called a dynamic graph visualization technique. The purpose of this project is to more deeply understand not merely a single technique, but rather the relationships between different techniques. We will construct and analyze a graph where the data points are techniques and the relationships are the similarities and differences between pairs of techniques. We will use this graph‐of‐techniques to define a new language for describing each dynamic graph visualization technique. We can then use this language to build software that takes as input a dynamic graph and a description of a technique in our new language and outputs a cognition‐amplifying display of the graph using the described technique.
Pre‐exercise carbohydrate consumption for the average exerciser
There is a high level of interest in how macronutrients impact sport performance outcomes. Previous studies have extensively examined the impacts of protein, carbohydrates, and fat on performance. More specifically, studies have examined the use of carbohydrates prior to exercise in order to increase performance. Unfortunately, there is a gap in the literature surrounding the benefits of macronutrient intake for the average exerciser. The average, adult exerciser has little scientifically-based guidance about whether they should eat prior to exercise, and if so, what they should eat. Many of the current recommendations are based on scientific data from studies looking at endurance athletes (exercising >60 minutes/bout). This is not applicable to the average, adult exerciser who typically participates in 45‐60 minutes of exercise/bout. This amount of exercise may or may not benefit from pre‐exercise intake. In addition, a pre‐exercise snack may increase daily caloric intake and negatively impact weight management. If the snack is not increasing the output of the exercise performed, it may not be beneficial to the participant. The purpose of this study is to identify if a carbohydrate snack prior to an average exercise bout at moderate intensity impacts the performance of the participant. In addition, we will examine if there is a difference based on the type of carbohydrate ingested.
Comparison of Supine and Prone Dolphin Kicking Mechanics Across Ability Levels
Anecdotally, the best swimmers in the sport are rapidly becoming the best dolphin kickers, which emphasizes the need to understand what elements of this movement are most important for success. While a number of articles in trade journals have suggested methods for developing an underwater dolphin kick, little research has been performed to evaluate what elements of the movement are related to success in this movement. Furthermore, to our knowledge, no work exists to describe how the ability to perform this movement changes with ability or age (and with motor skill/coordination acquisition). This information could prove valuable to swimmers of all ability levels and will inform coaches and athletes in how to develop effective underwater dolphin kicking. Beyond the applied aspect of these data, this work may provide a basic understand of the development of coordinated movement patterns across ages. Therefore, the purpose of this study is to compare dolphin kick performance, as defined by kinematic and kinetic measures, across age and skill level. Students involved in this work will gain experience in motion analysis and advanced statistical data analysis.
Exploring Choose Your Own Adventure Books with Graph Theory
This project uses the mathematical field of graph theory to analyze the Choose Your Own Adventure (CYOA) book series. We will first turn a collection of CYOA books into directed graphs and study their properties. Then, we will create a ranking algorithm combining various properties of the graph to decide what book is the “best read” and compare our results to rankings by actual readers. We will also analyze the mathematical structure of the books over time to see what (if any) changes were made. No mathematical background is needed, but a willingness to explore new mathematical ideas is required.
Creating a Wave‐Powered Robot
Marine robotic vehicles allow scientists to measure and better understand ocean conditions. As a result, these devices have become essential to a wide variety of applications including environmental monitoring. This project seeks to design a new type of aquatic robot that does not require external power to move but instead uses spring‐mounted fins to convert wave energy into forward movement. The initial tests of the propulsion unit will probably start in Southwestern’s pool and then later move to Lake Georgetown. After learning some basic electronics, you’ll then learn how to compute the position of the robot using a marine GPS unit and a magnetic compass. With this information we can adjust the position of the fins so that the robot moves along a predetermined path, collecting environmental data (such as water temperature) and storing it for later analysis. A willingness to get wet is required for this project!
Numerical Explorations of Dynamical Systems
Simple iterative equations known as mappings have been studied as models of plasma and fluid systems, particle accelerators, and the transition to chaos in dynamical systems. Maps contain rich behavior characteristic of more complicated systems and are much faster to compute than the full dynamics, but challenges exist in computing and visualizing many different initial conditions in parallel. Recent advances in graphics processing unit (GPU) computing (CUDA, OpenCL) have made massively parallel processing tasks readily available and accelerated machine learning, physics simulations, and data science. After a brief introduction to the basics, students will be guided through their own computational explorations and data visualizations of dynamical systems.
Balcones Escarpment Environmental Monitoring Experiment (BEEMEX)
A collaborative data collection and environmental monitoring experiment will be undertaken in Central Texas. Kestrel handheld weather observing meters will be used by participants to record meteorological data (wind speed, wind direction, temperature, and relative humidity) at a series of set locations on either side of the Balcones Escarpment, a topographical feature which divides the state into the Edwards Plateau to the west and the Coastal Plains to the east. Previous research suggests that this feature initiates and enhances thunderstorm activity in this region, potentially leading to life‐threatening flash flooding. Teams from the University of the Incarnate Word and St. Edward’s University will join with Southwestern personnel in a large‐scale data collection effort aimed at better understanding the effect the Balcones Escarpment has on regional meteorology. Data from the National Weather Service and from St. Edward’s ozonesonde program will also be used.