Undergraduate Research Symposium 2024

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  Isolation and Analysis of R130D Malate Dehydrogenase (MDH)

  Hayley Brunette, Abby Doyle, Ilsa Hoaglund, and Danielle Bolland

  Malate Dehydrogenase (MDH) is the enzyme that catalyzes the ninth step of the citric acid cycle, a regenerative step in the metabolism of glucose in which malate is converted to oxaloacetate. Conformational changes in the active loop region of MDH along with the coenzyme NAD+ drive catalysis. Previous studies suggested that mutating positively charged amino acids to negatively charged amino acids at residue 130 decreased the enzymatic activity of MDH. We hypothesized that if we change arginine 130 (positively charged amino acid) to aspartate (negatively charged amino acid), then the enzymatic activity of MDH would significantly decrease. In e. Coli cells, site-directed mutagenesis was performed to create the mutation (R130D). The mutated protein was purified using nickel affinity chromatography and confirmed by Bradford assay and SDS-PAGE gel of the protein purity. The kinetics of the mutated protein were measured and compared to the wild-type to examine the effects of the mutation. We found R130D has a lower Vmax and higher Km than wild-type MDH, suggesting that the mutant MDH protein catalyzes the reaction at a much slower rate, and the substrate oxaloacetate had a reduced binding affinity to the enzyme. Learning more about which amino acid sequences of MDH are important in its metabolic function has important implications regarding the regulation of carbohydrate metabolism, specifically the citric acid cycle.

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  The Relationship Between Fatalities in Police Violence and Their Identifying Characteristics: Age, Gender, Race, and Region

  Yuechu Hu

  Police violence, highlighted by the George Floyd incident in 2020, has intensified concerns about police brutality and perceived racism in U.S. law enforcement (AP News, 2022). Therefore, we intend to analyze Fatal Encounters data, which documents non-police deaths that occur in the presence of the police in the United States. By creating statistical tables and graphs, as well as applying time-series methods, classification and regression trees, and a multinomial logistic regression model, we find that males and transgender people are more likely than females to encounter victimization during police brutality enforcement for any cause of death. Victims older than 19 are more likely to die in police brutality enforcement than victims younger than 19.

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  "This is How the West Ends": A Content Analysis of Conservative Youtubers Notions of Western Excellence

  Michelle Johnson

  In 2023, YouTube was one of the most used social media platforms in the United States alone. While existing scholarship (Finlayson 2022) has observed linkages between right-wing social media and distrust in institutions of government, family, and others, I seek to understand how conservatives use YouTube as a means to teach their audience racialized, gendered, and nationalistic ideas about the Western hegemonic order. To examine this issue, I conducted an in-depth qualitative content analysis of three key conservative content creators: Ben Shapiro, Matt Walsh, and Michael Knowles. Two videos were chosen within each creator's profile using keyword searches such as “Anti White” and “DEI”. Preference was given to videos published within the last 6 months and for videos more than 5 minutes and less than 60 minutes. Total watch time amounted to 139 minutes. I found that these creators most commonly suggest that whiteness, masculinity, and Western society as we know it are under attack. The culprit of these attacks in their point of view are efforts that promote diversity, equity, and inclusion in the workplace, schools, and other institutions. By utilizing a “draw your own conclusions” framework, conservative creators can both distance themselves from their ideological teaching and create a community with which followers of this content can connect with. Ben Shapiro, Matt Walsh, and Michael Knowles have gained, maintained, and grown their following on the basis of this shared sense of community that promotes extremely violent, racialized, gendered, and nationalistic ideas.

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  Legal Process Durations in Domestic Violence Cases

  Gabrielle Meyers and Jon Anderson

  Slow court case processing is a significant concern, particularly in regard to their adverse implications for survivors of serious crimes such as domestic abuse and sexual assault. This study investigates a number of factors that may influence the duration of court case proceedings using court records from three Minnesota counties. Focusing on cases of domestic violence, sexual assault, kidnapping, harassment, stalking, and various other sex crimes, we employ survival analysis methods to explore the effects of various factors on the duration of court case processing. Our analysis considers the effects of factors such as type of crime, form of legal representation, judge, and various defendant characteristics. Our goal is to identify major factors that contribute to delays in court proceedings, providing helpful insight for advocacy groups and crime victims about what they can expect during trial. We find significant differences in completion durations between counties and between crimes charged. However, when we adjust for differences between judges such as the number and complexity of cases assigned to them, there is no evidence of county differences.

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  Enhancing Evolutionary Computation: Optimizing Phylogeny-Informed Fitness Estimation Through Strategic Modifications

  Chenfei Peng and Nic McPhee

  In evolutionary computation, programs are developed using evolution's basic principles, such as selection, mutation, and recombination, to iteratively improve problem solutions towards optimal outcomes in a reasonable amount of time. To save time and be more efficient, we are currently exploring a modified version of phylogeny-informed fitness estimation. The original version evaluates each individual program on a subset of the training cases and estimates the performance everywhere else according to its parent's performance. Our approach involves comprehensive evaluation of promising programs across all training cases, increasing computational investment where the sub-sampled results indicated potential gains. This method led to our modified algorithms finding solutions in fewer generations, but at the cost of increased computation time. One question is how to determine whether a solution is promising enough to warrant this additional evaluation. To address this, we used a threshold-k, requiring that a child should be better than its parent in at least k training cases. Analysis of 30 trials on a simple test problem showed threshold-3 enhanced time efficiency, while threshold-1 minimized the number of generations needed for success. A further 100-run analysis with much lower generation limits revealed that threshold-1 secured the highest success rates. To sum up, we did a lot of interesting experiments using a modified version of phylogeny-informed fitness estimation, including comparisons between modified version and original one, 30 runs and 100 runs, complex regression problem and fuel-cost problem.

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  Spring Burns and its Effects on Vernal Forbs

  Liam Poitra, Miriam Gieske, and Stuart Wagenius

  Grasslands are the least protected ecosystem on earth. In North America, protected native grasslands are typically burned in the spring, when native warm-season grasses are dormant, to reduce growth of invasive cool-season grasses; burn seasons historically included summer burns. This study aims to find how spring burns affect early spring flowering forbs (non-woody, non-grass plants).

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  Effect of Assay Medium pH on Inhibitory Ability of Streptomyces

  Trevor Swan and Miriam Gieske

  Streptomyces bacteria from soil often produce antibiotics which inhibit growth of other microbes. When comparing Streptomyces’ inhibitory ability between different soils, it may be important to match the pH of the medium used in assays to the pH of the soil they came from. We assayed Streptomyces isolates collected from a long-term agricultural experiment with nitrogen-fertilized and non-fertilized treatments to determine their ability to inhibit growth of other bacteria by producing antibiotics. Average soil pH was 6.8 in fertilized soil and 7.2 in non-fertilized soil. We dotted isolates on a glucose-asparagine agar medium adjusted to different pH values and overlaid them with a non-pathogenic Streptomyces standard to measure their inhibitory ability. Some isolates produced different inhibition zone sizes depending on medium pH. However, response to assay medium pH did not differ significantly among isolates from soils of different pH. More tests are needed to determine whether it is necessary to match the medium pH to the pH of the soil the isolates came from when comparing prevalence of antibiotic production among Streptomyces from different soils

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  Providing Beginners with Interactive Exploration of Error Messages in Clojure

  John Walbran and Elena Machkasova

  Programmers are imperfect, and will often make mistakes when programming and create a program error, for example, attempting to divide by zero. When a computer tries to run a program with an error, the program will halt and present the details of the error to the user in the form of an error message. These error messages are often very jargon-heavy, and are not designed to be palatable to a novice programmer. This creates significant friction for new programmers trying to learn programming languages. This work is a part of an ongoing project (called Babel) led by Elena Machkasova in an attempt to ease this friction in the Clojure programming language. Currently, Babel software is able to replace standard error messages with ones that are more helpful for a beginner audience. My contribution to this project is an exploration of potential tools to effectively display information about errors in an interactive and intuitive manner. The most promising of these tools up to this point has been Morse, created by the company Cognitect, owned by Nubank. As this project continues to explore the possibilities of Morse and how it can integrate with the existing Babel system, we are putting together potential setups that novice programmers can use to effectively understand and explore the causes of the errors they come across. This project presents the setups that have been developed and discuss their benefits and tradeoffs in helping novice programmers understand error messages.