Undergraduate Research Day 2024

Permanent URI for this collectionhttp://hdl.handle.net/1903/31825

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End date: 2024

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Now showing 1 - 10 of 127
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    Enhanced Computational Tool for Seismic Fault Sensitivity Screening
    (2024) Subramaniyan, Vishnu; Mandhan, Sai; Maheshwari, Raunak; Bensi, Michelle; Lundstern, Jens-Erik
    Earthquakes occur when stress exceeds the strength of pre-existing faults, potentially causing severe damage to the built environment. It is critical to identify the faults that are most likely to rupture, given our knowledge of various subsurface properties. Existing fault screening tools are closed-source or have limitations that affect their usefulness in research and engineering applications. Our team is developing a more efficient, open-source seismic fault sensitivity screening software program designed to support probabilistic seismic hazard analysis and geophysical research. Our research aims to improve upon existing tools by leveraging vectorization to increase calculation speeds and offering choice among multiple probabilistic distributions to capture uncertainty in input parameters. Moreover, the open-source nature of this tool enables researchers to adapt the program for their own purposes to support seismic hazard assessment.
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    Expression of Human RPS17 and RPS23 in E. Coli Bacterial Cells
    (2024-04) Bloom, Kaylee; Perera, Senanga; Outmezguine, Daniel; Patel, Tulsi; Hunter, Kennedi; Kothari, Yashi; Guevara, Ivan; Pham, Thong; Zeidan, Quira
    Ribosome biogenesis is vital for a cell to make proteins and proceed through the central dogma of molecular biology. Human ribosomal proteins (RPs) RPS17 and RPS23 are protein-encoding genes associated with the formation of ribosomes in cells. Serious diseases are linked to dysfunction of RPS17 and RPS23. Mutations in RPS17 have been linked to Diamond-Blackfan anemia, a rare inherited bone marrow disease that affects red blood cells, leading to anemia. RPS23 protein dysfunction is linked to Hepatocellular carcinoma, a severe form of liver cancer. In this study, RPS17 and RPS23 were cloned and expressed with two different bacterial expression plasmids, pNIC28-Bsa4 and pNH-TrxT, with 100% sequence confirmation. Plasmids were then transformed into BL21 E. coli cells, and IPTG induction was used to express RPS17 and RPS23. SDS-PAGE, followed by Coomassie staining, was conducted to confirm the successful expression of the proteins. Future research will determine how overexpression and posttranslational modifications of RPS17 and RPS23 link to cellular growth and homeostasis.
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    Cloning and Expression of Human RPS24 into E.coli and the HEK293 Cell Line
    (2024-04-26) Merrifield, Katherine; Apgar, Sofia; Jessica Whitney; Argueta, Vicky; Zeidan, Quira
    Ribosome biogenesis is the process of constructing ribosomes and requires ribosomal RNA, ribosomal proteins (RPs), and assembly factors. The products of eukaryotic ribosome biogenesis are the large 60S subunit and the small 40S subunit, of which RPS24 is crucial in its formation. In addition to its translational roles, RPS24 is associated with regulating cell growth and proliferation, apoptosis, and DNA damage response. We hypothesize that the extra-ribosomal functions of RPS24 are impacted by its post-translational modifications (PTMs). To elucidate the functions of these PTMs, the coding sequence of human RPS24 was cloned into pNH-TrxT and pNIC28-Bsa4 bacterial expression vectors via ligase-independent cloning. The recombinant plasmids were then transformed into BL21 E.coli cells, and initial trials were conducted to optimize growth and expression conditions for the two transformed strains. Protein expression was determined using SDS-PAGE and Coomassie staining, the results of which indicated moderate levels of the RPS24 fusion protein in cells transformed with both the recombinant plasmids. RPS24 expression was observed without IPTG induction, indicating leaky expression. In parallel experiments, we investigated the overexpression of RPS24 in HEK293 cells from the plasmid pcDNA3.1(C)DYK, and successful transfection was confirmed by SDS-PAGE and Western Blot analysis. We aim to investigate the role of RPS24 PTMs in cell proliferation and viability under various stress conditions to evaluate their impact on tumor development.
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    Expressing Human Ribosomal Proteins S20 and S26 in Modified E.coli (BL21) Cells
    (2024-04-26) Lee, Maia; Quenano, Erika; Owen, Jennifer; Ngouba, Andrea; Zahniser, Hannah; Tafesh, Talah; Ofoegbu, Stacie; Weber, Louis; Quira Zeidan
    Ribosomes are fundamental in creating proteins that contribute to the proper functioning of cellular processes. Thus, ribosome biogenesis must occur with integrity by appropriately expressing ribosomal proteins (RPs). Mutations in the genes of human RPS20 and RPS26 have been linked to disruption in the translation machinery and anomalies in the production of red blood cells, leading to diseases such as Diamond-Blackfan Anemia. To develop our understanding of the role of mutations in human RPS20 and RPS26, we performed ligase-independent cloning of their coding sequence into pNIC28-Bsa4 and pNH-TrxT and transformed these plasmids into a BL21 E. coli expression system. IPTG induction was used to determine conditions necessary to maximize the expression of soluble RPS20 and RPS26. After SDS-PAGE, Coomassie staining showed successful expression of RPS26 in response to IPTG induction, whereas RPS20 was produced regardless of IPTG presence. Human RPs expressed in bacteria are often purified from insoluble inclusion bodies; thus, determining the conditions for maximal solubility provides an optimal strategy for studying fusion proteins. Future research on the effects of the overexpression of RPS20 and RPS26 on human cell growth and viability will expand our understanding of the complex mechanisms of human ribosome biogenesis and its role in disease.
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    Stable accumulation of human ribosomal proteins SA, S2, S3, S4X, S6, S7 in rabbit reticulocyte cell-free expression system
    (2024) Neuheisel, Mary Louisa; Streit, Julia; Zeidan, Quira
    Mutations in human ribosomal proteins (RPs) contribute to severe, tissue-specific pathologies, indicating roles that extend beyond protein translation. RPSA is associated with pancreatic cell migration and congenital asplenia, while RPS3, RPS4X, and RPS7 are linked to Diamond-Blackfan anemia (DBA). While we understand the nucleolar assembly of RPs, the cytoplasmic events preceding RP translocation into the nucleus remain unclear. This work investigated the expression and posttranslational modifications (PTMs) of human RPSA, RPS2, RPS3, RPS4X, RPS6, and RPS7 using Rabbit Reticulocyte Lysate (RRL), an enucleated cell-free system that allows the study of cytosolic modifications crucial for RP stability. We conducted coupled transcription/translation experiments with Western blot analyses and immunoprecipitations with anti-FLAG antibodies and magnetic beads to analyze RP expression and cytosolic PTMs. Our results demonstrated the robust and stable expression of RPs, with distinct abundance and stability among different proteins despite expression from the same promoter under identical conditions. RPSA, RPS3, and RPS6 exhibited a molecular weight of approximately 8-10 kDa higher than predicted, suggesting PTM with a peptide. We also detected the presence of enzymes for O-GlcNAc modification within the RRL system. Treatment with TMG, an O-GlcNAcase inhibitor, resulted in increased O-GlcNAcylation levels. We propose that the RRL system is an invaluable tool for probing the roles of PTMs in the extraribosomal activity of RPs within the cytoplasm, representing a relevant and accessible model to deepen our understanding of ribosomopathies and their future therapeutic interventions.
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    Deciphering the Factors: Faculty Discretion in Academic Misconduct Referrals
    (2024) Groisser, Kara; Bersani, Bianca
    College campuses face widespread academic misconduct, with rates as high as 80-95%, but only 3-9% of cases are reported (Cochran 2017; Hard, Conway, Moran 2006; McCabe 2005; Vandehey, Diekhokk, LaBeff 2007). Examples include cheating during exams, collaborative assignments meant to be individual, and improper use of online sources. At the University of Maryland, common sanctions for academic misconduct include a 12-month "XF," and suspension or expulsion is possible for repeated or severe offenses. Despite university administrations implementing honor codes, such as the Code of Academic Integrity at the University of Maryland, academic misconduct persists. These codes outline policies, expectations, and disciplinary processes, with faculty required to report suspicions. Despite severe sanctions like course failure, suspension, and expulsion, students continue to cheat, and faculty are reluctant to report their suspicions of misconduct. The persistence of academic misconduct despite these measures raises questions about the motivations behind student behavior and the responses of faculty and administrations (Waltzer, Samuelson, Dahl 2022). Existing research underscores the crucial role of faculty in deterring cheating, with inconsistent responses to misconduct by faculty fostering a culture of dishonesty that further encourages misconduct. This research aims to address the inconsistency in formal referrals of students suspected of academic misconduct by faculty. Faculty discretion leads to unequal treatment, impacting the likelihood of students being caught for cheating and facing sanctions like suspension or expulsion. A comprehensive understanding of factors influencing faculty decisions to refer and identifying a profile of likely referrers would enhance the fairness and equity of the student judicial process.
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    Students' Use of Retrieval Practice
    (2024) Aliabadi, Farah; Oscilowski, Joseph; Wieczynski, Aleysa; Hartwig, Marissa
    Retrieval practice is the highly effective learning strategy of recalling facts and concepts from memory. Examples of retrieval practice include using flashcards, practice quizzes, open-ended recall, and other exercises where information is retrieved from memory. Research is mixed on whether or not students choose to use retrieval practice and whether they fully understand its benefits for their learning. Our research seeks to better understand student attitudes toward retrieval practice. We hypothesized that the type of retrieval under consideration–for example, ready-made quiz questions vs. free-recall summarization–might affect students’ inclination to study with retrieval practice. Two studies examined the popularity of two retrieval practice methods–practice quizzing and summarization–compared to passive studying (i.e., reviewing instructional materials). Study 1 was conducted with undergraduates in a laboratory setting (N = 93). Study 2 was conducted in high school math classes in four different high schools (N = 567). In both studies, participants were taught unfamiliar math lessons via computer tutorials. A study phase followed, where participants could restudy the materials in preparation for a test by selecting any of three study tools: quiz, summarize, or review. Participants could use any combination of tools and could also quit studying at any time. In both studies, the quiz tool was significantly more popular than reviewing or summarization. These results suggest that students’ inclination to use retrieval practice for studying may depend on the form of retrieval practice.
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    Skibbereen, Ireland: A Legacy of the Famine
    (2024) Weikert, Emma; Brighton, Stephen
    The Irish Potato Famine began in the mid-19th century, claiming the lives of millions. The Famine forever changed the culture and sociopolitical relations of Irish people, and these changes are reflected in the graveyards in the past and present. Symbols, imagery, and types of grave markers give insight into the ideologies of the time they were placed there. I visited three graveyards in West Cork in the summer of 2023 and examined databases of graveyards, to compare grave markings and graveyards before, during, and after the Famine. The question was posed: What are the long-term cultural implications of the famine, and how does this manifest in graveyards?
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    Quantum Finance: Exploring Asset Management with QAOA
    (2024) Henkle, Evan; Igur, Vismay; Karnik, Sara; Velaga, Sourabh; Jabeen, Shabnam; Khan, Alex
    Quantum computers are becoming more and more applicable to a variety of applications due to their ability to exponentially speed up computation. This project aims to utilize quantum technology to build a Quantum Approximation Optimization Algorithm (QAOA), to redefine portfolio optimization in finance. We aim to conduct a series of simulations to evaluate the effectiveness of our quantum based portfolio strategy, and compare the outcomes against those achieved through traditional optimization methods. Our preliminary research indicates that the quantum approach may result in faster and higher quality portfolio solutions, leading to more profitable and risk averse investments. By translating the challenge of finding the optimal combination of assets - balancing risk and return - into a problem that can be solved by quantum computing, we unlock new possibilities for financial analysis and decision making.
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    Exploring Olfactory Cues: Behavioral Responses in Cichlid Juvenile to Food and Amino Acid Stimuli
    (2024) Leary, Maurice; Gable Parker, Coltan; Juntti, Scott
    Cichlid fish have achieved a uniquely high rate of speciation, providing researchers the opportunity to better understand the sensory systems associated with speciation. Chemosensation, which includes both taste and olfaction and is used to detect food, must have evolved as cichlids evolved different lifestyles and diets. However, the specific neural mechanisms associated with chemosensory food detection in cichlids have not been discovered. In this experiment, we aimed to determine if cichlid juveniles show behavioral preference for food associated olfactory cues when presented with two types of stimuli: amino acids and food extract. We expect that both cues should be sufficient in evoking behavioral preference, as determined by time spent in odor compared to clean water, which would confirm the ability to confirm preference for food olfactory cues in cichlid juvenile. I tested a total of 28 cichlid juvenile, and their results revealed no overall significant preference when introduced to an olfactory cue. Nonetheless, we did observe 100% of fish spending over 50% of time in food extract order when administered, suggesting further research is required to determine if a possible stage in development is crucial in confidently proving this. Further research may entail an assay with a simpler food delivery system, a finer control of water flow, and histological studies in comparison of cichlid juvenile in various stages of development, as to determine significant olfactory or brain tissue differences.