Office of Undergraduate Research
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Emphasizing equitable and inclusive access to research opportunities, the University of Maryland's Office of Undergraduate Research (OUR) empowers undergraduates and faculty to engage and succeed in inquiry, creative activity, and scholarship. This collection includes materials shared by undergraduate researchers during OUR events. It also encompasses materials from Undergraduate Research Day 2020, Undergraduate Research Day 2021, and Undergraduate Research Day 2022, which were organized by the Maryland Center for Undergraduate Research.
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Item Exploring Olfactory Cues: Behavioral Responses in Cichlid Juvenile to Food and Amino Acid Stimuli(2024) Leary, Maurice; Gable Parker, Coltan; Juntti, ScottCichlid 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.Item Generating Algorithms for Hot Spots Policing(2024) Versace, Nathan Rios; Arellano, Trina; Chen, Alex; Du, Allen; Eichstadt, Andrea Maria; Lin, Aaron; Samuels, Coley; Tao, Grace; Tasneem, Zoya; Hajiaghayi, Mohammad TaghiLarge police departments have come to rely on algorithms to predict where crime will occur, such that they can better allocate resources to communities that need them. While these algorithms have been shown to reduce crime, they are not built to account for historical bias in training data, especially against racial and class minorities. As a result, they run the risk of reinforcing historical prejudice against these already persecuted groups. The aim of team GAHSP is to address these inherent issues with predictive policing while also improving on crime-prediction accuracy. Using modern Machine Learning techniques, better data cleansing/weighting, and algorithm stopgaps such as unfairness penalties, we aim to construct an algorithm which has the benefits of better crime prediction while minimizing bias in ways that past algorithms have not attempted or succeeded at doing.Item Gluten Quantitation in Fermented Sourdough Using a Multiplex-Competitive ELISA(2024) Parimi, Manasvini; Galanis, Christina; Panda, RakhiBackground: Gluten in wheat, barley, and rye can cause adverse reactions in individuals with Celiac disease, who need to follow a strict gluten-free diet. There are regulations in place that defines gluten-free. Accurate quantification of gluten in different foods, including fermented and hydrolyzed foods, is necessary to comply with the gluten-free regulations. Here we report a multiplex-competitive ELISA for the quantification of gluten in fermented sourdough. Methods: Gluten-incurred sourdough using four types of sourdough starters were prepared. The starter cultures were combined with rice flour, water, incurred with 8, 20, and 100 ppm wheat gluten, and fermented for 72 hrs. Samples collected every 24 hours were analyzed by a multiplex-competitive ELISA that uses a gluten-incurred yogurt calibrant and six gluten specific antibodies. Gluten concentrations in the samples were estimated using a four-parameter logistic (4 PL) regression. Results: The quantitative values from two out of six antibodies used in the ELISA were used to estimate the gluten concentrations in the sourdough samples. The average gluten recovery was between 55-195% for all samples. The coefficient of variation (%CV) ranged between 2-31%. Implications: The average % recovery for most sourdough samples were within acceptable range of 50-150%. Few samples showed recovery up to 200%. The %CV for most samples were ≤ 20%. These results indicate that the multiplex-competitive ELISA can provide accurate and precise quantitation of wheat gluten in fermented sourdough. The effects of heat treatment and several other variations in sourdough preparation on quantitation is currently being evaluated.Item Exploring the Effect of Putative PGF Synthase Genes in A. Burtoni Cichlid(2024) Amini, Cyrus; Jackson, Peter; Juntti, Scott; Li, Cheng-YuExploring the Effect of Putative PGF2α synthase genes in A. burtoni Cichlid ProstaglandinF2α (PGF2α) drives reproductive behaviors in different species as a hormone and pheromone. In African Cichlids, fertile females produce high levels of PGF2α which are converted to PGF2α metabolites. These metabolites signal and induce male preferential behavior. However, the mechanism behind the synthesis of PGF2α is widely unknown. Using A. Burtoni, we hypothesize that Aldo-Keto Reductase (AKR) enzymes are the putative PGF2α synthases; we proceeded to test the effect of a knockout of AKR using CRISPR-Cas9. In African Cichlids, two paralogs of AKR genes, LOC102291490 and LOC102291786, are hypothesized to be involved in PGF2α synthesis. However, individual knockout (KO) of either enzyme did not result in any significant change in the reproductive behaviors; we predicted that KO of both would result in lower PGF2α levels, circling bouts, and pecking in females. We targeted LOC102291490 in animals already carrying LOC102291786 d53/d53 homozygous mutations and recovered two mutant genotypes, d4 and d12d2. We had two tanks, each containing about 15 mixed-sex WT siblings or dual-KO fish, allowing undisturbed mating. Both tanks were live-recorded and reviewed to compare the male-female interactions between the genotypes. We surprisingly discovered a dual-KO male mouthbrooding eggs, complementing that PGF2α suppresses male mouthbrooding behavior via pheromone signaling. Additional investigation is necessary to examine whether PGF2α signaling suppresses male appetite and if males can discern between food and eggs. This study aids in our comprehension of reproductive behaviors and the mechanisms of hormone and pheromone-mediated behaviors.Item Instrument Design for Low-Temperature Infrared Spectroscopy of Materials(2024-04-17) Dietrich, Matthew; Dodson, LeahSolid material analysis has come a long way in its ability to accurately characterize the structure of bulk materials progressing from magnifying glasses to today’s atomic resolution instruments. Present common techniques include the use of various IR spectroscopies to determine the structural properties of these materials. Typically, these methods are low-resolution and are used to pinpoint only a few vibrational modes in the material’s structure. In addition, these studies are either done near room temperature or at one temperature setting. This poster presents a custom-built cryogenic FTIR instrument that is capable of characterizing a given material from room temperature down to 30K with < 2 cm-1 resolution. Shown to the right and below is the design, creation and specific components of the cryogenic instrument, future plans include incorporating gas-species dosing to allow for gas adsorption experiments. The Dodson laboratory is one of few labs capable of cryogenic IR analysis of various metal and covalent-organic frameworks using these necessary techniques to fully characterize the changes in structure and vibrational modes of these materials as they approach extremely low temperatures.Item Functional characterization of nuclear receptor NR1D1 on investigation of brain metastasis(2024) Berroya, Arryn Joeina Mercado; Klotz, Remi; Wang, Yiru; Yu, MinBrain metastasis is a fatal recurrence of advanced cancer that affects 20% of cancer patients. Capturing comprehensive brain metastasis landscape is critical to the establishment of sufficient and effective anti-tumor strategies. Ongoing research efforts in our team aim to better understand the biology of tumor cells in human brain metastasis. Preliminary data, generated by single cell sequencing of human brain metastases highlighted a potential role of the nuclear receptor NR1D1. Indeed, NR1D1 activity seems to be correlated with proliferation, immune evasion, and metabolism of brain metastatic tumor cells. The activity of this nuclear receptor can be controlled by its ligand Hemin (HEME) and is critical in retaining control of the circadian rhythm. Our aim is to investigate the functional properties of NR1D1 itself through breast cancer cell lines. Breast cancer cell lines, SUM190, MDA-MB-231 and JIMT1 were used to study NR1D1 function and undergone multiple treatments with conditions that consisted of exposing HEME and a synthetic agonist in various incubation times while adjusting media with no FBS, essentially starving the cells from creating their own HEME. In publicly available data sets it was found that low NR1D1 expression correlated with increase of Triradylglcerols metabolism and high NR1D1 expression with increase of amino acids and peptide metabolism. In addition, our data suggests that NR1D1 activation leads to cell morphology changes and future experiments will determine whether NR1D1 influences tumor cell proliferation and immune invasion. This will assist in determining discrete phenotypes of brain metastatic tumor cells and new approaches for treatment.Item Mapping the heterogeneity of the human senescent proteome(2023-08-04) Cunningham, Ana S.G.; Tsitsipatis, Dimitrios; Anerillas, Carlos; Banarjee, Reema; Gorospe, Myriam; Herman, Allison B.; Singleton, Andrew; Mazan-Mamczarz, Krystyna; Qi, Andy; Yi, Ziyi; Hao, Ying; Basisty, NathanCellular senescence is a unique response to sublethal stress characterized by at least two elements: persistent cell cycle arrest and a senescence-associated secretory phenotype (SASP). Recent evidence suggests a close link between senescence and aging, as selective elimination of senescent cells in mice improves longevity and overall health. Therefore, there is increased interest in identifying markers to develop drugs (senolytics) that selectively eliminate senescent cells without harming healthy, proliferating cells. However, senescent phenotypes vary across cell types and inducers, creating a need for tissue-specific markers of senescence. To this “senescence catalog” has three aims: 1) Identify protein and RNA markers of senescence; 2) Compare across models to find overlapping markers; and 3) Validate markers with scRNA-seq and IHC in culture and in mice.Item Cavity Ringdown Spectroscopy System Design for Astrochemical Studies(2024) Ganley, Shannon; Howard, Thomas; Dodson, LeahCavity ringdown spectroscopy (CRDS) is a highly sensitive technique that allows for the detection and analysis of extremely dilute chemical species. This tool is particularly useful for the collection of high-resolution spectra of molecules of astrochemical interest, which can be used to assist molecular detection efforts and improve our understanding of the chemistry that can occur in space. We present two iterations of a near-IR (1.5 µm) continuous-wave CRDS system which has been under development at the University of Maryland. HCN is chosen as a test molecule for each of these systems due to its importance in astrochemistry and its well-studied—experimentally and theoretically—spectra in the infrared. The rovibrational spectrum of the first overtone of the C-H stretch is analyzed on each system at room temperature, and in our newest system at cryogenic temperatures. The rotational temperature of HCN is calculated from this spectral data, and will be used in future work to quantify the rotational energy of neutral gaseous species for kinetics studies.Item Tracking animal identities with machine learning to analyze cichlid aggression(2024) Edwards, Michael; Westbrook, Molly; Juntti, ScottAggression is a central characteristic of social animal behavior that can drive early life development. We can use the social cichlid fish Astatotilapia burtoni as a model to study aggression by analyzing stereotyped chase behaviors defined by simple metrics such as changes in velocity. This enables a computer based data collection process, streamlined through the use of the SLEAP machine learning program. This method seeks to translate large quantities of cichlid video into positional coordinate data of multiple points on the animal’s skeletal limbs. Refining how SLEAP tracks animal identity through video improves the quality of positional data by labeling positional tracks with unique animal identities. SLEAP applies three primary parameters to match identities across frames: tracker methods create an initial positional estimate based on movement prediction, similarity methods connect two instances of identified fish from one frame to the next, and matching methods score each identity connection and optimize those scores. A variety of test cases examined the three parameters, Kalman filter application, and a diversified training data set to reduce the rate of identity swap based errors. Performance of these test cases were measured by the rate of identity errors relative to the other test cases, and tested across a variety of video examples differing by inclusion in the training data set and known machine learning model performance. The analysis of these relative error rates demonstrated a reduction of up to 79% of identity swap occurrences, which illustrates a significant improvement in the ability of the machine learning model to maintain separate animal identities.Item Identifying Difficidin in the Supernatant of Bacillus velezensis using High Resolution Mass Spectrometry(2024) Nasisi, Benjamin; Jenkins, Conor; Jermain, Madison; Winkler, WadeDifficidin is a naturally occurring extracellular antibiotic produced by Bacillus velezensis. The dfn operon encodes for the difficidin biosynthesis proteins. This operon (dfn) is transcriptionally regulated by intrinsic transcription termination sites that are spread throughout the 70 kilobase operon and that limit dfn expression. LoaP is a specialized transcription elongation protein that promotes readthrough of these terminators. We hypothesize that LoaP associates with RNA polymerase to promote readthrough of the termination sites; however, the LoaP regulatory mechanism is still unknown. We have constructed different bacterial strains containing mutations in LoaP. Yet, we do not have an assay for measuring the impact of these mutations on the regulation of the dfn operon. This study seeks to address this problem by developing a method to quantify difficidin. Specifically, we will establish a mass spectrometry-based detection assay to identify the levels of difficidin under various conditions. Three strains - wild-type, ΔloaP, and Δdfn - were utilized to test native levels, low levels, and absence of difficidin, respectively. Strains were grown overnight to an OD600 of 2 in 150 mL of rich medium (LB broth). Cells were pelleted and extraction of difficidin was performed by incubation of the supernatant at 4°C overnight with Amberlite XAD-16 resin. Metabolites were then eluted from the resin using 8 mL of methanol and analyzed by mass spectrometry. Data for the three strains were compared against each other to identify the retention time of difficidin. The WT strain had an intense cluster of peaks at a retention time of 17-19 minutes. These peaks completely disappeared in the Δdfn strain. The disappearance of a peak in the Δdfn strain that is present in the WT strain is a strong indication that difficidin has been identified. Further tests using the fragmentation of the metabolites at the retention time determined are required to confirm whether difficidin has been identified by mass spectrometry.