Summer Undergraduate Research Conference 2024
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Item Optimization of an in-house bacterial cell-free expression system to evaluate the design of toehold switch sensors for selected cervical precancer miRNA biomarkers(2024-07-19) Meyer, Jonathon; Zeidan, Quira; Spirito, CatherineCervical cancer is a significant health burden for women across the globe. However, over 94% of all cervical deaths occured in low and middle income countries (LMICs) in 2022 alone. This reflects a broader trend of a lack of access to quality treatment options for cervical cancer due to socioeconomic barriers including limited trained professionals, financial resources, and access to proper screening. We are partnering with UMaryland iGEM, an undergradutate-led synthetic biology research team, to assist in the development of a low-cost, point-of-care screening device for detecting commonly upregulated miRNAs in cervical precancer patients to address this issue. The functionality of this device relies on a cell-free expression kit, referred to as a lysate, in order to properly transcribe the desired toehold switches in the paper-based assay and translate the fluorescent protein output. However, common commercial cell-free lysates are expensive which increases the cost of producing our device – ultimately hindering its accessibility in LMICs. To address this problem, we propose a method for producing and optimizing our own in-house cell-free lysate. In our method, we compare three lysates – commercially available myTXTL, a lysate developed by the Aberdeen Proving Ground, and our own lysate – using varying ratios of energy mix, lysate, and T7p14 deGFP HP plasmid to evaluate the ideal composition of these components for a cell-free expression kit. We quantify these relationships using fluorescence in order to determine the efficacy of our lysate and the ideal ratio of components for a cell-free, paper-based assay.Item Using site-directed mutagenesis to engineer human ribosomal protein variants(2024-07-19) Neuman, Robert Keller; Bornhorst, Xavier; Liu, Annie; Guevara, Ivan; Zeidan, QuiraWe used a site-directed mutagenesis (SDM) protocol to create plasmid constructs through substitution and deletion. When the pmTurquoise plasmid containing the coding sequence for human ribosomal protein (RP) S6 was originally synthesized, a single nucleotide was added, shifting the reading frame of the mTurquoise gene out of line with RPS6. SDM was used to delete nucleotide 3619 and restore the fusion protein reading frame. Since we are using these plasmids to study the extraribosomal functions of RPS6, two different plasmids were constructed with this deletion: control (pmTurquoise-N1-RPS6) and one containing a nuclear export signal (pmTurquoise-NES-RPS6). On a pNH-TrxT bacterial expression plasmid containing the coding sequence for human RPS3A, SDM was also used to substitute amino acids at positions previously identified as post-translational glycosylation sites. On this plasmid, the serine at position 59 and the serine at position 154 in the wild-type RPS3A sequence were substituted individually with alanine to disrupt the residue targeted by the modification. Mutagenesis efficiency was estimated at >80% by blue-white colony screening of control reactions, and designed nucleotide changes were confirmed by plasmid DNA sequence analysis. The constructs on the pmTurquoise backbone will allow us to study the activity of RPS6 in the cytoplasm upon transfection into HEK293 cells. The pNH-TrxT-RP plasmids will enable bacterial protein expression and affinity purification of human RPs from soluble and insoluble fractions for subsequent in vitro glycosylation assays.Item Improved Silicone Fish Tail Actuator With Variable Stiffness(2024) Abrishamian, Shirah Shoshanah Ariel; Huertas-Cerdeira, Cecilia; Johnson, Lena; Huertas-Cerdeira, Cecilia; Johnson, LenaIn a continuation of research presented at The University of Maryland Undergraduate Research Day, this work will document improvements on a fish-inspired robot actuator. Bio-inspired robotics is an interdisciplinary field offering advantages that diversify robot designs and improve functionality. Incorporating soft robotics techniques into bio-inspired designs expands the potential of new robots. A common research subject is fish-inspired robots, due to the several possibilities of experimentation. A fish’s naturally flexible body and reaction to the hydrodynamics of its environment provide useful inspiration for robots of similar design. In the question of improving the efficiency of robot performance in water, it can be seen in nature that several fish such as tuna adjust their swimming behaviors through tunable musculature. Prior research has observed muscle stiffness to impact swimming efficiency. This study aims to develop a silicone fishtail capable of variable stiffening. Previous experimentation resulted in a molding process, producing a thick prototype fin with cavities in which stiffening material is placed and the air vacuumed out - stiffening the fin. This work details the refinement of this process to create a fin that further meets the design specifications. The tail must be 150 millimeters wide at the tip and 10 millimeters thick. The new design process introduced a higher-quality silicone rubber, and a more in-depth preparation process, including a vacuum chamber. The new mold designs are easily adjustable to 3D print cavities of more complex geometries. Furthermore, the new molding process improved the assembly and overall fin aesthetic. The internal cavities were successfully compressed after attaching the fin to a 4.5-volt combined vacuum and pump. Further design includes quantitatively measuring this stiffness and performance in a flow.Item Children’s evaluations of peers who confront gender bias in science contexts(2024-08-05) Kumar, Anusha; Forbes, Marley; Killen, MelanieBeliefs about gender and science, technology, engineering, and mathematics (STEM) abilities emerge early in childhood and negatively impact STEM belonging and motivation. This study examines how children and adolescents evaluate and reason about peers who confront gender bias in the context of science leadership opportunities within peer groups. Using individual interviews, an initial sample of ethnically and racially diverse 8- to 14-year-olds (N = 28, Mage = 10.99, SDage = 1.98) were shown vignettes about a group of kids their age at a science competition and were asked to give predictions, evaluations, and reasoning about the characters in the story. Initial results show that children and adolescents expected peers disadvantaged by bias (M = 4.57, SD = 1.26) to be more likely to confront the group's bias than peers advantaged by the bias (M = 4.07, SD = 1.25). However, participants viewed peers advantaged by bias as more effective in their confrontations (M = 4.46, SD = 1.29) compared to peers disadvantaged by bias (M = 4.11, SD = 1.13). This pattern was particularly strong when girls are the group disadvantaged by bias, but not when boys are the disadvantaged group. These preliminary results provide initial evidence that children understand that individuals occupying different positions in a system of bias differ in their likelihood of challenging such bias, but also in their effectiveness in changing the bias in the future. Results also suggest children recognition of the asymmetry of gender and status in STEM contexts. This study contributes important insights into children’s developing capacities to make science spaces more inclusive.Item Arianna's Mosaics: A Survey of the Villa Arianna's Mosaics(2024-07-19) Korth, Stephanie; Williams, JosephArianna’s Mosaics A Survey of the Villa Arianna’s Roman Mosaics investigates the art historical context behind the creation, function, and experience of the floor mosaics of the Villa Arianna in Roman Stabiae (1st century BCE - 1st century CE) based on original archaeological documentation in the form of measured line drawings of select floors and photographs throughout the excavations. The measured digital drawings are made with the assistance of Light Detection and Ranging (LiDAR) and Photogrammetry technologies. All data collection for this project was conducted on-site at the Villa Arianna, including photographs and measurements. Orthophotos (non-perspectival photographs created with photogrammetry) were made from some of the best preserved mosaiced rooms and door thresholds and then scaled to LiDAR measurements to produce high-quality measured line drawings. High-quality illustrations not only aid in the research project for which they are created but also contribute to the wider scholarly community as interpretative tools for facilitating understanding. The research from this project examines the chronology of the Villa Arianna’s mosaics in relation to the overall decoration of the rooms, particularly their response to the development of the villa’s fresco program. The Villa Arianna, located in Stabiae Italy, was preserved by ash from the eruption of Mt. Vesuvius in 79 CE and excavated in the eighteenth century. The mosaics have not been well studied, but the leaders of the University of Maryland Villa Arianna survey have recognized their substantial integration with the rest of the visual and spatial program, which included frescoes, gardens, water features, and framed views. This research applies a mixed methodology to the study of the mosaics within the villa, connecting their creation processes, functions of use, iconography, and concepts of space. Furthermore, this research investigates if there is a visual sequence within the decoration of the rooms intended to guide the movements of the viewer.Item Interactions Between Pdlim7 and Yap1 during Trigeminal Ganglion Neurodevelopment(2024) Young, Liesl; Leonard, Carrie; Taneyhill, LisaIn the genetic disorder familial dysautonomia (FD), mutations in elongator acetyltransferase complex subunit 1 (ELP1) cause severe nervous system phenotypes. Abnormal development of the trigeminal nerve results in decreased facial pain and temperature perception in FD, but the molecular mechanisms leading to these sensory deficits are poorly understood. Preliminary data from an FD mutant mouse model suggest loss of Elp1 increases expression of Pdlim7 and several proteins in the Yap1 signaling pathway. Pdlim7 promotes activation of Yap1 through direct binding in other contexts, but the role of Pdlim7 in trigeminal sensory neuron development has not been described. Furthermore, it is unclear how dysregulation of Yap1 through increased Pdlim7 expression may contribute to FD neuronal phenotypes. To address this, I characterized the normal expression of Pdlim7 and Yap1 in embryonic mouse trigeminal ganglion neurons. Through immunohistochemistry, I found that Pdlim7 is expressed in the cytoplasm of early trigeminal ganglion neurons. Yap1 is also expressed in several cell types, including some neurons, while the active form of Yap1 was enriched in neural crest cell precursors and placodal neurons. Using immunoblotting, I determined that Pdlim7 and Yap1 levels and activation change across developmental timepoints in trigeminal nerve target tissue. Co-expression and biochemical interaction of Pdlim7 and Yap1 indicates their potential role in trigeminal neurodevelopment. The results of this project have improved our understanding of the functions of Pdlim7 and Yap1 and provide a basis for further study of how altering Pdlim7 and Yap1 pathways may disrupt neurodevelopment in FD.Item Vanishing Ice: Simulating Changes in Atmospheric Circulation(2024-07-19) Majithia, Himani; Srinivasan, Sujay; Strey, Sara TItem IMPACT OF WRF-ARW CLOUD FRACTION ON ARCTIC ALBEDO FOLLOWING EXTREME SEPTEMBER SEA ICE CONDITIONS(2024-07-19) Chakraborty, Ishaan; Lingala, Divya; Mehra, Sophiya; Strey, Sara TItem Comparing Land Surface Models During the São Paulo February 2023 Flood(2024-07-19) Alvarenga, Mario; Fan, Vanessa; Vu, Tyler; Strey, Sara TItem Optimization of an in-house bacterial cell-free expression system to evaluate the design of toehold switch sensors for selected cervical precancer miRNA biomarkers(2024-07-17) Meyer, Jonathon; Zeidan, Quira; Spirito, CatherineCervical cancer is a significant health burden for women across the globe. However, over 94% of all cervical deaths occured in low and middle income countries (LMICs) in 2022 alone. This reflects a broader trend of a lack of access to quality treatment options for cervical cancer due to socioeconomic barriers including limited trained professionals, financial resources, and access to proper screening. We are partnering with UMaryland iGEM, an undergradutate-led synthetic biology research team, to assist in the development of a low-cost, point-of-care screening device for detecting commonly upregulated miRNAs in cervical precancer patients to address this issue. The functionality of this device relies on a cell-free expression kit, referred to as a lysate, in order to properly transcribe the desired toehold switches in the paper-based assay and translate the fluorescent protein output. However, common commercial cell-free lysates are expensive which increases the cost of producing our device – ultimately hindering its accessibility in LMICs. To address this problem, we propose a method for producing and optimizing our own in-house cell-free lysate. In our method, we compare three lysates – commercially available myTXTL, a lysate developed by the Aberdeen Proving Ground, and our own lysate – using varying ratios of energy mix, lysate, and T7p14 deGFP HP plasmid to evaluate the ideal composition of these components for a cell-free expression kit. We quantify these relationships using fluorescence in order to determine the efficacy of our lysate and the ideal ratio of components for a cell-free, paper-based assayItem Exploring the Impact of Prenatal Drug Exposure on Brain Development: Data Collection Framework(2024) Sare, Perfect; Jones, Morgan; Chi, Zehua; Riggins, TracyUnderstanding brain development is a critical area of neuroscience requiring comprehensive research. Numerous factors, including prenatal drug exposure (PDE), significantly influence both pre- and postnatal brain development. The HEALthy Brain and Child Development (HBCD) Study is a longitudinal study that aims to explore these impacts and advance our knowledge of early brain and child development. It utilizes multiple, carefully curated methods to obtain physiological data from participants, including diverse patient recruitment, biospecimen collection, and various MRI scans. This poster will address these methods of data collection and how they will contribute to future research. 2Item BioCascade Exhaled Breath Sampler (BEBS): Sample Viability(2024) Chartrand, Ansley; Coleman, KristenThe viability of samples collected in the BioCasade Exhaled Breath Sampler (BEBS) machine is to be measured by simulating an exhaled breath sampling event via a Collison nebulizer. There are four stages the nebulized stimulants are divided into within the BEBS system, they divide the particles based on size. The stages are labeled large, medium, small, and BioSpot and they collect particles of sizes >8.2µm, 3.3-8.2µm, 1.15-3.3µm, and <1.15µm respectively. Similar experiments have been done to examine the viability of collected samples in the BEBS system but all are done at lower collection flow rates, where this test collects at 12 lpm. In addition, this experiment collects the nebulized virus onto a hydrogel surface as opposed to previously used liquid mediums. PR8 virus will be used as the model to simulate the collection of influenza viruses. The purpose of this experiment is to recreate real-world collection data to ensure the BEBS efficacy for collecting culturable samples prior to clinical use in the EMIT-2 study.Item 222 nm UV Disinfection of Bacteriophages as Surrogates for Eukaryotic Viruses(2024) Lim, Mariana K.; Fadaka, Esther A.; Coleman, Kristen K.Germicidal ultraviolet (GUV) radiation, particularly shortwave UV-C (200-280 nm) is a promising technique used for disinfection of several microbiological targets. In the wake of the COVID-19 pandemic, its use for disinfecting eukaryotic viruses has garnered attention as an intervention to prevent transmission of airborne respiratory viruses. This study examines 222 nm GUV, primarily in liquid, and uses various bacteriophages (MS2, Phi6, T1, and T4) as surrogates to model eukaryotic viruses, aiming to broaden current understanding of GUV disinfection efficacy and virus models. Usage of bacteriophages (RG1 organisms) as virus surrogates serves as a low risk alternative to handling pathogenic viruses (RG2 organisms), allowing for safer infectious disease transmission mitigation research. UV exposures of bacteriophages were conducted in a collimated beam chamber designed according to Bolton and Linden (2003) [1], which was validated using iodide/iodate actinometry. For MS2 phage experiments, approximately 0.75, 1.1, 4.5, and 6.4 log reductions in PFU/mL were observed following UV exposures of 2.5, 5, 15, and 30 minutes (fluence of 7.60, 15.22, 45.65, 91.29 mJ/cm2), respectively. Liquid experiments with other phages are still ongoing. Continued efforts will also explore 222 nm disinfection in an aerosol state via a single pass flow chamber, using the same virus models as in liquid. Future work will also repeat all experiments with eukaryotic viruses such as influenza to compare virus behavior to that of the phages. [1] Bolton, J. R., & Linden, K. G. (2003). Standardization of methods for fluence (UV dose) determination in bench-scale UV experiments. Journal of environmental engineering, 129(3), 209-215.