Undergraduate Research Day 2024

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

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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, Nathan
Cellular 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.
Identification of fikk gene expression specific to severe malarial syndromes in Malian children
(2023-10-13) Kapadia, Sarika; Lawton, Jonathan; Stucke, Emily; Travassos, Mark
Plasmodium falciparum is the most common and virulent malaria parasite. As the primary species responsible for severe malaria, it continues to be a leading cause of mortality in the developing world. Children under the age of five are overwhelmingly affected, accounting for most deaths from malaria. P. falciparum is unique among Plasmodium species for having multiple members of the fikk multigene family, which encodes serine/threonine kinases. During intra-erythrocytic infection, P. falciparum actively exports 18-26 FIKKs into the infected erythrocyte. These kinases are predicted to facilitate the activation and trafficking of membrane proteins within infected erythrocytes, contributing to the remodeling of the erythrocytic membrane and its highly variable surface antigens. Given the association of parasite erythrocyte surface antigens and severe malarial disease, we hypothesized that severe malaria cases feature elevated expression of a subset of fikks compared to matched uncomplicated malaria controls. We investigated the differential expression of fikk kinases in severe clinical syndromes of P. falciparum malaria in a matched case-control study in Mali. Using a custom pipeline, we compared fikk expression in cases of cerebral malaria (CM), severe malaria anemia (SMA), and a combined syndrome featuring both CM and SMA (CM+SMA) to matched uncomplicated malaria controls (UM). Preliminary findings with 64 total subjects indicate the differential expression of several fikks in severe disease compared to matched controls. One fikk gene had significantly increased expression in CM cases compared to matched uncomplicated malaria controls (N=14 pairs, P<0.02; Wilcoxon signed-rank test). We identified a characteristic fikk expression profile specific to the combined CM+SMA syndrome involving four FIKKs. We are examining host immune responses to FIKK proteins using a custom protein microarray. We are assessing the suitability of a subset of FIKKs as targets for vaccine and therapeutic development for severe malaria, particularly if they are natural targets of the host immune system.
HIPPOCAMPAL VOLUME, CAREGIVER CHANGES, AND FAMILY COHESION IN ADOLESCENTS WITH PRENATAL DRUG EXPOSURE
(2023-10-15) Booker, Jonathan; Kohn, Brooke H.; Riggins, Tracy
Prenatal exposure to drugs has been associated with changes in neurocognitive development, such as delays in language development and sensorimotor development. However, the effects of prenatal drug exposure (PDE) can also be modified by the postnatal environment. The present study explored associations between PDE and postnatal family functioning on adolescent brain development. Parent-infant dyads were enrolled at delivery from an urban University Hospital. Eligibility included positive (cocaine/heroin) maternal/infant urine toxicology or maternal self-report of cocaine/heroin use during pregnancy. A Community Comparison (CC) sample, of the same age and key demographic, was enrolled at age 6 years. Caregiver changes were documented every six months throughout the first 7 years of the study. Adolescents (N = 50) completed structural MRI scans. Volumetric segmentation of the hippocampus was performed using FreeSurfer v5.2. Hippocampal volume was adjusted for intracranial volume, age, and sex. At this time, caregivers and adolescents also reported on family functioning by completing the Self-Report Family Instrument. The subscales of interest were family cohesion and health competence. Participants with PDE had more caregiver changes, reported less family cohesion, less health competence, and had larger hippocampal volumes compared to the CC group. Additionally, within the PDE group, caregiver changes were correlated with right hippocampal volume; however the bilateral hippocampal volumes of those with any history of caregiver changes vs none were not significantly different. Overall, findings demonstrate lasting impacts of PDE but suggest that postnatal caregiving environments may also contribute to neurodevelopment.
The Effect of Light Duration on Methane Emissions
(2023-12-07) Patel, Pooja; Paranthaman, Nivitha; Kesler, Elijah; Nguyen, Cat; Rivello, Elena; Cano, Elielka; Niu, Danielle
Lab-on-CMOS-Capacitance Sensor Array for Real-Time Cell Viability Measurements
(2024) Dasgupta, Prithwish; Nielsen, Kyle; Abshire, Pamela
This project addresses the need to enhance the functionality and reusability of existing CMOS chips for monitoring cell viability and facilitating visual inspection. The primary challenge tackled is the reduction of research downtime due to inefficient sensor replacement and the improvement of data collection methods. To achieve this, the project integrates PCB design software, CAD software, and programming languages, including VHDL, C, and MATLAB. PCB design is utilized to create strategic board configurations aimed at streamlining the data collection process and ensuring the creation of a reliable and replaceable cell viability measurement device. These methods synergistically enhance CMOS chip functionality and usability, with a focus on streamlining packaging, facilitating hot-swappable system development, and establishing a data readout system. Key achievements encompass the development of a hot-swappable system for effortless CMOS chip replacement, streamlined packaging to bolster chip longevity, and the establishment of a real-time data readout system. These advancements notably enhance research efficiency and data quality by minimizing downtime and improving the correlation of capacitance measurements with direct visual observations of cell behavior. In the broader context of lab-on-a-chip technology and sensor development, these achievements deepen our understanding of cell behavior and expedite progress in drug screening, disease diagnostics, and tissue engineering. The integrated approach presented in this research marks a significant advancement in pushing the boundaries of lab-on-a-chip technology and its applications in biomedical research.
Gamera-S: Designing and Flying a Manned Solar-Powered Helicopter
(2024) Yang, Han; Farren, Emma; McLenagan, Devin; Chopra, Inderjit; Nagaraj, Vengalattore
The University of Maryland's Solar Gamera, or Gamera-S, is a solar-powered quadrotor that has demonstrated piloted flights using only on-board solar panels. Made of carbon fiber and mylar, the structure remains lightweight yet durable, allowing for the achievements in flight accomplished by Gamera-S thus far. There are several solar-powered rotorcrafts that are unpiloted, most significantly being the NASA drone exploring the Martian surface. This creates a question: can we make a viable solar-powered rotorcraft for piloted flight? Gamera-S currently holds the record of 9 seconds in hover at an altitude of 0.1 meters. The team aims for a new flight record of 60 seconds in sustained hover. To achieve this, rotor blade twists are being studied through parametric modeling and finite element analysis to optimize the power efficiency. Scale prototypes of the rotors will also be developed and tested in wind tunnels to validate the optimization outcome. In addition, attitude feedback control methods are being surveyed to improve flight stability and pilot control in the presence of gusts and ground effects. The control law will be verified in SiL simulations prior to being implemented on custom avionics hardware. Furthermore, methods to mitigate power fluctuations and losses, including the addition of bypass diodes and MPPT charging circuits, will be investigated. The effectiveness of such methods will be tested and quantified through solar panel shade testings. Lastly, full-scale flight tests will be conducted to demonstrate that a sustained, or even perpetual, flight through a manned solar-powered helicopter is possible.
Optimizing the expression, solubility, and purification of human ribosomal proteins SA, S2, S7, and S12 in E. coli to analyze post-translational modifications in vitro
(2024) Goshtasbi-Gowharrizi, Athra; Martin, Jacob; Streit, Julia; Zeidan, Quira
DNA Aptamers Against Airway Mucin Proteins for Therapeutics and Diagnostics
(2024) Dwomoh, Deborah; Welte, Linara; Savage, Colin; McDonald, Cyan; Shpilman, Zackary; Srinath, Priyanka; Spirito, Catherine
Mucus is a viscous bodily fluid composed of mucin proteins, inorganic salts, and water. MUC5AC and MUC5B are the two mucin proteins that makeup airway mucus. Elevated levels of MUC5AC can indicate certain diseases, like asthma and Chronic Obstructive Pulmonary Disease (COPD). Current treatments for mucus-associated respiratory diseases include using enzymes and chemical agents to clear mucus buildup. These existing treatments are limited in their ability to selectively target specific mucin proteins within mucus. Our research aims to select DNA aptamers that bind to MUC5AC or MUC5B, within mucus samples. We are optimizing a One-Pot SELEX or in vitro selection methodology previously used by other researchers to select aptamers against MUC16. Selected DNA aptamers with high binding affinity and specificity can detect airway mucin proteins and deliver engineered proteases to cleave and destroy them.
Investigating the Role of Glutamine Metabolism on Bacteriophage Replication
(2024) Goodwin, Gabriel ; Altberger, Hannah ; Varghese, Riya ; O'Hara, Jessica
The emergence of antimicrobial resistance demands more effective alternative treatments such as phage therapy. To further explore treatments, this research attempts to better understand bacteriophage replication. The TCA cycle is a crucial metabolic pathway in E. coli, responsible for providing bacteria with energy, which includes pathways such as glutamine-synthesis and glutamine degradation. It is known that bacteriophage requires energy and nutrients to perform viral replication. We chose to knock out genes glnA (present in glutamine-synthesis), glsA, and glsB (both present in glutamine degradation). This research examines the importance of glutamine in these metabolic pathways. To determine the role of glutamine in T4 bacteriophage replication, growth and phage replication dynamics in the different strains were compared. Growth and lysis curves were conducted in rich LB media to understand patterns in optimal nutrient conditions, while also in M9 minimal media with a small glucose concentration and varied glutamine concentrations. This data was used to determine optimal glutamine concentrations for growth and lysis. Phage replication differences in the strains were further analyzed via phage titer and burst size. The glsB strain showed increased phage replication, and glnA had decreased replication. These results indicate what genes are necessary for optimal phage replication. Our research will assess the selected knockout genes to understand which aspects of the metabolic pathway are more influential on bacterial lysis. Further research will help illuminate the role of glutamine metabolism in T4 phage replication and have implications for improving phage therapy.
Alterations in Retinal Blood Flow Autoregulation in Human Subjects with Early Glaucoma as measured with Laser Speckle Imaging
(2024) Porwal, Yash; Gill, Amrik; Ventimiglia, Mary; Mansoor, Shaiza; Sinha, Avigyan; Rege, Abhishek; Saeedi, Osamah
Attention! Data Helps Diagnoses: A machine learning approach to predicting ADHD
(2024) Navaleza, Irene; Coutts, Jacob
Attention deficit hyperactivity disorder (ADHD) is often dismissed as a “childhood condition”, since easy-to-identify features (e.g., hyperactivity) are more prevalent in children. Yet, for almost half of diagnosed individuals, the effects of ADHD persist through adulthood, impacting important areas such as jobs/academic performance and relationships. These implications make early diagnoses and effective treatments salient issues for medical professionals. However, as ADHD affects brain development, symptoms often greatly vary person to person. Further, research suggests that the high comorbidity of ADHD with other disorders compounds this issue, explaining why many diagnoses do not come until adulthood. One solution to more accurate diagnoses is machine learning, a class of models that have become increasingly prevalent in research. However, few researchers have developed models to predict ADHD diagnoses. In this study, we performed a secondary data analysis from a study on 103 anonymous participants (51 diagnosed with ADHD, 52 clinical controls). We employed a K-nearest neighbors algorithm to identify key features of ADHD (e.g., prevalence of comorbid disorders) that can accurately predict one’s diagnosis. The results of our analysis suggest: 1.) Objective metrics like this may improve ADHD diagnoses, since current methods are subjective and vary by physician, 2.) Some comorbidities are more predictive than others, and 3.) Research should continue in this area to include more predictive features. Implications for practitioners and researchers are discussed.
Exploring Mental Health Stigma: Associations Between Health History and Social Stigma
(2024) Clarke, Jason; Fuchs, Joelle; Gard, Arianna
Forty-six million people aged 12 or older met the DSM-5 criteria this past year for substance use disorder (SUD). SUD, marked by the inability to control or cut down on substance use paired with clinical impairment, is linked to negative health and well-being across the life course. Individuals with mental illnesses face self-stigma, social stigma, and institutional stigma. Levels of stigma vary based on mental illness, with SUD being one of the most stigmatized disorders due to the belief that addiction is a personal choice. The overarching question for this project is, what is the association between individual health and mental health history and ratings of social stigma? We hypothesize that greater internalizing symptoms will be associated with greater social stigma towards substance use but less stigma towards general health. In addition, individuals with a disability will endorse greater social stigma towards substance use but less stigma towards general health. Data was sourced from the General Social Survey (GSS). Data included 3,544 participants (45.6% Male). Respondents were adults 18 or older in the United States who lived in noninstitutional housing at the time of interviewing. Chi-squared tests, One-way ANOVA with posthoc Tukey tests, and correlations were used to test the hypotheses. Only greater depressive and anxiety symptoms (but not disability) were associated with less social stigma towards general health. No psychopathology symptoms (i.e., anxiety or depressive symptoms) were associated with stigma towards substance use. The next step in this project is to examine whether other forms of mental illnesses are associated with social stigma toward SUD.
Examining Convective Froude Number as a Fire Spread Rate and Plume Structure Predictor Using WRF Model
(2024) Maynard, Nichola; Eghdami, Masih
Fire responders and local authorities face significant challenges when dealing with extreme wildfires. These fires are unpredictable and exhibit varying spread rates and plume structures depending on whether the fire regime is plume-driven or wind-driven. To better predict fire spread in these uncertain scenarios, it is crucial to gain a deeper understanding of the drivers of the fire regime. Here, we examine the Froude Number to predict the plume structure and fire spread rate using idealized simulations run with the Weather Research and Forecasting (WRF) model. Changing levels of relative humidity in the atmosphere as well as different fuel types can provide further insight into how fire spreads in varying conditions. The intensity of wildfires has greatly increased over the past several years and that trend is predicted to continue in the near future. By improving predictions of fire spread and plume structure during wildfire events, our results directly help the work of firefighters, potentially leading to less infrastructure damage and more lives saved.
Impact of Racial Disparities in Home Mortgage Lending Outcomes on Intergenerational Mobility
(2024) Wychulis, Matthew; Reck, Daniel
This paper evaluates the level of racial disparities within the home mortgage lending market and their relationship with intergenerational upward mobility. Using data from the Home Mortgage Disclosure Act (HMDA) 2010 dataset and Opportunity Insights datasets, this study scrutinizes lending disparities and intergenerational upward mobility at the Commuting Zone (CZ) level. By only evaluating lending outcomes for first-lien home purchase loans, I am able to capture the cohort of prospective home buyers moving to better neighborhoods and self-sorting themselves into geographical regions. I estimate the relationship between the disparities in mean denial rates between specified race groups within a given CZ, with the disparities in CZ-level predicted intergenerational childhood outcomes for the specified race groups. I find that disparities in denial rates between Black/Hispanic individuals and non-Hispanic whites disproportionately negatively affect Black and Hispanic children's expected future outcomes, especially those with parents at lower income percentile ranks in the national income distribution.
Exploring the Effect of Putative PGF Synthase Genes in A. Burtoni Cichlid
(2024) Amini, Cyrus; Jackson, Peter; Juntti, Scott; Li, Cheng-Yu
Exploring 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.
Silicone Fish Tail Actuator Capable of Variable Stiffening
(2024) Abrishamian, Shirah Shoshanah Ariel; Lena, Johnson; Huertas-Cerdeira, Cecilia
This work documents the creation of a fish-inspired robot actuator - from the conceptual design to a functional silicone model. The effect between the variable stiffness of a fish body and swimming efficiency has been a research subject in recent years. Often anatomy or function of an organism will inspire technological designs, particularly within the study of robotics. Animals have flexible anatomy for a range of possible maneuvers, and why fish-inspired robots are a popular choice in research. Studies have suggested a key to swim speed and efficiency in fish has been through tunable musculature. While muscle stiffness is difficult to measure in live fish, there is strong, natural evidence from several species, such as sunfish and tuna fish, showcasing this idea. Promoting inspired designs is the next step in improving robot performance. The deceptively simple appearance of typical fish combined with the numerous species' traits provides several possible robot designs. The robots can be objectively simple, with a trivial body and motor design to observe simple caudal fin motion. Or they can be exceptionally complicated if the research chooses to explore the nuances of fish anatomy and physiology, and how the impact on fish swimming in nature translates into an engineered construct. This would be beneficial due to the close relationship between bio-inspired design and soft robotics, fish bodies make a prime testing ground for soft robotics. No matter the simplicity, these robot designs can then be tested to gather valuable experimental data. This collaboration of technology and analysis then results in robots with advanced designs and special maneuvering capabilities. This research project aims to develop a tuna-inspired tail actuator capable of variable stiffness via a pneumatic system. Once attached to a 3D-printed fish body, it will be used to observe vorticity changes in fluid.
Decreased Host-Cell ATP Levels Affects Bacteriophage Replication in Knockout E. coli Strains
(2024) Alumyar, Marrie; Beitzell, Lauren; Bradish, Kristin; Kato, Rion; Vozna, Alina; O'Hara, Jessica
Bacteriophages are viruses that use host cell metabolic resources for replication. Altering Escherichia coli's ATP production pathway can inhibit bacteriophage replication, offering a new approach to bacteriophage therapy.The atp genes encode ATP synthase subunits crucial for ATP generation in E. coli. Knockouts ΔatpA, B, D, E, and H, alongside the parent strain, were studied. Focus narrowed to ΔatpA and B due to significant deviations from the parent strain. It is hypothesized that these knockout strains reduce growth in E. coli and bacteriophage due to decreased ATP production, vital for metabolism and phage replication. Comparative growth assays of E. coli parent and ATP knockout strains were conducted in LB-rich media and M9 minimal media. T4 bacteriophage replication was measured through lysis curves, plaque assays, and two time-point phage titer experiments, chosen for consistent replication. Characterization of T4 bacteriophage replication revealed ΔatpA's crucial role, showing difficulties in growth and lysing. ΔatpA required 10-4 dilutions in phage titer experiments due to low PFU/mL, contrasting with 10-7 dilutions for other strains. ATP assay data showed significantly lower ATP concentration (319nM) in ΔatpB compared to the parent strain, also implying its crucial role in ATP synthesis.Future research will focus on characterizing phage replication in ATP synthase knockout strains using E. coli ATP synthase inhibitors to deepen understanding of phage-host interactions. Controlled bacteriophage manipulation can be studied further to have a better understanding of the application of bacteriophage therapy and to potentially improve its clinical efficacy.
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.
Preparation and Application of In-House E. coli Cell-Free Protein Expression Kits
(2024) Murthy, Maya; Philip, June; Ryan, Blaise; Heber, Audrey; Aronsky, Morgan; Spirito, Catherine; Zeidan, Quira; Spirito, Catherine; Zeidan, Quira
Cell-free expression technology is cutting-edge research that would allow for increased flexibility, reliability, and versatility in the development of biosensors. This project is a joint between the Molecular Diagnostics and Cell-Ex labs in the FIRE program at the University of Maryland, in which we examine the usability of cell-free expression for workflows that differ from what they have been designed for, and conduct research into the feasibility of creating our own cell-free extract for further experimentation. In doing so, we determine the feasibility of using cell-free extract across different lab workflows, the possibility of creating it , and the cost-effectiveness of doing so versus commercial alternatives.
Ligation-LAMP to Detect miR-221 Cancer Biomarker
(2024) Kaiser, Jillian; Lee, HaeSung Lola; Patel, Khushi; Sugg, Bethany; Spirito, Catherine
Breast cancer is the second most common cancer in women and can be fatal. Current breast cancer diagnostic tools such as mammograms, MRIs, and biopsies are invasive, costly, time-consuming, and inefficient. Isothermal amplification assays, such as loop-mediated isothermal amplification (LAMP), can be designed to detect miRNA cancer biomarkers in blood samples. The focus of our project is to detect miRNA-221, a breast cancer biomarker, using a ligation-LAMP assay with high specificity and sensitivity. During ligation LAMP, miR-221 is reverse transcribed to cDNA. The cDNA acts as a splint to ligate two hairpins that form the dumbbell needed for LAMP amplification by Bst Polymerase. LAMP amplification can be detected through colorimetric methods, using phenol red and HNB. Intercalating fluorescent dye can also be used, or a CRISPR system can be used and yield a fluorescent output as well. Our primary findings include successful tests using colorimetric LAMP. We have seen nonspecific amplification causing false positives, but by adding betaine, a reagent that hinders nucleic acid amplification rate, to our reactions, the positive control amplifies sooner than the negative. Using the colorimetric and fluorescent methods described, ligation LAMP can be used to efficiently detect breast cancer biomarker miR-221.