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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Subject: search.filters.subject.Microbiology

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Now showing 1 - 8 of 8
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    DNA Aptamers against Parkinson's Disease Biomarker Alpha-Synuclein
    (2024) Cabrera Martin, Maria; Lynch, Margaret; Marin, Andrea; Saluja, Jasmine; Spirito, Catherine
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    Effects of the aceE Gene on E. coli Growth and Bacteriophage Replication
    (2024) Lippert, Celia; Lynskey, Julie Anne; Lee, James; Dasgupta, Ruben; O'Hara Jessica
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    The Effect of the E.coli lysA Gene on Viral Replication
    (2024) Godnick, Bill; Pullmann, Evan; Searls, Olivia; Solomon, Mary; O'Hara, Jessica
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    Investigating the effect of biofilm pathways on Bacillus subtilis anti-termination
    (2024-04-14) Robertello, Nathan; Tran, Thao; Jenkins, Conor; Winkler, Wade
    Biofilms are communities of bacteria ensconced in a blanket of exopolysaccharides and proteins. They can form in a variety of clinically important contexts such as the surfaces of teeth, contact lenses, and medical implants. Biofilm communities are more resistant to antibiotics than planktonic cells. Hence, it is important to understand the underlying mechanisms which promote biofilm formation. Bacillus subtilis is an important model system for studying biofilm-synthesis genes. The biosynthetic genes for B. subtilis exopolysaccharide are found in one, unusually long, operon (eps). A previously discovered processive anti-termination (PA) mechanism promotes readthrough of transcription termination sites within this operon. PA occurs when regulatory factor(s) modify the transcription elongation complex (TEC) such that it becomes resistant to downstream termination events. The PA mechanism of the eps operon requires a highly conserved RNA element called eps-associated RNA (EAR). It is not currently known how EAR exerts its influence on the TEC. The eps operon itself is only one of many biosynthetic genes necessary to biofilm formation and maintenance. In this study, we investigate the impact of a few key regulatory pathways on EAR anti-termination. We combined deletions of genes involved in these pathways with a genetic reporter assay for EAR anti-termination activity. Our preliminary data do not support a connection between these genes and the PA efficiency of EAR. These data suggest that anti-termination of the eps operon is not necessarily coupled to other known biofilm-regulatory pathways.
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    Automated Workflow for Advanced Single Cell and Bacterium Tracking in Host-Pathogen Interactions
    (2024) Augenstreich, Jacques; Poddar, Anushka; Belew, Ashton T.; El-Sayed, Najib; Briken, Volker; Briken, Volker
    In the study of intracellular pathogens like Mycobacterium tuberculosis, time-lapse microscopy is a valuable tool for understanding dynamic cellular processes involved in host cell defense. Quantification of signals at localized compartments within the cell and around bacteria can provide even deeper insight into interactions between bacteria and host cell organelles. However, existing quantitative analysis at a single-bacterial level remains limited and dependent on manual tracking methods. We developed a near-fully automated workflow that performs unbiased, high-throughput cell segmentation and quantitative tracking of both single cells and single bacteria/phagosomes within multi-channel, z-stack, time-lapse confocal microscopy videos. We took advantage of the PyImageJ library to bring Fiji functionality into a Python environment and combined deep-learning-based segmentation from Cellpose with tracking algorithms from Trackmate and visualization within ImageJ. Following both cell and bacteria tracking, our workflow provides a versatile toolkit of functions for measuring relevant signal parameters at the single-cell level (such as velocity or bacterial burden) and at the single-bacteria level (for assessment of phagosome maturation). Ultimately, our workflow’s capabilities in both single-cell and single-bacteria quantification can help decipher the virulence factors of pathogens and pave the way for the development of innovative therapeutic approaches. The customizable nature of the methods extends the applications of the workflow far beyond the field of mycobacteria and presents opportunities for advancement in host-pathogen interaction research in a variety of systems.
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    INVESTIGATING THE ROLE OF E. COLI TCA CYCLE METABOLISM IN BACTERIOPHAGE REPLICATION
    (2024) Kavalov, Lilith; Weaver, Trinity; O'Hara, Jessica
    Bacteriophages are viruses that specifically infect and hijack Escherichia coli's metabolic processes to proliferate, ultimately destroying the host cell in the process. The Tricarboxylic Acid Cycle (TCA Cycle) is a multi-step aerobic enzyme-catalyzed pathway that occurs in the cytoplasm of E. coli and is responsible for generating the electron-carrier molecules NADH and FADH2 which are crucial for generating ATP for the cell in future steps of cellular respiration. The E. coli genes, acnB, and acnA, encode enzymes that catalyze different reactions that are necessary for the TCA cycle. We hypothesize that the removal of these genes would negatively impact the growth rate and ATP levels of E. coli and, as a result, inhibit or slow the replication of bacteriophage. To determine the effects of the removal of these genes, enzyme assays, comparative growth curves of the knockout strains, and plaque assays of bacteriophage replication were measured and investigated. Furthermore, we quantified the knockout’s effects by collecting lysis curves as well as performing an ATP assay using bioluminescence.
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    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.
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    Spread Prevention and Eradication of Resistant Bacterial Growth
    (2024) Sripathi, Neha; Kim, Joshua; Dinh, Phuclam; Rayford, Amber; Breymaier, Nicholas; Zhang, Cristina; Hillman, Mackenzie; Stein, Daniel; Stein, Daniel
    Diseases caused by drug resistant bacteria are becoming a pressing public health threat due to a lack of new antibiotics and the evolution of multidrug resistance. Drug resistance is caused by mutant or novel genes known as resistance genes. CRISPR-Cas9 gene editing has been shown in recent studies to successfully edit resistance genes to increase susceptibility to antibiotics. We aim to use bacteriophage M13 to transduce a CRISPR-Cas9 system into nalidixic acid resistant Escherichia coli and resensitize it to nalidixic acid. We aim to improve upon the efficiency of previous studies.