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.Host-Pathogen Interactions

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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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    Implications of the TCA Cycle on Escherichia coli Growth and Phage Replication
    (2020) Suriaprakash, Aiswarya; Bokil, Eesha; Koudouovoh, Carlos; Chuck, Marissa; O'Hara, Jessica
    ATP provides energy for the cellular processes in E. coli. The E. coli icd gene encodes the enzyme isocitrate dehydrogenase which is used in the tricarboxylic acid (TCA) cycle to make ATP. We hypothesize that T4 phage is dependent on ATP production in the host cell in order to successfully replicate. Our research aims to find if an E. coli bacteria strain lacking the icd gene will show decreased T4 phage replication because of its decreased ATP production compared to E. coli bacteria strains that possess the icd gene with normal ATP production. Decreased ATP production in the E. coli host will result in a decrease in bacterial growth rate and T4 phage replication. Plaque assays, growth curves, and lysis curves were used to monitor bacterial growth and phage replication. Host cells lacking the icd gene had decreased bacterial growth. T4 phage replication is slower in the host cells lacking the icd gene. It is the hope that these results and future research will contribute to phage therapy, a promising development in treating bacterial diseases.
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    Impact of Inhibition of the TCA cycle on ATP and NADH levels in Escherichia coli during Bacterial Replication
    (2021) Suriaprakash, Aiswarya; Mercado, Briana; De La Cruz, Raina; O'Hara, Jessica
    Bacteriophage are bacteria-eating viruses that utilize the host cell’s metabolic pathways for components for phage replication. The tricarboxylic acid (TCA) cycle, an important metabolic pathway within cellular respiration, uses oxygen to break down organic molecules to make adenosine triphosphate (ATP) for energy. In E. coli, the fumarase A gene codes for the enzyme fumarase, which catalyzes fumarate to (S)-malate and NAD+ in the TCA Cycle, used to create NADH, pyruvate, high-energy electron carriers, and ATP. The icd gene encodes the enzyme isocitrate dehydrogenase which is also used in the TCA cycle to make ATP. In our previous research, we discovered that the removal of the fumA and icd genes resulted in a delay in T4 and/or T4r bacteriophage replication. Currently, we are aiming to quantify ATP and NADH levels before and after cell lysis to further understand the impacts of each knockout on cellular metabolism and the resulting impact on T4 replication. This research is made to further understand ways to treat bacterial diseases in the face of antibiotic resistance, specifically phage therapy.