Undergraduate Research Day 2021

Permanent URI for this collectionhttp://hdl.handle.net/1903/27016

With students involved in so many research opportunities, Undergraduate Research Day provides the perfect opportunity for them to share their work with the campus community. Held each April, Undergraduate Research Day showcases current research, scholarship, and artistic endeavors.

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End date: 2021Subject: search.filters.subject.FIRE

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Now showing 1 - 6 of 6
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    Identification of Clostridium Phage Endolysins with Novel Multimeric Genetic Sequences
    (2021) Bokil, Eesha; Baker, Charley; Nelson, Daniel; O'Hara, Jessica
    The endolysin CD27L is produced by the Clostridium phage phiCD27. This phage targets the bacteria and uses the endolysin’s enzymatic properties to lyse cells from within and release new replicated phages. Past studies have characterized the two domains of CD27L’s genetic sequence, the enzymatically active domain (EAD) at the N-terminus and the cell wall binding domain (CBD) at the C-terminus connected by a linker sequence. The gene sequence order is EAD-linker-CBD. A unique aspect of CD27L is its ability to form a multimeric enzymatic structure from these two domains where one EAD and multiple CBDs are present in one structure. This multimeric endolysin is formed from one gene, so translation of the one sequence uses two ribosome binding sites and two start codons. One ribosome binding site and start codon is before the EAD and the other in the linker sequence before the CBD. Our goal is to analyze the sequences of other Clostridium phage endolysins to find multimeric endolysins similar to CD27L. We are specifically looking for multiple ribosome binding sites with start codons or alternate start codons downstream in close proximity on one gene sequence.
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    Investigating Arginine Biosynthesis in Viral Replication
    (2020-11) Lee, Harrison; Griffin, Ryleigh; Stecklein, Sabrina; Chaudry, Daniel; O'Hara, Jessica
    When a virus infects a cell, it must hijack that host cell’s inner machinery, normally used to manufacture necessary molecules for the host cell, and divert that machinery to producing new viruses. Previous research has indicated that arginine, an amino acid, plays an important role in viral infection. We investigated the role arginine plays in infection in two ways. First, we compared how well bacteriophage, a type of bacteria-infecting virus, replicated in normal (parent) E. coli and genetically modified E. coli that could not produce their own arginine. These genetically modified E. coli are called a knock-out strain because the gene for a particular protein, in this case an enzyme involved in producing arginine, is removed. The gene in question is called argH and thus the knock-out strain is named ΔargH. Here we found that when arginine was available from outside the cell, there was no significant difference between bacteriophage replication in the two E. coli strains. Second, we observed how the levels of certain small molecules (metabolites), including arginine, inside a human cell changed after it was infected with the Human Cytomegalovirus (HCMV). We found that HCMV infected cells had altered levels of metabolites from throughout the arginine biosynthesis pathway, including increased levels of arginine.
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    Characterizing a Chimera: Comparative Analysis of Pal Endolysin and its Homologs
    (2021-04) Griffin, Ryleigh; Lee, Harrison; O'Hara, Jessica; Nelson, Daniel
    Once a virus infects a cell and produces more virus particles (virions), it must find a way to release those virions so they can infect more cells. Bacteriophage, or viruses that infect bacteria, accomplish this goal by producing endolysins, proteins that cause bacterial cells to lyse by breaking down their cell walls. Many endolysins have a modular structure consisting of an enzymatically active domain (EAD), which catalytically breaks bonds in peptidoglycan, the main component of bacterial cell walls, and a cell wall binding domain (CBD), which attaches the endolysin to the cell wall and determines host specificity. By combining EADs and CBDs from different endolysins, researchers can produce new “chimeric” endolysins in order to kill disease-causing bacteria in a targeted fashion, which can be more effective than the original enzymes. Chimeric endolysins can also form naturally. Bacteriophage Dp-1, which infects Streptococcus pneumoniae bacteria, produces a chimeric endolysin called Pal. Pal’s CBD has the ability to bind to choline and is very similar to a portion of the LytA enzyme produced by S. pneumoniae. Pal’s EAD breaks down amide bonds in peptidoglycan and is very similar to a portion of the endolysin produced by a Bacteriophage BK5-T, which infects Lactococcus lactis bacteria. In our research, we used bioinformatics techniques to find other proteins that share homology with Pal and to investigate the evolutionary relationships between these proteins. We hope that a better understanding of this natural chimeric endolysin could be useful to researchers attempting to engineer new ones.
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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.
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    HGCAL Electromagnetic Calorimeter Performance
    (2021-04) Garcia, Fred Angelo; Morrissey, Wil; Mehta, Samyak; Karagoz, Muge
    The High-Granularity Calorimeter (HGCAL) is an important component of the High Luminosity LHC (HL-LHC) upgrade for the CMS experiment. With electromagnetic (CE-E) and hadronic (CE-H) sections, these calorimeters are designed to withstand and operate in high radiation environments. We primarily studied the CE-E region at the TeV and GeV regimes. Motivations for this research include identifying software inconsistencies and calibration issues, as well as overall design limitations; it supplements efforts in shower leakage correction for the detector as a whole by investigating electron energy reconstruction. Using electron and positron particle gun simulations, generated with CMSSW (CMS Offline Software), our study tries to answer questions related to detector performance at specific regions of the HGCAL, focusing on pseudorapidity (η) ranges of 1.5 to 1.6 and 2.9 to 3.0 at two different energy values. We quantified the η dependence of electrons and found that not only are electron reconstruction energy resolutions energy dependent, they are also η dependent. We assert that this is an underlying detector geometry issue that may be addressed by future updates to HGCAL detector geometry, as well as more advanced reconstruction techniques. Hence, our next step will include conducting the same study with a sample simulated with updated detector geometries.