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An Antiviral Response Unleashed: Deciphering The Relationship Between Shiftless And Rna Granules During Kshv Infection, David C. Hatfield 2024 University of Massachusetts Amherst

An Antiviral Response Unleashed: Deciphering The Relationship Between Shiftless And Rna Granules During Kshv Infection, David C. Hatfield

Masters Theses

Herpesviruses persist as a parasitic actor among many species. These viral agents can rapidly seize control over host cells by influencing global gene expression. Through a process known as host shutoff, herpesviruses cause a widespread degradation event of host transcripts within the cytoplasm. Specifically, Kaposi Sarcoma associated herpesvirus (KSHV) encodes for an endoribonuclease, termed SOX, that orchestrates this manipulation of gene expression. We and others have discovered certain transcripts that escape this fate; we suggest that this is an active escape, where transcripts have 3’ UTR elements that disallow SOX cleavage. One of the escapees that has been found is …


Vitro Bacteriophage Treatment For A Staphylococcus Aureus And Pseudomonas Aeruginosa Co-Culture, Alexis Perry 2024 Ouachita Baptist University

Vitro Bacteriophage Treatment For A Staphylococcus Aureus And Pseudomonas Aeruginosa Co-Culture, Alexis Perry

Arkansas Women in STEM Conference

Recent studies show that up 27-36% of all infections are polymicrobial, involving more than one bacteria species. In all categories, polymicrobial infections are often more virulent and harmful to the patient. Since different types of bacteria can communicate with each other through quorum-sensing when in the presence of each other, they can display different genomic characteristics. Further research into polymicrobial infections needs to be done because these changing characteristics can prevent treatment from working, such as antibiotics or bacteriophage therapy. This experiment focused on the co-culture between the two bacteria, Pseudomonas aeruginosa and Staphylococcus aureus, which can be found co-existing …


Investigating The Escape Mechanism Of Sre Bearing Mrna Transcripts During Viral Host Shutoff, Daniel MacVeigh-Fierro 2024 University of Massachusetts Amherst

Investigating The Escape Mechanism Of Sre Bearing Mrna Transcripts During Viral Host Shutoff, Daniel Macveigh-Fierro

Doctoral Dissertations

During viral infection, the virus and host clash for control over gene expression in an evolutionarily arms race that has raged for thousands of years. During lytic replication, Kaposi’s sarcoma associated herpesvirus (KSHV) triggers a massive RNA decay event known as host shut off. This causes over 70% of all RNA to be degraded suppressing the host antiviral response while freeing resources for viral replication. Our lab focuses on a subset of transcripts that escape from this viral degradation event using a cis acting 3’ UTR element known as a “SOX resistant element” or SRE. Although we have identified a …


Using Single Cell Genomics To Explore The Impact Of Marine Viruses On Microbial Respiration., Paxton Tomko 2024 University of Connecticut - Storrs

Using Single Cell Genomics To Explore The Impact Of Marine Viruses On Microbial Respiration., Paxton Tomko

MCB Articles

Viral metabolic reprograming of marine prokaryotes, through the use of virally encoded auxiliary metabolic genes (AMGs), plays a critical role in marine ecosystem function by influencing biochemical cycles and genetic diversity in these environments. Despite the fundamental role viruses play in global environmental ecosystems, they remain an understudied aspect of microbial ecology and evolution, in part due to the methods available for studying virus host interactions in natural systems. Thus far, metagenomic analyses have been used to study the interactions of virus host pairs, but these types of analyses have their limitations in accurately linking viruses to hosts, or culture-based …


Developing Disinfection Strategies For Controlling Human Norovirus, Sars-Cov-2, And Clostridioides Difficile Endospores In Long-Term Care Facilities, Jinge Huang 2023 Clemson University

Developing Disinfection Strategies For Controlling Human Norovirus, Sars-Cov-2, And Clostridioides Difficile Endospores In Long-Term Care Facilities, Jinge Huang

All Dissertations

Long-term care facilities (LTCFs) provide an environment favorable for the transmission of three critical human pathogens: human norovirus (HuNoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Clostridioides difficile. Given residents in LTCFs are susceptible to infections due to their advanced ages and compromised immune systems, effective environmental surface disinfection plays a crucial role in controlling the spread of human pathogens within these settings and, therefore, mitigates the risk of infections caused by these pathogens. This dissertation aimed to assess the efficacy of various types of disinfectants against two HuNoV surrogates [feline calicivirus (FCV) and Tulane virus (TuV)], two …


Cell Surface And Plasma Biomarkers Of Kaposi Sarcoma, Sara R. Privatt 2023 University of Nebraska-Lincoln

Cell Surface And Plasma Biomarkers Of Kaposi Sarcoma, Sara R. Privatt

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

Kaposi sarcoma-associated herpesvirus is the etiological agent of several pathologies including Kaposi sarcoma, primary effusion lymphoma, and multicentric Castleman’s disease. Here, we investigated both the tumor microenvironment (TME) in KS lesions as well as plasma from KSHV-infected individuals and how metabolic dysfunction and dysregulated cytokines might have a systemic effect on KS tumorigenesis. Based on previously published KS tumor transcriptomics, one aspect of our investigation involved characterizing cell surface glycoproteins with potential to serve as therapeutic targets against KSHV-infected cells or KS tumors or as biomarkers for disease. Expression patterns of such markers may also suggest the cellular origin of …


Detection And Control Of Environmentally Transmissible Viruses, Anand R. Soorneedi 2023 University of Massachusetts Amherst

Detection And Control Of Environmentally Transmissible Viruses, Anand R. Soorneedi

Doctoral Dissertations

Viruses, owing to their ubiquitous nature and ability to infect almost every other species, have long been a subject of interest for scientists. Some of the virus species can be very deadly to humans and animals alike and can impose a huge economic and health burden across the world. The recent CoVID-19 pandemic underscores the importance of timely detection for developing effective intervention strategies. Unfortunately, some of the virus species that cause significant health and economic impacts do not have robust and reliable detection methods due to several reasons. In some cases, despite having gold standard methods for detection of …


Climate Change, Giant Viruses And Their Putative Hosts, Sarah K. Tucker 2023 University of Massachusetts Amherst

Climate Change, Giant Viruses And Their Putative Hosts, Sarah K. Tucker

Masters Theses

Viruses hold our attention for the horrific impact they have on human health and welfare. However, viruses are a critical part of our ecosystem and facilitate the cycling of carbon and other important nutrients. The cycle of virus infection, followed by host resistance and the subsequent evolution of new strains enables adaptation to changing hosts and the environment. Giant viruses, some with particle sizes large enough to be visible in light microscopes and their bewildering array of accessory genes, have captivated scientists and the general public since their discovery two decades ago. Giant viruses are part of the Nucleocytoviricota (NCV) …


Mycobacteriophage: A Demonstration Of The Reduction Of M. Smegmatis In Various Matrices., Laura O'Connell 2023 Department of Biological Sciences, Munster Technological University, Cork, Ireland.

Mycobacteriophage: A Demonstration Of The Reduction Of M. Smegmatis In Various Matrices., Laura O'Connell

ORBioM (Open Research BioSciences Meeting)

Background

Mycobacterial disease is a major cause of fatality worldwide, with approximately 1.5 million deaths for every 10 million infections. These infections are difficult to treat due to the intrinsic resistance of its mycolic acid rich cell wall to many antibiotics. There is potential for mycobacteriophage (MP) to be used therapeutically for multidrug- and extensively-drug resistant infections. Mycobacterium smegmatis mc2 155 is a useful substitute for slow-growing pathogenic mycobacteria, as it propagates quickly under lab conditions. This feature of M. smegmatis increases the pace of analysis, by ensuring the quick isolation and characterisation of MP and acting as a …


Bactericidal Effects Of Chlorine And Bacteriophages On Mycobacteria In Conventionally Treated Water., Max Kevane-Campbell 2023 Department of Biological Sciences, Munster Technological University, Cork, Ireland.

Bactericidal Effects Of Chlorine And Bacteriophages On Mycobacteria In Conventionally Treated Water., Max Kevane-Campbell

ORBioM (Open Research BioSciences Meeting)

Introduction

Mycobacteria are members of the order Actinomycetales and the only genus in the family Mycobacteriaceae. The distinguishing characteristics that are found in mycobacteria include acid-fastness and the presence of mycolic acids. Mycobacteria can be commonly classified as non-spore-forming, aerobic, slender rod-shaped, and are slow-growers. Natural reservoirs that mycobacteria can be found in are aquatic and terrestrial environments. Recent studies have shown that mycobacteria that can cause skin lesions, immune and/or pulmonary dysfunctions and chronic diseases, i.e., Mycobacterium avium subsp. Paratuberculosis, M. kansasii, and M. xenopi, can be isolated from common household tap water. Tap water can originate from …


Sars-Cov-2: Tale Of A Microscopic Murderer, Josiah P. Garner 2023 Collin College

Sars-Cov-2: Tale Of A Microscopic Murderer, Josiah P. Garner

Quest

Independent Study

Research in progress for BIOL1406: Biology for Science Majors I

Faculty Mentor: Amina Tassa, Ph.D.

I am delighted to introduce Josiah Garner’s “SARS-CoV-2: Tale of a Microscopic Murderer.” This independent study assignment explores the impact of a novel, deadly, and worldwide virus. The assignment also examines the fast development of vaccines to control the spread and reduce the symptoms of the virus.

Josiah’s paper focuses on the early history of the emergence of COVID-19, the world response, and vaccine development. He demonstrates critical thinking skills and effectively utilizes various research methods to obtain and communicate his information. Josiah …


Predicted Structure And Analysis Of The Glycoprotein From Sars-Cov-2 Variants Of Interest, Boris Shabaltiy 2023 University of Nebraska - Lincoln

Predicted Structure And Analysis Of The Glycoprotein From Sars-Cov-2 Variants Of Interest, Boris Shabaltiy

Honors Theses

SARS-CoV-2 has had a devastating effect on the world, and while the public concern and severity of the diseased caused by it have decreased, it is still crucial to monitor the virus for mutations so we can rapidly identify new variants of concern, and then rapidly prepare new vaccines and treatments. The SARS-CoV-2 spike (S) protein from the first isolates of the virus (root variant) was structurally characterized in early 2021. The spike protein structure, designated 7CZW, was uploaded to RCSB Protein Data Bank (RCSB PDB). All subsequent mutations the S protein has accumulated are based on the amino acid …


Functional Characterization Of The Human And Murine Schlafen Family Group Iii, Carlos A. Valenzuela 2023 University of Texas at El Paso

Functional Characterization Of The Human And Murine Schlafen Family Group Iii, Carlos A. Valenzuela

Open Access Theses & Dissertations

The Schlafen (SLFN) family of proteins are known for being encoded by interferon stimulated genes. The family is divided into three groups (I, II, III), for which the largest in size belong to the subgroup III. In humans, group III has the most members (SLFN5, SLFN11, SLFN13 and SLFN14); there is no member of group I and only one member of group II (SLFN12). All human SLFNs belonging to group III have been reported to impair viral protein expression or infection across a variety of viruses. The antiviral function is mediated in SLFN11 and SLFN13 by their tRNase activity, and …


Multiple Rsv Strains Infecting Hep-2 And A549 Cells Reveal Cell Line-Dependent Differences In Resistance To Rsv Infection, Anubama Rajan, Felipe-Andres Piedra, Letisha Aideyan, Trevor McBride, Matthew Robertson, Hannah L. Johnson, Gina Marie Aloisio, David Henke, Cristian Coarfa, Fabio Stossi, Vipin Kumar Menon, Harshavardhan Doddapaneni, Donna Marie Muzny, Sara Joan Javornik Cregeen, Kristi Louise Hoffman, Joseph Petrosino, Richard A. Gibbs, Vasanthi Avadhanula, Pedro A. Piedra 2023 Baylor College of Medicine

Multiple Rsv Strains Infecting Hep-2 And A549 Cells Reveal Cell Line-Dependent Differences In Resistance To Rsv Infection, Anubama Rajan, Felipe-Andres Piedra, Letisha Aideyan, Trevor Mcbride, Matthew Robertson, Hannah L. Johnson, Gina Marie Aloisio, David Henke, Cristian Coarfa, Fabio Stossi, Vipin Kumar Menon, Harshavardhan Doddapaneni, Donna Marie Muzny, Sara Joan Javornik Cregeen, Kristi Louise Hoffman, Joseph Petrosino, Richard A. Gibbs, Vasanthi Avadhanula, Pedro A. Piedra

Research Symposium

Background: Respiratory syncytial virus (RSV) is the major viral driver of a global pediatric respiratory disease burden disproportionately borne by the poor1. Thus, RSV, like SARS-CoV-2, combines with congenital and environmental and host-history-dependent factors to create a spectrum of disease with greatest severity most frequently occurring in those least able to procure treatment.

Methods: Here we apply whole genome sequencing and a suite of other molecular biological techniques to survey host-virus dynamics in infections of two distinct cell lines (HEp2 and A549) with four strains representative of known RSV genetic diversity.

Results: We observed non-gradient patterns of RSV …


Modeling Nonsegmented Negative-Strand Rna Virus (Nnsv) Transcription With Ejective Polymerase Collisions And Biased Diffusion, Felipe-Andres Piedra 2023 Baylor College of Medicine

Modeling Nonsegmented Negative-Strand Rna Virus (Nnsv) Transcription With Ejective Polymerase Collisions And Biased Diffusion, Felipe-Andres Piedra

Research Symposium

Background: The textbook model of NNSV transcription predicts a gene expression gradient. However, multiple studies show non-gradient gene expression patterns or data inconsistent with a simple gradient. Regarding the latter, several studies show a dramatic decrease in gene expression over the last two genes of the respiratory syncytial virus (RSV) genome (a highly studied NNSV). The textbook model cannot explain these phenomena.

Methods: Computational models of RSV and vesicular stomatitis virus (VSV – another highly studied NNSV) transcription were written in the Python programming language using the Scientific Python Development Environment. The model code is freely available on GitHub: …


Sero-Epidemiology Of Rotavirus Gastroenteritis In Children In Ilorin, Kwara State, Omosigho Omoruyi Pius, Izevbuwa Osazee Ekundayo, Saheed Ibrahim Damilare 2023 Department of Medical Laboratory Science, Faculty of Applied Health Sciences, Edo State, Uzairue

Sero-Epidemiology Of Rotavirus Gastroenteritis In Children In Ilorin, Kwara State, Omosigho Omoruyi Pius, Izevbuwa Osazee Ekundayo, Saheed Ibrahim Damilare

Journal of Bioresource Management

Rotavirus is responsible for the most severe dehydrating diarrhea among young children due to gastroenteritis. In this study, we aimed to ascertain the occurrence of childhood gastroenteritis caused by Rotavirus among infants and young children who are younger than 5 years of age in Ilorin, Kwara State and determined the risk factors posing the challenges to be susceptible to diarrhea associated with rotavirus in Ilorin, Kwara State. Diarrhea stool samples were collected from children who passed watery stools, who met predetermined inclusion criteria and who presented at the study hospitals Viz: General Hospital and Specialist Hospital Alagbado and Children Specialist …


Evolution Of Overlapping Reading Frames In Virus Genomes, Laura Muñoz Baena 2023 Western University

Evolution Of Overlapping Reading Frames In Virus Genomes, Laura Muñoz Baena

Electronic Thesis and Dissertation Repository

Viruses are formidable pathogens that represent the majority of biological entities in our planet, and their genomes are a source of interesting enigmas. One feature in which virus genomes are usually rich, is the presence of overlapping reading frames (OvRFs) — portions of the genome where the same nucleotide sequence encodes more than one protein. OvRFs are hypothesized to be used by viruses to encode proteins more compactly and to regulate transcription. In addition, OvRFs might be a source of gene novelty, facilitating the creation of new open reading frames (ORF) within the transcriptional context of existing ones.

To characterize …


Mutation-Induced Changes In The Stability, B-Cell Epitope, And Antigenicity Of The Sars-Cov-2 Variant Spike Protein: A Comparative Computational Stud, Nira Meirita Wijayanti, Muhammad Hermawan Widyananda, Lailil Muflikhah, Nashi Widodo 2023 Biology Department, Faculty of mathematics and Natural Sciences, Brawijaya University, Malang, Indonesia

Mutation-Induced Changes In The Stability, B-Cell Epitope, And Antigenicity Of The Sars-Cov-2 Variant Spike Protein: A Comparative Computational Stud, Nira Meirita Wijayanti, Muhammad Hermawan Widyananda, Lailil Muflikhah, Nashi Widodo

Karbala International Journal of Modern Science

The spike (S) protein is a major antigenicity site that targets neutralizing antibodies and drugs. The growing number of S protein mutations has become a severe problem for developing effective vaccines. Here, we investigated four severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that were the most infectious and widespread during the COVID-19 pandemic to determine the trends and patterns of mutation-induced changes in the stability, B-cell epitope, and antigenicity of the SARS-CoV-2 S protein. The data showed that the Beta and Gamma variants had three mutations on the receptor-binding domain (RBD), which is the specific site on the S …


Analyzing Pseudomonas Aeruginosa With Bacteriophage Tags Using Photoacoustic Flow Cytometry, Jennifer C. Schinke 2023 Duquesne University

Analyzing Pseudomonas Aeruginosa With Bacteriophage Tags Using Photoacoustic Flow Cytometry, Jennifer C. Schinke

Electronic Theses and Dissertations

The number of daily bacterial infections is climbing and the CDC explains that this is due to the antibiotic-resistant threat in the United States. Finding a faster way of bacterial identification is necessary as it currently takes 1-4 days for a medical lab to culture and identify bacteria. Photoacoustic flow cytometry (PAFC) can be used as an alternative method resulting in swift identification within an hour (Edgar, 2019). Pseudomonas aeruginosa, cell line PA01, will be coated in up to a few hundred red dyed phages making it detectible by the photoacoustic flow cytometry system. Bacteriophages (phages) are viruses that …


A Shift In Rna Fate: Investigating The Role Of C19orf66 During Kshv Lytic Replication, William Rodriguez Jr. 2023 University of Massachusetts Amherst

A Shift In Rna Fate: Investigating The Role Of C19orf66 During Kshv Lytic Replication, William Rodriguez Jr.

Doctoral Dissertations

During viral infection, virus and host clash for control of the cell in a conflict that ultimately drives the evolution of both sides and has lasting consequences in the form of pathogenesis. At the heart of this struggle is a contest for control of cellular gene expression, a struggle epitomized by an evolutionary tug-of-war for supremacy over RNA fate. During lytic replication, Kaposi’s sarcoma-associated herpesvirus (KSHV) triggers a massive RNA decay event known as viral “Host Shutoff” which decimates greater than 70% of the host transcriptome, simultaneously suppressing the cellular anti-viral response and freeing host resources for viral replication. However, …


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