Organisms Commons^™

Host Cell Responses To Zika Virus Infection, Bikash Ranjan Sahoo

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

The re-emergence of Zika virus (ZIKV) in 2015 as a significant human pathogen causing neurological diseases in infants as well as adults is a serious global health concern. A clear understanding of the mechanisms involved in ZIKV replication in infected host cells as well as the host responses to virus infection are keys to the development of therapeutic strategies against ZIKV. Studies conducted in this dissertation demonstrate that ZIKV infection induces the activation of mTOR signaling cascade that promotes viral protein accumulation and infectious progeny production. While both mTORC1 and mTORC2 are essential for ZIKV replication, the observation that depletion …

Virus-Targeted Transcriptomic Analyses Implicate Ranaviral Interaction With Host Interferon Response In Frog Virus 3-Infected Frog Tissues, Yun Tian, Francisco De Jesús Andino, Collins N. Khwatenge, Jiuyi Li, Jacques Robert, Yongming Sang

Agricultural and Environmental Sciences Faculty Research

Ranaviruses (Iridoviridae), including Frog Virus 3 (FV3), are large dsDNA viruses that cause devastating infections globally in amphibians, fish, and reptiles, and contribute to catastrophic amphibian declines. FV3’s large genome (~105 kb) contains at least 98 putative open reading frames (ORFs) as annotated in its reference genome. Previous studies have classified these coding genes into temporal classes as immediate early, delayed early, and late viral transcripts based on their sequential expression during FV3 infection. To establish a high-throughput characterization of ranaviral gene expression at the genome scale, we performed a whole transcriptomic analysis (RNA-Seq) using total RNA samples containing both …

Development Of Vaccines And Antivirals Against Zika Virus, Aryamav Pattnaik

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

The re-emergence of Zika virus (ZIKV), an arbovirus, poses a major global human health concern because of its ability to cause congenital abnormalities and neurological diseases. While many candidate vaccines and antiviral drugs are in the developmental pipeline, none have been approved for use against ZIKV infection. This dissertation describes the characterization of one vaccine and two antiviral drug candidates against ZIKV infection. A bacterial ferritin-based nanoparticle vaccine, termed zDIII-F, is designed to display multiple copies of ZIKV E protein domain III on its surface. These stable nanoparticles are shown to induce robust antibody-mediated protection against lethal ZIKV infection in …

Preventing Transmission Of Covid 19 In Hvac Duct Systems: Implementations Of Hvac System Design Upgrade, Jacob S. Lopez, Adama Barro

Publications and Research

The recent pandemic outbreak has triggered a global alarm to increase efforts on finding the best methods to mitigate contagious viral pathogens. This project is a continuation of our mission to study engineering guidelines needed to implement upgrades to HVAC Systems in order to deter airborne pathogens such as the covid-19 virus. In our previous projects we researched how covid-19 can possibly flow through the ambient air inside of restaurants, office spaces, and locomotive train cabins. As we continued our research, we were able to find some solutions that will be best used to deactivate and prevent the virus from …

Analysis Of Single Cell Rna-Seq Data Revealed Interferon Gamma Signaling Alteration In Severe Covid Patients, Ahmed Elbaz

Theses and Dissertations

Background: SARS-COV2 virus detected in December 2019, and was considered a pandemic in March 2020 by the WHO. Symptoms range from asymptomatic to life threatening ones. Studying cell-cell interactions in patients' blood samples may lead to novel diagnosis and treatment approaches.

Aim: This study aims to analyze single-cell RNA sequencing data to identify differences in cell-cell communications between healthy and COVID patients and differentially expressed T-cells genes that contributed to immune system antiviral activity.

Materials and methods: Single-Cell RNA sequencing data from seven COVID patients and five healthy individuals were collected from (GEO accession GSE155673). Cell types were identified and …

Epidemiology And Outcomes Of Hospitalized Adults With Sars-Cov-2 Community-Acquired Pneumonia In Louisville, Kentucky, Julio A. Ramirez, T'Shura Ali, Thomas Chandler, Stephen P. Furmanek, Daniya Sheikh, Vidyulata Salunkhe, Steven Gootee, Mohammad Tahboub, William A. Mattingly, Demetra Antimisiaris, Jiapeng Huang, Jose Bordon, Rodrigo Cavallazzi, Paul Schulz, William P. Mckinney, Dawn Balcom, Mark Burns, Ruth Carrico, Forest W. Arnold, Cerid Covid-19 Study Group

The University of Louisville Journal of Respiratory Infections

Background: During the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SARS-CoV-2 community-acquired pneumonia (CAP) has been the primary cause of hospitalization. The objective of this study was to evaluate the clinical characteristics and outcomes of 1,013 patients hospitalized with SARS-CoV-2 CAP from September 2020 through March 2021 in Louisville, Kentucky.

Methods: This was a retrospective observational study of 1,013 patients hospitalized with SARS-CoV-2 CAP at eight of the adult hospitals in the city of Louisville from September 2020 through March 2021. Patients with 1) a positive reverse transcriptase-polymerase chain reaction (RT-PCR) for SARS-CoV-2, 2) fever, cough, or …

Sociodemographic, Clinical Characteristics, And Outcomes Of Influenza Pneumonia Patients Admitted In A Tertiary Care Hospital In Karachi, Pakistan: Findings From A Cross-Sectional Study, Fazal Ur Rehman, Muhammad Arslan Ahmed, Kashif Aziz, Mahmooda Jabeen Ashraf, Tazein Amber, Sumera Aziz Ali

Section of Internal Medicine

Objective: To determine the sociodemographic, clinical characteristics, and outcomes of influenza pneumonia patients in tertiary care hospital, Karachi Pakistan.
Study design: A cross-sectional study.
Place and duration of study: The Aga Khan University Hospital Karachi Pakistan from January 2013 to December 2018. Methodology: All adult patients who were older than 18 years and suspected to have viral pneumonia were included in the study. Data were abstracted on 105 patients and were entered on preformed proforma after reviewing the files of patients.
Results: Ninety-four (89.5%) patients were influenza positive and 15.2% (n=16) had been vaccinated. Around 92.4% (n=97), 81.9% (n=86) and …

Covid-19 Presenting With Spontaneous Pneumothorax, Intisar Ahmed, Hunaina Shahab, Muhammad Arslan Ahmed, Muhammad Sohaib

Section of Cardiology

The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease mainly affects respiratory system. Its common clinical findings include fever, cough and shortness of breath. Characteristic radiological features of the disease include peripherally distributed, bilateral ground-glass opacities, predominantly involving the lower lung zones. In this report, we present a case of COVID-19 disease presenting with spontaneous pneumothorax. A 26-year male patient was admitted to the Emergency Department with fever, dry cough, shortness of breath and right-sided chest pain. Radiographic imaging of the patient revealed pneumothorax on the right and peripherally distributed non-homogenous opacification. …

Covid19 Disease Map, A Computational Knowledge Repository Of Virus–Host Interaction Mechanisms, Marek Ostaszewski, Tomáš Helikar, Bhanwar Lal Puniya, A Host Of Co-Authors, Covid-19 Disease Map Community

Department of Biochemistry: Faculty Publications

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, …

Evolution, Ecology, And Zoonotic Transmission Of Betacoronaviruses: A Review, Herbert F. Jelinek, Mira Mousa, Eman Alefishat, Wael Osman, Ian Spence, Dengpan Bu, Samuel F. Feng, Jason Byrd, Paola A. Magni, Shafi Sahibzada, Guan K. Tay, Habiba S. Alsafar

Research outputs 2014 to 2021

Coronavirus infections have been a part of the animal kingdom for millennia. The difference emerging in the twenty-first century is that a greater number of novel coronaviruses are being discovered primarily due to more advanced technology and that a greater number can be transmitted to humans, either directly or via an intermediate host. This has a range of effects from annual infections that are mild to full-blown pandemics. This review compares the zoonotic potential and relationship between MERS, SARS-CoV, and SARS-CoV-2. The role of bats as possible host species and possible intermediate hosts including pangolins, civets, mink, birds, and other …

Covid-19: Race For Vaccine, L. Hayley Burgess, Jason J. Braithwaite, Emily Singleton, Aaron M. Young, Mandelin K. Cooper

HCA Healthcare Journal of Medicine

The world is in the midst of a pandemic from COVID-19, a disease caused by the virus SARS-CoV-2. Despite broad mitigation efforts, new cases continue with 74 million cases and 1.6 million deaths worldwide. Regardless of previous research efforts, there is no commercially available vaccine for any coronavirus. Novel vaccine development has historically taken at least 10 years from discovery to availability with only a 6% market entry probability.

With the global impact, there is an urgency to expedite a vaccine to protect the population. The U.S. government launched Operation Warp Speed with the goal to produce and deliver 300 …

Parillo, Sophia - Covid-19 Journal, Sophia Parillo

Personal Journals

Personal diary of EIU college student and junior Elementary Education major with a minor in orchestra. Her journal documents the holiday season of 2020 and includes documentation that illustrates life during the pandemic.

Arguelles, Ceci - Covid-19 Journal, Ceci Arguelles

Personal Journals

Personal diary of EIU student Ceci Arguelles documenting her early experience with the Covid-19 pandemic. Submission includes photos and a description of the images.

Tagtmeier, Daniel - Covid-19 Journal, Daniel Tagtmeier

Personal Journals

EIU student, Daniel Tagtmeier writes about the effect of the pandemic on his learning and homelife, particularly his relationship with his grandmother and the inability to see her in the early stages of the pandemic.

Elliott, Santasia - Covid-19 Journal, Santasia Elliott

Personal Journals

Personal journal of Santasia Elliot that includes images of business signs a snippets of social life in the Fall of 2020 as it relates to the effect of the pandemic on communities. In this instance, the documentation is from Danville, IL.

Stutzman, Kelsi - Covid-19 Journal, Kelsi Stutzman

Personal Journals

Personal journal of Kelsi Stutzman, a student in Dr. Laughlin-Schultz's HIS3810 History of Illinois course during Fall, 2020

Vitamin D In Covid-19 Pneumonia: High Yield With Low Risk, Shahan Waheed, Emaduddin Siddiqui

Department of Emergency Medicine

No abstract provided.

Genomic Diversity Of Bacteriophages Infecting Microbacterium Spp, Deborah Jacobs-Sera, Lawrence A. Abad, Richard M. Alvey, Kirk R. Anders, Haley G. Aull, Suparna S. Bhalla, Lawrence S. Blumer, David W. Bollivar, J. Alfred Bonilla, Kristen A. Butela, Roy J. Coomans, Steven G. Cresawn, Tom D'Elia, Arturo Diaz, Ashley M. Divens, Nicholas P. Edgington, Gregory D. Frederick, Maria D. Gainey, Rebecca A. Garlena, Kenneth W. Grant, Susan M.R. Gurney, Heather L. Hendrickson, Lee E. Hughes, Margaret A. Kenna, Karen K. Klyczek, Hari Kotturi, Travis Mavrich, Angela L. Mckinney, Evan C. Merkhofer, Jordan Moberg Parker, Sally D. Molloy

Life Sciences Faculty Research

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, …

Understanding Human Astrovirus From Pathogenesis To Treatment, Virginia Hargest

Theses and Dissertations (ETD)

While human astroviruses (HAstV) were discovered nearly 45 years ago, these small positive-sense RNA viruses remain critically understudied. These studies provide fundamental new research on astrovirus pathogenesis and disruption of the gut epithelium by induction of epithelial-mesenchymal transition (EMT) following astrovirus infection. Here we characterize HAstV-induced EMT as an upregulation of SNAI1 and VIM with a down regulation of CDH1 and OCLN, loss of cell-cell junctions most notably at 18 hours post-infection (hpi), and loss of cellular polarity by 24 hpi. While active transforming growth factor- (TGF-) increases during HAstV infection, inhibition of TGF- signaling does not hinder EMT induction. …

Characterization Of A Plasmid-Based Dna Vaccine For Simian Immunodeficiency Virus, Priya Sanipara

Honors Theses

Described as one of the world’s worst pandemics, HIV (Human Immunodeficiency Virus) infects millions of people each year and is the cause for AIDS (Acquired Immunodeficiency Syndrome). Despite the development of vaccines for numerous infectious diseases such as polio, small pox, and influenza, a vaccine for HIV remains elusive due to the virus’s high mutation rate and ability to evade the immune system. HIV causes depletion of CD4+ lymphocytes, resulting in a weakened immune system. However, the development of a plasmid-based DNA vaccine approach may help revolutionize vaccine development for HIV due to its ability to confer cellular and humoral …

Life During A Pandemic, Srinivasan Ragothaman

Creative Work

This is a short poem (6 stanzas) about the current pandemic and the trials and tribulations people are going through. This describes the heroic efforts by the doctors, nurses, and other frontline warriors in tackling the virus related illnesses and pays a rich tribute to all heroes from every walk of life who are in the front fighting this disease. It hopes for a plan, a vaccine, and a cure soon. This poem also describes the switchover to remote instruction at a reginal University, student and faculty adjustments to the pandemic and pokes gentle fun at the opportunity to watch …

Messer, Braden - Covid-19 Journal, Braden Messer

Personal Journals

EIU student Braden Messer recounts the transition from Spring Break to online classes. He talks of quarantine life at home, and his stepmother's role as an attorney working with forced quarantine orders.

Zamora, Celeste - Covid-19 Journal, Celeste Zamora

Personal Journals

EIU student Celeste Zamora recounts life while quarantining in Charleston, IL while maintaining her studies and also working at a local hotel. She details Covid policies as they develop, including hotel practices such as the constant wearing of gloves, putting in place a new glass window, and no admittance of out of state people.

Osborne, Ethan - Covid-19 Journal, Ethan Osborne

Personal Journals

EIU student Ethan Osborne recounts in detail the experience and frustration of living at home and working on his family farm in the early months of the pandemic, March-May 2020. He also details his observations of and feelings about the news coverage of the pandemic as well as the disregard (particularly by young people) for shelter in place mandates.

Klepzig, Logan - Covid-19 Journal, Logan Klepzig

Personal Journals

EIU student Logan Klepzig documents travel from Charleston, IL to Mohomet, IL (approximately 1 hour) to deliver groceries to, and visit his grandparents. He also describes the difficulty of not being able to celebrate birthdays, and see family. His journal also includes a number of links to regional and national news stories from the months of March and April of 2020, as well as images documenting pandemic restrictions around the EIU campus.

Mchale, Marguerite - Covid-19 Journal, Marguerite Mchale

Personal Journals

Marguerite McHale, and EIU student in Professor Mark Dries' HIS 1595 class maintains an upbeat journal documenting the challenges of the pandemic. Of particular note, she describes the growing divide between those supportive of the social distancing and masking initiatives, as well as the impact on high school students who she maintains friendships with as one who graduated a year early from high school. She includes a number of pieces of high school student commentary as well as memes related to the pandemic, and links to news stories. She also describes her home life, and finding ways to keep busy …

Drake, Benjamin - Covid-19 Journal, Benjamin Drake

Personal Journals

EIU student Benjamin Drake (freshman at the time of his journal writing in Spring, 2020), and History of Illinois (HIS 3810) student, reflects on the early months of the pandemic. He discusses the frustrations of the disruption of social life, not being on campus with friends, and also experiences with activities like playing virtual Dungeons and Dragons.

Spencer, Julia - Covid-19 Journal, Julia Spencer

Personal Journals

EIU student Julia Spencer describes the challenges adjusting to the new normal of the pandemic as it sets in. In particular she writes about struggles staying motivated to keep up with her studies, and the oddity of having classes on zoom. Her experience is compounded by health scares involving her mother and a friend.

Klein, Will - Covid-19 Journal, Will Klein

Personal Journals

EIU student and baseball player (drafted by the Kansas City Royals in the 5th round of the 2020 draft) documents the upheaval of life in Charleston and at EIU in the early weeks of the pandemic. In particular he describes the distress of day he found out about the cancellation of the baseball season, while the EIU baseball team was travelling.

Smrt Sequencing Of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability In Adenines Targeted By Restriction Modification Systems, Samantha R. Coy, Eric R. Gann, Spiridon E. Papoulis, Michael E. Holder, Nadim J. Ajami, Joseph F. Petrosino, Erik R. Zinser, James L. Van Etten, Steven W. Wilhelm

James Van Etten Publications

Chloroviruses (family Phycodnaviridae) infect eukaryotic, freshwater, unicellular green algae. A unique feature of these viruses is an abundance of DNA methyltransferases, with isolates dedicating up to 4.5% of their protein coding potential to these genes. This diversity highlights just one of the long-standing values of the chlorovirus model system; where group-wide epigenomic characterization might begin to elucidate the function(s) of DNA methylation in large dsDNA viruses. We characterized DNA modifications in the prototype chlorovirus, PBCV-1, using single-molecule real time (SMRT) sequencing (aka PacBio). Results were compared to total available sites predicted in silico based on DNA sequence alone. SMRT-software detected …