Virology Commons^™

Virology: Mutagenizing The Proteolytic Cleavage Site In The Major Capsid Protein In Ssv1, Thejanee Liyanaarachchi

University Honors Theses

SSV1, spindle-shaped virus 1, is an archaeal virus with a unique shape that belongs to the family of fuselloviruses and infects hyperthermophilic archaea that thrive at 80°C and pH 3. SSV1 has two capsid proteins, VP1 and VP3, that presumably produce the lemon-shaped virion structure characteristic of fuselloviruses. The VP1 amino acid sequence is highly conserved among SSVs. Here, we investigate the importance of the proteolytic cleavage site in position E66 in VP1 by changing its glutamic acid to the other 19 amino acids. We have developed a new protocol for creating SSV1 mutants through HiFi Assembly (NEB) to increase …

Kshv Susceptibility And Transmission Within Tonsillar Specimens, Farizeh Aalam

Pharmaceutical Sciences (PhD) Dissertations

Despite nearly three decades of research, not much is known regarding the early stages of development for KSHV lymphoproliferative disorders, hindering our ability to develop prophylactic measures or effective treatments. This dissertation will focus on the host and viral factors influencing the magnitude and dynamics of KSHV infection in the human tonsil to pave the way for future interventions directed at limiting person-to-person transmission of KSHV.

To understand the contribution of host factors to KSHV susceptibility in B lymphocytes, we generated a library of 40 tonsillar specimens. Our results indicate that the immunological composition of tonsillar lymphocytes varies across our …

Examination Of The Association Between C - Reactive Protein(Crp) And Covid-19 Infection Severity And Length Of Hospitalization, Abdulahi Aremu Ayanwale

Open Access Theses & Dissertations

Chronic stress can lead to many systemic complications and low-grade systemic inflammation including increased levels of inflammatory cytokines, such as C-reactive protein (CRP). CRP is a marker of systemic inflammation and is associated with depression and perceived stress. Elevations can result in ineffective immune responses, thereby increasing the risk of complications and mortality from infections. Recent evidence suggests that uncontrolled inflammatory responses associated with COVID 19 are a major determinant of disease severity.  The COVID 19 is transmitted from one person to another through droplets from coughing, sneezing, talking, touching droplets on surfaces and contamination by hand-to-mouth routes. The mechanism …

Study Of The D-Dimer, C-Reactive Protein, And Autoantibodies Markers Among Hbv Infected Patients In Babylon Province, Iraq, Ahmed Abdul-Abbas Bayram, Hussein O.M. Al-Dahmoshi, Noor S.K. Al-Khafaji, Raheem Tuama Obayes Al Mammori, Ali Husain Shilib Al-Shimmery, Morteza Saki

BioMedicine

Background: Hepatitis B can be defined as one of the dangerous diseases caused by the hepatitis B virus (HBV), which infects the liver and causes liver failure, cirrhosis, and death.

Aims: This study aimed to evaluate the D-dimer, C-reactive protein (CRP), and autoantibodies markers among HBV- infected patients in Babylon province, Iraq, compared to a healthy control group.

Methods: In this cross-sectional study, all patients referred to GIT and liver centers in Merjan Medical City, Babylon, Iraq from January 2016 to January 2018 were screened for HBV infection by quantitative real-time polymerase chain reaction (qPCR). Antinuclear antibody (ANA), dsDNA, D-dimer, …

The Temperature-Dependent Conformational Ensemble Of Sars-Cov-2 Main Protease (Mpro), Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean Mcsweeney, Daniel A. Keedy

Publications and Research

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M^pro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of M^pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M^pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for M^pro, including …

Contact Normalization And The Role Of Maackia Amurensis Seed Lectin As A Novel Chemotherapeutic And Antiviral Agent, Stephanie A. Sheehan

Graduate School of Biomedical Sciences Theses and Dissertations

Cells communicate with each other to coordinate tissue function and homeostasis. Diseases including cancer, arthritis, and acute respiratory disease syndrome (ARDS) require a breakdown in this intercellular communication. For example, cancer progression is suppressed by junctional communication between nontransformed and transformed cells. This process is called contact normalization. Junctional communication must be disrupted to enable transformed cells to grow into malignancies. However, the junctions and mechanisms by which nontransformed cells normalize cell behavior have not been clearly defined. My project aimed to identify junctions and elucidate mechanisms underlying contact normalization. We discovered that cadherins, specifically N-cadherin, form junctions that enable …

Investigation Of An Alternative Protocol For The Production Of Sars-Cov-2 Antigenic Proteins, Nichole Ninaltowski

USF Tampa Graduate Theses and Dissertations

With the COVID-19 pandemic showing no signs of slowing down, large-scale antigenic protein production is still needed for surveillance using serologic assays. From screening to vaccines to biotherapeutics, being able to produce the proteins for these assays is essential; however, the current gold standard method for producing SARS-CoV-2 spike proteins is prohibitively expensive for most research groups.

Alternative methods of transfecting mammalian cells to produce recombinant proteins that are relatively inexpensive have been used for years. Unlike the expensive, commercially available lipid-based methods, other established methods such as polyethyleneimine (PEI), are considerably easier, and cheaper to meet the needs of …

Immunometabolic Dysregulation At The Intersection Of Obesity And Covid-19, Collins N. Khwatenge, Marquette Pate, Laura C. Miller, Yongming Sang

Agricultural and Environmental Sciences Faculty Research

Obesity prevails worldwide to an increasing effect. For example, up to 42% of American adults are considered obese. Obese individuals are prone to a variety of complications of metabolic disorders including diabetes mellitus, hypertension, cardiovascular disease, and chronic kidney disease. Recent meta-analyses of clinical studies in patient cohorts in the ongoing coronavirus-disease 2019 (COVID-19) pandemic indicate that the presence of obesity and relevant disorders is linked to a more severe prognosis of COVID-19. Given the significance of obesity in COVID-19 progression, we provide a review of host metabolic and immune responses in the immunometabolic dysregulation exaggerated by obesity and the …

A Bioinformatic And Biochemical Analysis Of Cruciviruses, George William Kasun

Dissertations and Theses

Cruciviruses are novel ssDNA viruses discovered through metagenomics and direct environmental DNA amplification and cloning. The genomes of cruciviruses suggest that gene transfer between RNA and DNA viruses occurred due to the presence of putative protein-encoding genes that are homologous to both ssRNA and ssDNA viruses. In order to gain a better understanding of this group of viruses both bioinformatic analyses and in vitro biochemical experiments were employed. The results of the bioinformatic analyses show that cruciviruses are a highly diverse group of ssDNA viruses. Their placement within established ssDNA phylogenies is difficult due to heterogeneity in their putative replication-associated …

Harness Organoid Models For Virological Studies In Animals: A Cross-Species Perspective, Yongming Sang, Laura C. Miller, Rahul K. Nelli, Luis Gabriel Giménez-Lirola

Agricultural and Environmental Sciences Faculty Research

Animal models and cell culture in vitro are primarily used in virus and antiviral immune research. Whereas the limitation of these models to recapitulate the viral pathogenesis in humans has been made well aware, it is imperative to introduce more efficient systems to validate emerging viruses in both domestic and wild animals. Organoids ascribe to representative miniatures of organs (i.e., mini-organs), which are derived from three-dimensional culture of stem cells under respective differential conditions mimicking endogenous organogenetic niches. Organoids have broadened virological studies in the human context, particularly in recent uses for COVID19 research. This review examines the status and …

Editorial: Pathogens, Pathobionts, And Autoimmunity, Linda A. Spatz, Gregg J. Silverman, Judith A. James

Publications and Research

No abstract provided.

Biocontrol Of Foodborne Pathogens Using Bacteriophages, Dzhuliya Ignatova, Erion Hogan, Simone Dakare, Jean Lu

Symposium of Student Scholars

Biocontrol of Foodborne Pathogens Using Bacteriophages

Dzhuliya Ignatova, Erion Hogan, Simone Dakare, and Jean Lu

Department of Molecular and Cellular Biology

Abstract

Salmonella and Shigella are two important groups of foodborne bacterial pathogens. Salmonella cause an illness called salmonellosis while Shigella cause shigellosis (bacillary dysentery). The most common symptoms of these illnesses are abdominal cramps, diarrhea, and fever. Shigella can also cause bloody diarrhea. It was estimated that each year Salmonella cause 93.8 million cases of gastroenteritis and 155,000 deaths globally. Shigella causes 164.7 million cases and 1.1 million deaths throughout the world yearly. People get these illnesses mainly by …

Bacteriophages Infecting Enterobacter Cloacae To Reduce Bloater Damage In Fermented Cucumbers

Symposium of Student Scholars

Fermented cucumbers are one of the most important fermented vegetables consumed worldwide. During cucumber fermentations, certain undesirable changes may occur. One of such changes is known as bloater defect (hollow cavities in fermented cucumbers), which is primarily caused by gas-producing bacteria including Enterobacter cloacae. Bloater defect lowers product quality and leads to significant economic loss to the pickle industry, and effective preventative methods are needed. Bacteriophages (phages) are highly host-specific bacterial killers. Use of phages to control unwanted bacteria in foods is a promising approach because phages do not change food properties. This research was to isolate, characterize, and …

Effectiveness Of Bacteriophages Against Bloater-Causing Bacteria Enterobacter Cloacae In A Model Food System, Ashley Reed, Dzhuliya Ignatova, Sandra Kopic, Unique Sardeneta

Symposium of Student Scholars

Effectiveness of bacteriophages against bloater-causing bacteria Enterobacter cloacae in a model food system

Department of Molecular and Cellular Biology

Ashley Reed, Dzhuliya Ignatova, Sandra Kopic, Unique Sardeneta, and Jean Lu

Abstract

Cucumber fermentation is one of the most important vegetable fermentations in the United States and Europe. Enterobacter cloacae and other gas-producing bacteria can cause bloater defect (the gas pockets or hollow cavities formed in fermented cucumbers) which lowers the quality and the yield of fermented cucumbers, thereby resulting in significant economic losses to the pickling industry. Cost-effective strategies to control E. cloacae and other microbiota need to be …

Roles Of A Bradykinin Storm And A Cytokine Storm In Covid-19 Cases, Nouha H. Odeh

Honors College Theses

In the light of recent events, it is imperative to understand the key inflammatory response elements that appear to be the source of more severe ailments resulting from a SARS-CoV-2 viral infection known as Covid-19 The more severe cases of Covid-19 are characterized by a severe inflammatory response resulting in tissue damage. My research proposal aims to investigate the two possible culprits of this response: a bradykinin (BK) storm and an interleukin-6 (IL-6) mediated cytokine storm. In both systems respectively, the excess release of these signals subsequently signals the production of even more of the same response element, resulting in …

A Review Of Novel Coronavirus: Cross-Disciplinal Perspective, Iram Asim, Hafsa Rehman, Rabeea Anwar, Humaira Yasmeen

Journal of Bioresource Management

The whole world is under the influence of coronavirus after its first report from Wuhan, China in December 2019. The virus is from coronaviridae family which has zoonotic viruses that can spread from animals to humans. The coronavirus like other viruses of this family produces mild flu-like symptoms within 2-14 days in the human host which progresses to death in severe cases. Unlikely coronavirus spread fast among humans-infectious diseases. Up till now (27/04/2020) around 2.97M cases and 207K deaths have been reported. The presence of a virus in respiratory secretions is diagnosed through molecular methods and chest scans. For this …

Interleukin-17a Facilitates Chikungunya Virus Infection By Inhibiting Ifn-Α2 Expression, Biswas Neupane

Dissertations

Interferons (IFNs) are the key components of innate immunity and are crucial for host defense against viral infections. Here, we report a novel role of interleukin-17A (IL-17A) in inhibiting IFN-α2 expression, thus promoting chikungunya virus (CHIKV) infection. CHIKV infected IL-17A deficient (Il17a^-/-) mice expressed a higher level of IFN-α2 and developed diminished viremia and milder footpad swelling in comparison to wild-type (WT) control mice, this was also recapitulated in IL-17A receptor-deficient (Il17ra^-/-) mice. Interestingly, IL-17A selectively blocked IFN-α2 production during CHIKV, but not West Nile virus (WNV) or Zika virus (ZIKV), infections. Recombinant IL-17A …

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 …

Determinants Of Fine-Scale Heterogeneity In Mosquito-Borne Virus Systems, Elizabeth Handly Mayton

LSU Doctoral Dissertations

ABSTRACT

Arthropod-borne viruses (arboviruses) are the etiological agents of much morbidity and mortality, especially in low- and middle-income countries. Many of these viruses are spread and maintained by mosquitoes, particularly the urban mosquito Aedes aegypti. Zika virus (ZIKV) is responsible for one of the largest vector-borne disease outbreaks in the past decade, affecting millions in Central and South America including a wave of microcephaly among newborns. Mayaro virus (MAYV) is a mosquito-borne virus endemic to South America and is predicted to become an emergent public health threat. Describing the vector-virus transmission systems are critical for understanding the potential spread …

Novel Scalable And Simplified System To Generate Microglia-Containing Cerebral Organoids From Human Induced Pluripotent Stem Cells, Brittany Bodnar, Yongang Zhang, Jinbiao Liu, Yuan Lin, Peng Wang, Zhengyu Wei, Sami Saribas, Yuanjun Zhu, Fang Li, Xu Wang, Wenli Yang, Qingsheng Li, Wen-Zhe Ho, Wenhui Hu

Nebraska Center for Virology: Faculty Publications

Human cerebral organoid (CO) is a three-dimensional (3D) cell culture system that recapitulates the developing human brain. While CO has proved an invaluable tool for studying neurological disorders in a more clinically relevant matter, there have still been several shortcomings including CO variability and reproducibility as well as lack of or underrepresentation of certain cell types typically found in the brain. As the technology to generate COs has continued to improve, more efficient and streamlined protocols have addressed some of these issues. Here we present a novel scalable and simplified system to generate microglia-containing CO (MCO). We characterize the cell …

Functional And Phenotypic Evaluation Of Murine Cytomegalovirus Infection Of The Heart, Cassandra Marie Bonavita

LSU Doctoral Dissertations

Human Cytomegalovirus (HCMV) is a ubiquitous pathogen which infects 50-90% of the world population and results in lifelong latent infection with periodic transient reactivations. In immunocompetent populations acute infection is generally asymptomatic but seropositivity is associated with many chronic diseases, including cardiovascular disease. Despite 139 years of research into HCMV pathogenesis there is still no licensed vaccine and many gaps in the general knowledge of the virus. This includes the role of long term infection as it pertains to chronic diseases. In these studies, murine cytomegalovirus (MCMV) was used as a model of HCMV pathogenesis in the heart. MCMV shares …

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 …

Protective Role Of Palmitoleate Against Zika Virus-Induced Apoptosis In Placental Trophoblasts, Philma Glora Muthuraj

College of Education and Human Sciences: Dissertations, Theses, and Student Research

Zika virus (ZIKV) infection in pregnant women causes congenital Zika syndrome which involves birth defects such as intrauterine growth restriction (IUGR), retinal defects and microcephaly in the fetus. ZIKV infection results in placental pathology which plays a crucial role in disease transmission from mother to fetus. Currently, there is no Food and Drug Administration (FDA) approved vaccine or therapeutic drug against ZIKV. In this thesis, we have elucidated the cell signaling pathways connected to ZIKV-induced apoptosis in trophoblasts and also the protective effect of palmitoleate against ZIKV-induced apoptosis. First, we demonstrated the molecular mechanism behind ZIKV-induced apoptosis using an in …

The Persistence Of Human Norovirus Surrogate In Leafy Greens Production System, Wenjun Deng

Graduate Theses and Dissertations

Since mostly consumed raw, foodborne pathogen contamination of leafy greens has led to a large number of foodborne disease outbreaks and illnesses each year in the United States. Human noroviruses (hNoV) are the most common viral pathogen transmitted by leafy greens. In this dissertation, the persistence of the hNoV surrogate Tulane virus (TV) on pre-harvest lettuce and microgreens was investigated. Lettuces are the most studied leafy green model, while previous hNoV research has mainly focused on the post-harvest stage of production. Here, pre-harvest hydroponically grown lettuce were used to determine TV persistence on leafy greens. After inoculation on leaves at …

Development And Validation Of An Isothermal Amplification Assay For Eastern Equine Encephalitis Virus, Mikayla D. Maddison

USF Tampa Graduate Theses and Dissertations

Eastern Equine Encephalitis virus (EEEV) is a neurotrophic alphavirus for which there is no effective treatment or vaccine for humans. Periodic outbreaks in the Eastern United States represent an ongoing public health problem; Florida serves as the reservoir for EEEV for the rest of the country. Reverse transcription-polymerase chain reaction (RT-PCR) is the current gold standard for molecular diagnostic testing of the presence of EEEV in vectors. However, RT-PCR is technically complex and can be difficult for mosquito control districts to utilize. In order to provide a simple, cost-effective alternative for mosquito surveillance and control, a novel one step reverse …

Global Analysis Of High Cited Papers On “Impact Of Covid-19 On Mental Health” During 2020-21, Ghouse Modin Nabeesab Mamdapur Mr., Brij Mohan Gupta Dr., Sandeep Grover Dr.

Library Philosophy and Practice (e-journal)

A bibliometric analysis based on 160 highly cited papers extracted from the Scopus international database was carried out to provide insights into literature characteristics and publication performances of various participating actors on “Impact of COVID-19 on Mental Health”. Quantitative and qualitative Indicators were applied to measure the productivity and citation impact of most productive participating countries, organizations, authors, journals and significant keywords and to visualise and measure collaborative interaction among them using VOSviewer software. Results obtained from this study can provide valuable information for researchers and policy-makers to identify present and future hotspots in research on “Impact of COVID-19 on …

Ruvb-Like Protein 2 Interacts With The Ns1 Protein Of Influenza A Virus And Affects Apoptosis That Is Counterbalanced By Type I Interferons, Yimeng Wang, Jianhong Zhou, Samuel G. Mackintosh, Yuchun Du

Biological Sciences Faculty Publications and Presentations

The NS1 protein of influenza A virus (IAV) plays important roles in viral pathogenesis and host immune response. Through a proteomic approach, we have identified RuvB-like proteins 1 and 2 (RuvBL1 and RuvBL2) as interacting partners of the NS1 protein of IAVs. Infection of human lung A549 cells with A/PR/8/34 (PR8) virus resulted in reductions in the protein levels of RuvBL2 but not RuvBL1. Further studies with RuvBL2 demonstrated that the NS1-RuvBL2 interaction is RNA-independent, and RuvBL2 binds the RNA-binding domain of the NS1. Infection of interferon (IFN)-deficient Vero cells with wild-type or delNS1 PR8 virus reduced RuvBL2 protein levels …

Psychological Impact Of Novel Coronavirus Covid-19 Across The Globe-A Review, Sadaf Shaheen, Iram Asim, Rida Zainab, Humaira Yasmeen

Journal of Bioresource Management

The recent outbreaks of novel coronavirus disease have unprecedent impact on mental health of patients, front-line healthcare workers and local population. However, the impact is not fully documented. This review explores stress-driven factors, stress-vulnerable groups and stress management interventions. Repetitive exposure to mass media and inappropriate health protective measures has heightened stress responses. Fear of not getting recovered from COVID-19 and disaffection has profound impact of infected individuals and their families. They may experience fear, anxiety, anger, sleep deprives and anorexia which may weakens their immune system thus making them vulnerable to COVID-19. The COVID-19 pandemic has underscored potential gaps …

Mucormycosis (Black Fungus) Maiming Covid Patients: Scientometrics Analysis Through Prism Of Biblioshiny, Sivankalai S, K Sivasekaran

Library Philosophy and Practice (e-journal)

This study analyses the global level outlook of research publications on Mucormycosis output between the period of 1923 to 2021 (May) on different limitations including contribution of authors, communication channel, publications on Institutions, countries, Journals, cited articles and mode of languages. 4451 data was downloaded from core collection of Web of Science bibliographic database using the search term ‘Mucormycosis’ and limited the publications 1900 to 2021, first publication was started in 1923 onwards. 3798 institutions and 8562 different disciplines contributed and 2808 records are in Articles. 4451 records published by 17320 authors and 23552 collaborated authors, documents per author are …

Investigating The Sars-Cov-2 Orf 8 Accessory Protein: Expression, Purification, And Structural Determination, Laney Hedgeman, Caroline Salha

Symposium of Student Scholars

Abstract

In order to provide insight into potential therapeutic breakthroughs for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more research must be done to understand the structure and function of its proteins. The open reading frame 8 (ORF 8) accessory protein is particularly unstable on its own outside of the viral envelope but can be stabilized when bound to the small ubiquitin-related modifier (SUMO) protein. The stable ORF 8-SUMO protein complex can be expressed and purified using familiar techniques and later characterized with nuclear magnetic resonance (NMR) spectroscopy, thus allowing us to gain knowledge about the role it plays …