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Virology: Mutagenizing The Proteolytic Cleavage Site In The Major Capsid Protein In Ssv1, Thejanee Liyanaarachchi 2021 Portland State University

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 …


Response Of Soil Viral And Microbial Functional Diversity To Long-Term Agricultural Management In Jackson, West Tennessee, Ning Duan 2021 Biosystem Engineering and Soil Science

Response Of Soil Viral And Microbial Functional Diversity To Long-Term Agricultural Management In Jackson, West Tennessee, Ning Duan

Doctoral Dissertations

Soil microbial communities are a critical component for ecosystem stability and function. Viruses, as an important biotic controller, have the potential to regulate the abundance and diversity of bacterial communities through infection. Soil is known to harbor abundant and diverse viral assemblages but their ecological role and influence on microbial processes has not been fully elucidated. Microbes can be influenced by viruses not only from infection but though biogeochemical feedbacks of the “microbial (bacterium–phage–DOC) loop” or “viral shunt”. However, we know relatively little about the microbial community and function under the regulation of viruses in soil and how they respond …


Examination Of The Association Between C - Reactive Protein(Crp) And Covid-19 Infection Severity And Length Of Hospitalization, Abdulahi Aremu Ayanwale 2021 University of Texas at El Paso

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 …


Kshv Susceptibility And Transmission Within Tonsillar Specimens, Farizeh Aalam 2021 Chapman University

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 …


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 2021 College of science, University of Babylon, Babylon, Hilla City, Iraq

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 2021 CUNY Advanced Science Research Center

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 Mpro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of Mpro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded Mpro 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 Mpro, including …


Investigation Of An Alternative Protocol For The Production Of Sars-Cov-2 Antigenic Proteins, Nichole Ninaltowski 2021 University of South Florida

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 2021 Tennessee State University

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 2021 Portland State University

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 2021 Tennessee State University

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 2021 CUNY City College

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 2021 Kennesaw State University

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, 2021 Kennesaw State University

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 2021 Kennesaw State University

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 …


Regulation Of Host-Microbe Interactions In Autoimmunity And Antiviral Immunity By Cytosolic Nucleic Acid Sensing And Interferon Signaling, Derek Jerome Platt 2021 Washington University in St. Louis

Regulation Of Host-Microbe Interactions In Autoimmunity And Antiviral Immunity By Cytosolic Nucleic Acid Sensing And Interferon Signaling, Derek Jerome Platt

Arts & Sciences Electronic Theses and Dissertations

Cytosolic nucleic acid sensing and interferon (IFN) signaling are central to the host immune response to microbial pathogens. However, dysregulation of immunological pathways such as these can result in devastating autoimmune disease. In order to provide a robust immune response to pathogen without causing harm to self, the host immune system must engage in a delicate balancing act, interacting with microbes and determining whether they are commensal or pathogenic. The cGAS-STING pathway is a key regulator of host-microbe interactions by cytosolic nucleic sensing and IFN signaling. Loss of function in the cGAS-STING pathway leads to increased susceptibility to pathogenic threats, …


Roles Of A Bradykinin Storm And A Cytokine Storm In Covid-19 Cases, Nouha H. Odeh 2021 Wayne State University

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 2021 Department of Microbiology and Molecular Genetics, The Women University Multan, Pakistan

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 2021 The University of Southern Mississippi

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 …


Determinants Of Fine-Scale Heterogeneity In Mosquito-Borne Virus Systems, Elizabeth Handly Mayton 2021 Louisiana State University and Agricultural and Mechanical College

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 2021 Temple University Lewis Katz School of Medicine

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

Virology Papers

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 …


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