Virology Commons^™

Clinical And In Vitro Evidence Favoring Immunoglobulin Treatment Of A Chronic Norovirus Infection In A Patient With Common Variable Immunodeficiency, Jeroen J A Van Kampen, Virgil A S H Dalm, Pieter L A Fraaij, Bas B Oude Munnink, Claudia M E Schapendonk, Ray W Izquierdo-Lara, Nele Villabruna, Khalil Ettayebi, Mary K Estes, Marion P G Koopmans, Miranda De Graaf

Faculty, Staff and Students Publications

BACKGROUND: Immunocompromised individuals can become chronically infected with norovirus, but effective antiviral therapies are not yet available.

METHODS: Treatments with nitazoxanide, ribavirin, interferon alpha-2a, and nasoduodenally administered immunoglobulins were evaluated sequentially in an immunocompromised patient chronically infected with norovirus. In support, these components were also applied to measure norovirus inhibition in intestinal enteroid cultures in vitro. Viral RNA levels were determined in fecal and plasma samples during each treatment and viral genomes were sequenced.

RESULTS: None of the antivirals resulted in a reduction of viral RNA levels in feces or plasma. However, during ribavirin treatment, there was an increased accumulation …

The “Big Six”: Hidden Emerging Foodborne Bacterial Pathogens, Mona G. Alharbi, Rashad R. Al-Hindi, Ahmed Esmael, Ibrahim A. Alotibi, Sheren A. Azhari, Mazen S. Alseghayer, Addisu D. Teklemariam

Nebraska Center for Virology: Faculty Publications

Non-O157 Shiga toxin-producing Escherichia coli (STEC) are emerging serogroups that often result in diseases ranging from diarrhea to severe hemorrhagic colitis in humans. The most common non-O157 STEC are O26, O45, O103, O111, O121, and O145. These serogroups are known by the name “big six” because they cause severe illness and death in humans and the United States Department of Agriculture declared these serogroups as food contaminants. The lack of fast and efficient diagnostic methods exacerbates the public impact of the disease caused by these serogroups. Numerous outbreaks have been reported globally and most of these outbreaks were caused by …

Butyrate-Producing Bacteria And Insulin Homeostasis: The Microbiome And Insulin Longitudinal Evaluation Study (Miles), Jinrui Cui, Gautam Ramesh, Martin Wu, Elizabeth T Jensen, Osa Crago, Alain G Bertoni, Chunxu Gao, Kristi L Hoffman, Patricia A Sheridan, Kari E Wong, Alexis C Wood, Yii-Der I Chen, Jerome I Rotter, Joseph F Petrosino, Stephen S Rich, Mark O Goodarzi

Faculty, Staff and Students Publications

Gut microbiome studies have documented depletion of butyrate-producing taxa in type 2 diabetes. We analyzed associations between butyrate-producing taxa and detailed measures of insulin homeostasis, whose dysfunction underlies diabetes in 224 non-Hispanic Whites and 129 African Americans, all of whom completed an oral glucose tolerance test. Stool microbiome was assessed by whole-metagenome shotgun sequencing with taxonomic profiling. We examined associations among 36 butyrate-producing taxa (n = 7 genera and 29 species) and insulin sensitivity, insulin secretion, disposition index, insulin clearance, and prevalence of dysglycemia (prediabetes plus diabetes, 46% of cohort), adjusting for age, sex, BMI, and race. The genus Coprococcus …

Viruses In Astrobiology, Ignacio De La Higuera, Ester Lázaro

Biology Faculty Publications and Presentations

Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very …

Sars-Cov-2 Omicron (B.1.1.529) Variant: Structural Features, Biological Characteristics, Impact On Scientific Research, General Precautions And Protective Procedures; A Systematic Review, Prithivi Nagarajan, Anitha Vetrivel, Jayanthi Kumar, Anusheela Howlader, Kumar Rangarajalu, Satheesh Kumar Sabapathy, Muthu Gopal, Saravanaavel Kumar

Journal of Mind and Medical Sciences

The SARS-CoV-2 mutations that have occurred have alarmed the entire medical community. Thus, global concerns have been expressed regarding the transmission, pathogenicity and immune evasion of the Omicron strain, which shares mutations with the variants of concern Alpha, Beta, and Gamma strains. Still, Omicron transmission has crossed numerous borders worldwide compared to other types of SARS-CoV-2. The number of confirmed cases has increased and is reappearing in India. Given the worrisome situation created by the Omicron outbreak, scientists and postgraduates have had to make decisions about current research programs at institutions around the globe. The Omicron variants under development have …

Proteômica Plasmática Quantitativa De Pacientes Sobreviventes E Não Sobreviventes De Covid-19 Internados No Hospital Revela Potenciais Biomarcadores Prognósticos E Alvos Terapêuticos, D C. Flora, A D. Valle, H Abs Pereira, T F. Garbieri, L. T. Grizzo, T J. Dionisio, A L. Leite, D Mc Rosa, C F. Santos, M Ar Buzalaf

Nebraska Center for Virology: Faculty Publications

O desenvolvimento de novas abordagens que permitam a avaliação precoce de quais casos de COVID-19 provavelmente se tornarão críticos e a descoberta de novos alvos terapêuticos são importantes. Neste estudo de coorte, foi avaliado o perfil proteômico e laboratorial do plasma de 163 pacientes internados no Hospital Estadual de Bauru (Bauru, SP, Brasil) entre 4 de maio e 4 de julho de 2020, que foram diagnosticados com COVID-19 por RT-PCR a partir de amostras de swab nasofaríngeo amostras. Amostras de plasma foram coletadas na admissão para análises laboratoriais de rotina e análise proteôomica quantitativa shotgun livre de marcadores. De acordo …

Maternal Gut Microbiota Mediate Intergenerational Effects Of High-Fat Diet On Descendant Social Behavior, Claudia M Di Gesù, Lisa M Matz, Ian J Bolding, Robert Fultz, Kristi L Hoffman, Antonella Marino Gammazza, Joseph F Petrosino, Shelly A Buffington

Faculty, Staff and Students Publications

Dysbiosis of the maternal gut microbiome during pregnancy is associated with adverse neurodevelopmental outcomes. We previously showed that maternal high-fat diet (MHFD) in mice induces gut dysbiosis, social dysfunction, and underlying synaptic plasticity deficits in male offspring (F1). Here, we reason that, if HFD-mediated changes in maternal gut microbiota drive offspring social deficits, then MHFD-induced dysbiosis in F1 female MHFD offspring would likewise impair F2 social behavior. Metataxonomic sequencing reveals reduced microbial richness among female F1 MHFD offspring. Despite recovery of microbial richness among MHFD-descendant F2 mice, they display social dysfunction. Post-weaning Limosilactobacillus reuteri treatment increases the abundance of short-chain …

Bird Species Define The Relationship Between West Nile Viremia And Infectiousness To Culex Pipiens Mosquitoes, Jefferson A. Vaughan, Robert Newman, Michael J. Turrell

Biology Faculty Publications

The transmission cycle of West Nile virus (WNV) involves multiple species of birds. The relative importance of various bird species to the overall transmission is often inferred from the level and duration of viremia that they experience upon infection. Reports utilizing in vitro feeding techniques suggest that the source and condition of blood in which arboviruses are fed to mosquitoes can significantly alter the infectiousness of arbovirus to mosquitoes. We confirmed this using live hosts. A series of mosquito feedings with Culex pipiens was conducted on WNV-infected American robins and common grackles over a range of viremias. Mosquitoes were assayed …

Role Of Tetraspanins In Sars-Cov-2 Fusion And Entry, Marcos Saul Santiago Figueroa

Master's Theses

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the pandemic the world has been facing in recent years. Even as new countermeasures are developed, there is still much we don’t know in terms of its entry into host cells. Tetraspanins are transmembrane proteins that are near ubiquitous amongst cell types. They fulfill numerous roles, including that of a viral co-receptor. Here, we considered whether tetraspanins, specifically CD9, CD63, and CD81 influence SARS-CoV-2 fusion and entry. Using ACE2-LgBit and tetraspanin overexpressing EVs and HeLa cells, we find that the presence of excess tetraspanins inhibit fusion and entry. However, we …

Forty Years Without Family: Three Novel Bacteriophages With High Similarity To Spp1 Reveal Decades Of Evolutionary Stasis Since The Isolation Of Their Famous Relative, Veronique A. Delesalle, Brianne E. Tomko, Albert C. Vill, Katherine B. Lichty, Gregory P. Krukonis

Biology Faculty Publications

SPP1, an extensively studied bacteriophage of the Gram-positive Bacillus subtilis, is a model system for the study of phage–host interactions. Despite progress in the isolation and characterization of Bacillus phages, no previously fully sequenced phages have shared more than passing genetic similarity to SPP1. Here, we describe three virulent phages very similar to SPP1; SPP1 has greater than 80% nucleotide sequence identity and shares more that 85% of its protein coding genes with these phages. This is remarkable, given more than 40 years between the isolation of SPP1 and these phages. All three phages have somewhat larger genomes and more …

Pathogenesis Of Tobacco-Associated Lung Adenocarcinoma Is Closely Coupled With Changes In The Gut And Lung Microbiomes, Casey T Finnicum, Zahraa Rahal, Maya Hassane, Warapen Treekitkarnmongkol, Ansam Sinjab, Rhiannon Morris, Yuejiang Liu, Elizabeth L Tang, Sarah Viet, Jason L Petersen, Philip L Lorenzi, Lin Tan, Joseph Petrosino, Kristi L Hoffman, Junya Fujimoto, Seyed Javad Moghaddam, Humam Kadara

Faculty, Staff and Students Publications

Microbial dysbiosis has emerged as a modulator of oncogenesis and response to therapy, particularly in lung cancer. Here, we investigate the evolution of the gut and lung microbiomes following exposure to a tobacco carcinogen. We performed 16S rRNA-Seq of fecal and lung samples collected prior to and at several timepoints following (nicotine-specific nitrosamine ketone/NNK) exposure in Gprc5a^−/− mice that were previously shown to exhibit accelerated lung adenocarcinoma (LUAD) development following NNK exposure. We found significant progressive changes in human-relevant gut and lung microbiome members (e.g., Odoribacter, Alistipes, Akkermansia, and Ruminococus) that are closely associated with …

Phage Resistance Accompanies Reduced Fitness Of Uropathogenic Escherichia Coli In The Urinary Environment, Jacob J Zulk, Justin R Clark, Samantha Ottinger, Mallory B Ballard, Marlyd E Mejia, Vicki Mercado-Evans, Emmaline R Heckmann, Belkys C Sanchez, Barbara W Trautner, Anthony W Maresso, Kathryn A Patras

Faculty, Staff and Students Publications

Urinary tract infection (UTI) is among the most common infections treated worldwide each year and is caused primarily by uropathogenic Escherichia coli (UPEC). Rising rates of antibiotic resistance among uropathogens have spurred a consideration of alternative treatment strategies, such as bacteriophage (phage) therapy; however, phage-bacterial interactions within the urinary environment are poorly defined. Here, we assess the activity of two phages, namely, HP3 and ES17, against clinical UPEC isolates using in vitro and in vivo models of UTI. In both bacteriologic medium and pooled human urine, we identified phage resistance arising within the first 6 to 8 h of coincubation. …

Integrated Relationship Of Nasopharyngeal Airway Host Response And Microbiome Associates With Bronchiolitis Severity, Michimasa Fujiogi, Yoshihiko Raita, Marcos Pérez-Losada, Robert J Freishtat, Juan C Celedón, Jonathan M Mansbach, Pedro A Piedra, Zhaozhong Zhu, Carlos A Camargo, Kohei Hasegawa

Faculty, Staff and Students Publications

Bronchiolitis is a leading cause of infant hospitalizations but its immunopathology remains poorly understood. Here we present data from 244 infants hospitalized with bronchiolitis in a multicenter prospective study, assessing the host response (transcriptome), microbial composition, and microbial function (metatranscriptome) in the nasopharyngeal airway, and associate them with disease severity. We investigate individual associations with disease severity identify host response, microbial taxonomical, and microbial functional modules by network analyses. We also determine the integrated relationship of these modules with severity. Several modules are significantly associated with risks of positive pressure ventilation use, including the host-type I interferon, neutrophil/interleukin-1, T cell …

The Roles Of Gut Microbiome And Plasma Metabolites In The Associations Between Abo Blood Groups And Insulin Homeostasis: The Microbiome And Insulin Longitudinal Evaluation Study (Miles), Ruifang Li-Gao, Kirk Grubbs, Alain G Bertoni, Kristi L Hoffman, Joseph F Petrosino, Gautam Ramesh, Martin Wu, Jerome I Rotter, Yii-Der Ida Chen, Anne M Evans, Richard J Robinson, Laura Sommerville, Dennis Mook-Kanamori, Mark O Goodarzi, Gregory A Michelotti, Patricia A Sheridan

Faculty, Staff and Students Publications

Non-O blood groups are associated with decreased insulin sensitivity and risk of type 2 diabetes. A recent study pinpointed the associations between ABO blood groups and gut microbiome, which may serve as potential mediators for the observed increased disease risks. We aimed to characterize associations between ABO haplotypes and insulin-related traits as well as potential mediating pathways. We assessed insulin homeostasis in African Americans (AAs; n = 109) and non-Hispanic whites (n = 210) from the Microbiome and Insulin Longitudinal Evaluation Study. The ABO haplotype was determined by six SNPs located in the ABO gene. Based on prior knowledge, …

Intrinsic Cardiac Effects Of Severe Acute Respiratory Syndrome Coronavirus 2 In Coronavirus Disease 2019, Brittany Danielle Brumback

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cardiac arrhythmias, particularly ventricular arrhythmias, can be life-threatening and caused by both congenital genetic mutations and acquired cardiac injury. My thesis work was originally focused on delineating the effects of genetic mutation-driven dysregulation of a protein called Hey2 in Brugada Syndrome, a complex disease characterized by a predisposition to dangerous arrhythmias originating in the right ventricular outflow tract. In response to the pandemic, my thesis work shifted toward understanding the mechanisms of cardiovascular injury in Coronavirus disease 2019 (COVID-19), which is associated with serious cardiovascular complications, including ventricular arrhythmias and sudden cardiac death as well as endothelial dysfunction and coagulopathies. …

Neural Stem Cells: Age-Dependent Outcomes During Viral Infections In The Central Nervous System, Manisha N. Chandwani

Electronic Theses and Dissertations

Viral infections in the central nervous system (CNS) are associated with neurodevelopmental and neurobehavioral deficits. The outcomes of viral infections can be driven by damage and death of neurons. Neural stem cells (NSCs) play key roles in neurodevelopment, repair, and physiological brain function. During a viral infection, NSC activity can disturbed by direct infection of NSCs by the virus or by anti-viral immune response. Here, we aimed to assess whether the anti-viral immune response can impact NSC activity during an immunocompetent response in the adult brain. We utilized a transgenic mouse model of Measles virus infection where only the CNS …

Investigating The Role Of Sphingosine Kinases During Alphavirus Infection, Opeoluwa Oyewole

Theses & Dissertations

Several alphaviruses, critical human pathogens, have re-emerged in recent years. Alphaviruses are found on all continents and infect both invertebrates and vertebrates, including some aquatic animals. They are classified as arboviruses because hematophagous arthropods transmit them. Based on the symptoms they cause, alphaviruses are classified as either arthritogenic or encephalitic.

Rising global travel has led to outbreaks of infections in new regions, increasing the geographical ranges of alphaviruses and causing new infections in susceptible hosts. Currently, there are no approved prophylactic or therapeutic measures to prevent or treat alphavirus infections; prevention measures have focused on vector control. These measures are …

Functional Characterization Of Mycobacterium Smegmatis Phage Moomoo Gene Products: Identification Of Toxic Genes, Whitney Heard

Masters Theses & Specialist Projects

Mycobacteriophages are a group of phages that infect members of the genus Mycobacteria. Previous studies have conducted extensive comparisons of the mycobacteriophage genomes and amino acid sequences to establish different phage families. MooMoo is a singleton mycobacteriophage that has been characterized due to its lack of appreciable homology to other phages. Some of its unique properties include its structure and the isolation of a mutant that causes clear plaque phenotypes. The experiments described in this thesis identified three MooMoo phage (gp87, gp90, and gp91) encoded proteins that are toxic to the bacterial host, Mycobacterium smegmatis.Through the use of a …

Salivary Biomarker Evaluation Of Chronic Pancreatitis Patients Reveals Alterations In Human Proteins, Cytokines, Prostaglandin E2 Levels, And Bacterial Diversity, Richard T Waldron, Elaina K Jones, Vincent I Anani, Jolaine M Hines, Jing Zhao, Aurelia Lugea, Marcio A Diniz, Sungjin Kim, Aida Habtezion, Kristi L Hoffman, Joseph F Petrosino, William E Fisher, Liang Li, Ryan J Lennon, Ravinder Jit Singh, Santhi Swaroop Vege, Stephen J Pandol, Mark D Topazian

Faculty, Staff and Students Publications

OBJECTIVES: Chronic pancreatitis (CP) is a chronic fibroinflammatory condition of the pancreas difficult to diagnose in early stages. Novel biomarkers useful to facilitate early diagnosis or treatment responses may be found in biofluids. Although saliva can be easily and noninvasively collected from patients, useful salivary biomarkers from CP patients have not yet been identified.

METHODS: Here, we analyzed the proteome by quantitative proteomics, cytokine/chemokine levels by Luminex analysis, prostaglandin E2 (PGE2) levels by a mass spectrometry-based assay, and bacterial species diversity by 16S ribosomal ribonucleic acid sequencing in saliva samples from confirmed CP patients and healthy controls.

RESULTS: Our results …

Defining The Importance Of The Hnrnp I Interaction To The Sindbis Virus Subgenomic Viral Rna Using An Innovative Tethering Approach., Claire Westcott

Electronic Theses and Dissertations

Old World alphaviruses cause significant outbreaks of illness and debilitating multi-joint arthritis for prolonged periods. Currently, there are no FDA approved vaccines or antiviral therapies; and thus, there is a critical need to identify and characterize the molecular biology of alphaviruses. Alphaviruses rely on the host cell machinery to complete the viral lifecycle and are dependent on interactions with host RNA binding proteins. Accordingly, several host heterogenous nuclear ribonucleoprotein proteins (hnRNPs) have been found to bind to the Sindbis virus (SINV) RNAs. Disrupting the interaction sites in the viral RNAs of these RNA:Protein interactions results in decreased viral titers in …

Genomic And Functional Characterization Of Vancomycin-Resistant Enterococci-Specific Bacteriophages In The Galleria Mellonella Wax Moth Larvae Model, Lynn El Haddad, Georgios Angelidakis, Justin R Clark, Jesus F Mendoza, Austen L Terwilliger, Christopher P Chaftari, Mark Duna, Serena T Yusuf, Cynthia P Harb, Mark Stibich, Anthony Maresso, Roy F Chemaly

Faculty, Staff and Students Publications

Phages are naturally occurring viruses that selectively kill bacterial species without disturbing the individual’s normal flora, averting the collateral damage of antimicrobial usage. The safety and the effectiveness of phages have been mainly confirmed in the food industry as well as in animal models. In this study, we report on the successful isolation of phages specific to Vancomycin-resistant Enterococci, including Enterococcus faecium (VREfm) and Enterococcus faecalis from sewage samples, and demonstrate their efficacy and safety for VREfm infection in the greater wax moth Galleria mellonella model. No virulence-associated genes, antibiotic resistance genes or integrases were detected in …

Dietary Fatty Acid Intake And The Colonic Gut Microbiota In Humans, Anthony A Xu, Luke K Kennedy, Kristi Hoffman, Donna L White, Fasiha Kanwal, Hashem B El-Serag, Joseph F Petrosino, Li Jiao

Faculty, Staff and Students Publications

A high-fat diet has been associated with systemic diseases in humans and alterations in gut microbiota in animal studies. However, the influence of dietary fatty acid intake on gut microbiota in humans has not been well studied. In this cross-sectional study, we examined the association between intake of total fatty acids (TFAs), saturated fatty acids (SFAs), trans fatty acids (TrFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), n3-FAs, and n6-FAs, and the community composition and structure of the adherent colonic gut microbiota. We obtained 97 colonic biopsies from 34 participants with endoscopically normal colons. Microbial DNA was used to …

Temporal Changes In Gastrointestinal Fungi And The Risk Of Autoimmunity During Early Childhood: The Teddy Study, Thomas A Auchtung, Christopher J Stewart, Daniel P Smith, Eric W Triplett, Daniel Agardh, William A Hagopian, Anette G Ziegler, Marian J Rewers, Jin-Xiong She, Jorma Toppari, Åke Lernmark, Beena Akolkar, Jeffrey P Krischer, Kendra Vehik, Jennifer M Auchtung, Nadim J Ajami, Joseph F Petrosino

Faculty, Staff and Students Publications

Fungal infections are a major health problem that often begin in the gastrointestinal tract. Gut microbe interactions in early childhood are critical for proper immune responses, yet there is little known about the development of the fungal population from infancy into childhood. Here, as part of the TEDDY (The Environmental Determinants of Diabetes in the Young) study, we examine stool samples of 888 children from 3 to 48 months and find considerable differences between fungi and bacteria. The metagenomic relative abundance of fungi was extremely low but increased while weaning from milk and formula. Overall fungal diversity remained constant over …

Resolving The Repression Pathway Of Virulence Gene Hila In Salmonella, Alexandra King, Lon Chubiz Phd, Brenda Pratte, Lauren Daugherty

Undergraduate Research Symposium

Salmonella is a relatively abundant, virulent species of bacteria that is most known for spreading gastrointestinal diseases through food. These illnesses result in approximately 1.35 million infections, including over 25,000 hospitalizations each year, in the U.S. alone (CDC.gov). As antibiotic resistance becomes an increasingly urgent public health problem, the importance of developing alternative treatment methods is only becoming more crucial. One of the genes responsible for this virulence is known as hilA. HilA is the main transcriptional regulator of Salmonella Pathogenicity Island-1 gene (UniProt). SPI-1 plays an important role in the invasion of Salmonella into epithelial cells. The proteins encoded …

Discovery Of The First Lyticstaphylococcus Pseudintermedius/ Staphylococcus Aureus Polyvalent Bacteriophages, Haroldo Hernandez Santos, Justin Clark, Austen Terwilliger, Anthony Maresso

Faculty, Staff and Students Publications

Background:

There are no verified lytic Staphylococcus pseudintermedius phages in the literature and few temperate phage genomes in databases. S. pseudintermedius is an opportunistic zoonotic pathogen of great importance in veterinary and human medicine.

Materials and Methods:

We discovered phages against canine-derived S. pseudintermedius isolates by screening dog feces, hair, and skin swabs. Fourteen new phages were isolated and characterized by genomic analysis, transmission electron microscopy, and host range determination.

Results:

Three phages—DH2, DH5, and DS10, a phage K variant—were predicted lytic by sequencing, a designation supported by mitomycin C induction. All three are S. pseudintermedius and Staphylococcus aureus polyvalent …

Gut Commensals Modulate Siv/Shiv Pathogenesis And Therapeutics, Samuel Johnson

Theses & Dissertations

Despite significant advancements in combination antiretroviral therapy (cART), ongoing inflammation in the brain and gut remain two of the most significant hurdles in the health of people living with human immunodeficiency virus (HIV). Additionally, a viral reservoir in each compartment inhibits cure efforts by allowing rapid viral rebound following cART interruption. Emerging understanding of the gut-brain axis (GBA) implicates each compartment in the modulation of the other in a complex bi-directional interaction mediated by vagus innervation, circulating lymphocytes, and microbiome composition and biproducts. Using multiple models of the simian (and simian-human) immunodeficiency virus (SIV/SHIV) and therapeutic intervention, I present how …

The Impact Of Processing Body Proteins On An Adenovirus Infection, La`Quita Randolph

Biology Theses

Adenovirus is a nonenveloped, double-stranded DNA virus that contains a 36 Kbp genome. The E4 ORF3 region of its genome consists of an E4 11k protein that can reorganize host cell components by relocalizing cellular proteins. One such cellular component is the cytoplasmic processing body, which consists of proteins involved in translational repression of mRNA and mRNA degradation. During an adenovirus infection, processing body proteins Ddx6 and Pat1b have been shown to colocalize and form aggresomes. Aggresomes induced by E4 11k are specific to the adenovirus serotype 5 (Ad 5). In this study, cytoplasmic Pat1b foci were observed and quantified …

Systems Biology Approach To Functionally Assess The Clostridioides Difficile Pangenome Reveals Genetic Diversity With Discriminatory Power, Charles J Norsigian, Heather A Danhof, Colleen K Brand, Firas S Midani, Jared T Broddrick, Tor C Savidge, Robert A Britton, Bernhard O Palsson, Jennifer K Spinler, Jonathan M Monk

Faculty, Staff and Students Publications

Combatting Clostridioides difficile infections, a dominant cause of hospital-associated infections with incidence and resulting deaths increasing worldwide, is complicated by the frequent emergence of new virulent strains. Here, we employ whole-genome sequencing, high-throughput phenotypic screenings, and genome-scale models of metabolism to evaluate the genetic diversity of 451 strains of C. difficile. Constructing the C. difficile pangenome based on this set revealed 9,924 distinct gene clusters, of which 2,899 (29%) are defined as core, 2,968 (30%) are defined as unique, and the remaining 4,057 (41%) are defined as accessory. We develop a strain typing method, sequence typing by accessory genome (STAG), …

Characterization Of The Role Of The Replicase And Quasispecies Diversity In Flaviviral Evolution And Host Adaptation, Haley Caldwell

Legacy Theses & Dissertations (2009 - 2024)

Flaviviruses include several emerging and re-emerging arboviruses that cause millions of infections each year. Although relatively well-studied, much remains unknown regarding the mechanisms and means by which these viruses adapt to different hosts and rapidly alternate between hosts. Different aspects of flaviviral biology impact host switching, viral fitness, and the generation of viral diversity during genome replication by the NS3 and NS5 proteins. Together these factors may impact host plasticity.

Mathematical Modeling Of Potassium Modulated Viral Infection, Zaira Elizabeth Mather

Open Access Theses & Dissertations

In recent years, there is a growing interest in the investigation of using potassium to treat virus infections. In the region of infection, there is a biological observation of extracel- lular potassium level being typically very low whereas the intracellular potassium levels are much higher. There are numerous biological studies showing that elevated potassium levels in the extracellular membrane tends to block virus infections. A recent effort in this direction is a collaborative research conducted by mathematicians and biologists from the University of Texas at El Paso, New Mexico State University, and the University of New Mexico, where we develop …