Microbiology Commons^™

The 20th Anniversary Meeting Of The Rocky Mountain Virology Association, Joel Rovnak, Laura A. St Clair, Carley Mcalister, Chinemerem P. Ogbu, Jessica Smolenske, Randall J. Cohrs, Rushika Perera

Nebraska Center for Virology: Faculty Publications

Due to the COVID-19 pandemic and multiple devastating forest fires, the 2020 meeting of the Rocky Mountain Virology Association was held virtually. The three-day gathering featured talks describing recent advances in virology and prion research. The keynote presentation described the measles virus paradox of immune suppression and life-long immunity. Special invited speakers presented information concerning visualizing antiviral effector cell biology in mucosal tissues, uncovering the T-cell tropism of Epstein-Barr virus type 2, a history and current survey of coronavirus spike proteins, a summary of Zika virus vaccination and immunity, the innate immune response to flavivirus infections, a discussion concerning prion …

Chlorovirus Pbcv-1 Multidomain Protein A111/114r Has Three Glycosyltransferase Functions Involved In The Synthesis Of Atypical N-Glycans, Eric Noel, Anna Notaro, Immacolata Speciale, Garry A. Duncan, Cristina De Castro, James L. Van Etten

Nebraska Center for Virology: Faculty Publications

The structures of the four N-linked glycans from the prototype chlorovirus PBCV-1 major capsid protein do not resemble any other glycans in the three domains of life. All known chloroviruses and antigenic variants (or mutants) share a unique conserved central glycan core consisting of five sugars, except for antigenic mutant virus P1L6, which has four of the five sugars. A combination of ge- netic and structural analyses indicates that the protein coded by PBCV-1 gene a111/114r, conserved in all chloroviruses, is a glycosyltransferase with three putative domains of approximately 300 amino acids each. Here, in addition to in silico sequence …

Strategies Targeting Hemagglutinin As A Universal Influenza Vaccine, Brianna L. Bullard, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

Influenza virus has significant viral diversity, both through antigenic drift and shift, which makes development of a vaccine challenging. Current influenza vaccines are updated yearly to in- clude strains predicted to circulate in the upcoming influenza season, however this can lead to a mismatch which reduces vaccine efficacy. Several strategies targeting the most abundant and im- munogenic surface protein of influenza, the hemagglutinin (HA) protein, have been explored. These strategies include stalk-directed, consensus-based, and computationally derived HA immunogens. In this review, we explore vaccine strategies which utilize novel antigen design of the HA protein to improve cross-reactive immunity for development …

Zika Virus Infection Induces Endoplasmic Reticulum Stress And Apoptosis In Placental Trophoblasts, Philma Glora Muthuraj, Prakask K. Sahoo, Madison Kraus, Taylor Bruett, Arun S. Annamalai, Aryamav Pattnaik, Asit K. Pattnaik, Siddappa N. Byrareddy, Sathish Kumar Natarajan

Nebraska Center for Virology: Faculty Publications

Zika virus (ZIKV) infection to a pregnant woman can be vertically transmitted to the fetus via the placenta leading to Congenital Zika syndrome. This is characterized by microcephaly, retinal defects, and intrauterine growth retardation. ZIKV induces placental trophoblast apoptosis leading to severe abnormalities in the growth and development of the fetus. However, the molecular mechanism behind ZIKV-induced apoptosis in placental trophoblasts remains unclear. We hypothesize that ZIKV infection induces endoplasmic reticulum (ER) stress in the trophoblasts, and sustained ER stress results in apoptosis. HTR-8 (HTR-8/SVneo), a human normal immortalized trophoblast cell and human choriocarcinoma-derived cell lines (JEG-3 and JAR) were …

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, …

Comparisons Of Oral, Intestinal, And Pancreatic Bacterial Microbiomes In Patients With Pancreatic Cancer And Other Gastrointestinal Diseases, Mei Chung, Naisi Zhao, Richard Meier, Devin C. Koestler, Guojun Wu, Erika De Castillo, Bruce J. Paster, Kevin Charpentier, Jacques Izard, Karl T. Kelsey, Dominique S. Michaud

Department of Food Science and Technology: Faculty Publications

Background: Oral microbiota is believed to play important roles in systemic diseases, including cancer. Methods: We collected oral samples (tongue, buccal, supragingival, and saliva) and pancreatic tissue or intestinal samples from 52 subjects, and characterized 16S rRNA genes using high-throughput DNA sequencing.

Results: Bray–Curtis plot showed clear separations between bacterial communities in the oral cavity and those in intestinal and pancreatic tissue samples. PERMANOVA tests indicated that bacterial communities from buccal samples were similar to supragingival and saliva samples, and pancreatic duct samples were similar to pancreatic tumor samples, but all other samples were significantly different from each …

Molecular And Genetic Studies On A Sipd/Ipad-Related Virulence Spike Protein From Immune-Suppressive Particles Of A Drosophila Parasitoid, Carlo Miguel A. Sevilla

Dissertations and Theses

Parasitoid wasps are effective biological control agents that have evolved intricate host immune suppression strategies to overcome host immune defenses. The most important anti-parasite defense mechanism is encapsulation, where the host’s blood cells surround the wasp egg. In the Drosophila/Leptopilina host-parasitoid system, extracellular vesicles (EVs) are oviposited along with the wasp egg. The EVs possess spikes and contain hundreds of proteins, some of which enable wasp eggs to escape encapsulation by changing the morphology and function of hemocytes, or killing them. Previous studies have identified an abundant surface/spike protein (SSp40) from Leptopilina heterotoma EVs. While p40, a predicted …

Initial And Advanced Stages Of Microbiota Establishment Within The Tsetse Fly, Miguel Eduardo Medina Munoz

Graduate Theses, Dissertations, and Problem Reports (ETD)

Symbiosis is a long-term physical association between two or more species, although little is known regarding its evolutionary origins, particularly at the genetic level. Tsetse flies are the vector of African trypanosomes, causative agents of Human and Animal African Trypanosomiases. Tsetse provide an ideal model for studying initial and advanced stages of symbiosis. Tsetse have a simple digestive tract microbiota primarily consisting of two bacteria; the ancient mutualist Wigglesworthia glossinidia and the recently acquired Sodalis glossinidius. This work presents a chronological study in evolutionary terms of the history of a microbial-insect association. First, I present concepts on symbiosis and …

A Snapshot Of Ancient Microbial Life: Microorganisms And Organic Compounds In Primary Fluid Inclusions In Bedded Halite, Neoproterozoic Browne Formation Of Central Australia, Sara I. Schreder-Gomes

Graduate Theses, Dissertations, and Problem Reports (ETD)

Modern shallow brine environments contain an abundance of microorganisms. Microorganisms, mineral crystals, and air bubbles can be trapped with those brines in primary fluid inclusions in bedded halite as it grows in shallow saline surface waters. Primary fluid inclusions and their contents can be preserved, unaltered, for millions of years.

The ~830 million-year-old Browne Formation of central Australia contains intervals of bedded halite with unaltered primary fluid inclusions. Intervals of bedded halite were sampled in the Empress 1A core from ~1480 m – 1520 m depths. Here, I used petrography to describe suspect microorganisms and organic compounds that were trapped …

Pseudomonas Aeruginosa Vaccine Development Using Dual-Species Whole Cell And Subunit Vaccines, Catherine Bell Blackwood

Graduate Theses, Dissertations, and Problem Reports (ETD)

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen which can cause severe, recurrent, and chronic infections. The pathogen is highly adaptable, and pneumonia caused by it is associated with high morbidity and mortality, especially in individuals with the genetic disorder cystic fibrosis. Antibiotic resistance amongst clinical isolates of P. aeruginosa is steadily increasing, and multi-drug resistant strains are prevalent. There is currently no vaccine available for commercial use against P. aeruginosa. For these reasons, we sought to understand the immunity to P. aeruginosa induced by whole cell vaccination and identify antigens for development of future subunit vaccines. In this dissertation, …

Remnant Assessment And Soil Inoculation To Inform Large-Scale Prairie Restoration At Eastern Washington University, Erik E. Peterson

EWU Masters Thesis Collection

The Palouse Prairie of Eastern Washington and Western Idaho, characterized by rolling hills of deep loess soil, is one of the most endangered ecosystems in the world, with more than 99% converted to tilled farmland. To mitigate this loss, Eastern Washington University has begun prairie restoration on a tilled wheat field adjacent to campus, in the northern extent of the Palouse Prairie Ecoregion. However, effective restoration requires understanding reference conditions, and there are relatively few studies of remnant prairie plant communities or soils, particularly in the Northern Palouse. From north to south in the Palouse Prairie Ecoregion, there are gradients …

Tree Species Influence On Microbial Functional Gene Abundance And N Cycling In Riparian Soil, Elizabeth Matejczyk

Graduate Theses, Dissertations, and Problem Reports (ETD)

Little is known about how above-ground vegetation may differentially influence the below-ground microbial community structure, abundance, and function. Abundance of soil microbial N cycling genes responsible for nitrification (amoA), denitrification (nirK and nirS), and nitrous oxide reduction (nosZ) may vary with tree species and increasing N availability, and these variables may be used to predict production of NO₃^- and N₂O from soil. Variability of nitrification and denitrification rates have also been linked to tree mycorrhizal associations, with soil beneath tree species associated with arbuscular mycorrhizal (AM) exhibiting greater denitrification rates …

Stomatal Conductance And Reed Canary Grass Suppression Of Native Michigan Trees, David E. Martinez Vasquez, Martin L. Vanderschoot, David Warners

Faculty and Professional Research

Reed canary grass (Phalaris arundinacea), a prominent invasive understory species, threatens native Michigan biodiversity statewide. A notable affected area includes a stretch of agricultural land along Schooley Drain in Caledonia, MI, located in the headwaters of the Plaster Creek watershed. Our study pursues the following questions: “Do native trees provide enough shade to reduce the growth of Reed canary grass?” and “Which native trees best transpire water from a floodplain?”: To answer these questions, we initiated a long-term evaluation of seven different species of native Michigan trees to investigate which species best inhibits the growth of reed canary grass and …

Plaster Creek Floodplain And Adjacent Ravines Near Stanaback Park: Botanical Inventory Highlights And Management Considerations, David Warners, Garrett Crow, Haley Weesies

Faculty and Professional Research

In the summer of 2021, the research team visited this area of ravines and floodplain a total of twenty-one times to conduct our field research. During the visits, they carefully walked throughout different sections of the study site, identifying each vascular plant species they saw growing there and observing how the flora developed throughout the season. In addition to keeping detailed field notes, they documented permanent records of the findings of our inventory by collecting voucher specimens that have been deposited in the Calvin University Herbarium. Additionally, they sent duplicate specimens to the Michigan State University Herbarium and/or University of …

Botanical Inventory Highlights And Management Considerations For Covenant Park, David Warners, Garrett Crow, Haley Weesies

Faculty and Professional Research

In the spring and summer of 2021, Calvin University students and faculty conducted a botanical inventory and assessment of the natural areas in Covenant Park, located at 3724 Shaffer Avenue SE, Kentwood, MI 49512. Given that the property was recently acquired by the City of Kentwood Parks & Recreation, the purpose of this inventory is to inform Kentwood Parks and Recreation staff about the site’s floristic quality, diversity, and ecological significance. The specific objectives of this study are to 1) provide a comprehensive inventory of the species of plants occurring on the property, 2) identify particular areas that would benefit …

The Gut Microbiome Of Hapalemur Griseus Griseus, Propithecus Diadema, And Propithecus Coquereli: A Comparative Study Between Wild And Captive Lemur Species, Brenna Ritchie

Graduate Research Theses & Dissertations

Madagascar is home to thousands of endemic species, making it a biodiversity hotspot that is rapidly losing its fauna due to deforestation and human expansion. Efforts to restore and preserve this unique island are ongoing and several researchers have placed their focus on preventing species extinctions. One research avenue that can help contribute to these efforts is to study health and wellness of animals located in areas affected by these changes. In this study, I sought to characterize microbial community composition of two native lemur species found in Madagascar and compare those profiles to similar species found in captivity in …

Characterizing A Novel Cocksackievirus B3 Protease Mutant And Its Response To Polyamine Depletion, Bridget Hulsebosch

Master's Theses

Enteroviruses, including Coxsackievirus B3 (CVB3), are pervasive pathogens that cause significant disease, including cardiomyopathies. Unfortunately, no treatments or vaccines are available for infected individuals. We identified the host polyamine pathway as a potential drug target, as inhibiting polyamine biosynthesis significantly reduces enterovirus replication in vitro and in vivo. Here, we show that CVB3 is sensitive to polyamine depletion through the polyamine analog diethylnorspermidine (DENSpm) which enhances polyamine catabolism through induction of polyamine acetylation. We demonstrate that CVB3 acquires resistance to DENSpm via mutation of the 2A protease, which enhances proteolytic activity in the presence of DENSpm. Resistance to DENSpm occurred …

Review: Formation And Metabolic Function Of Coral Rubble Biofilms In The Reef Ecosystem, Andres Sanchez-Quinto, Luisa I. Falcon

Gulf and Caribbean Research

When coral dies, their calcareous skeletons constitute coral rubble in conjunction with the cementing activity of coralline algae and bacteria, creating a secondary reef structure which takes from years to decades to form. Healthy coral reefs differ from coral—rubble dominated reefs in microbial taxonomic composition and metabolic functional roles. The metabolisms of healthy reefs are dominated by autotrophic pathways, where carbon and nitrogen fixation dominate, while the metabolism of rubble—dominated reefs predominate in degradation of organic matter. Nitrogen fixation is 3 orders of magnitude lower in rubble—dominated reefs than in healthy reefs. Coral—rubble harbors a vast diversity of microbes that …

Investigating The Roles Of Lipids In Staphylococcus Aureus Infection, Xi Chen

Dissertations

The Gram-positive bacterium Staphylococcus aureus is a major threat to public health and causes a multitude of infections, ranging from mild skin and soft infection, to more severe diseases including sepsis, osteomyelitis and infective endocarditis. As a successful pathogen, S. aureus employs various mechanisms to invade host tissues, evade immune responses, and survive in the host environment. One critical adaptive trait of S. aureus that promotes virulence and survival is the ability to maintain membrane homeostasis via flexible modifications to its lipid composition in response to the surrounding lipid environment. Phospholipids are the major component of the bacterial membrane and …

F Plasmids In Escherichia Coli Decrease Permissivity To Coliphage, Cesar Eber Montelongo Hernandez

Dissertations

The urinary tract contains a community of bacteria called the urinary microbiota (urobiota) thatmay be relevant to health; the genomic component of the urobiota is the urinary microbiome (urobiome). Urinary bacteria have been associated with both asymptomatic states and disease conditions, such as urinary tract infection (UTI), overactive bladder (OAB), and urge urinary incontinence (UUI). Some bacteria, such as E. coli, are considered urinary pathogens (uropathogens) but also can be commensals. Bacteriophage (phage) are ubiquitous in nature and likely shape bacterial populations in every niche; thus, phage may be one factor that modulates the urobiota. Phages have a specific host …