Microbiology Commons^™

Pancreatic Ductal Adenocarcinoma And New Treatments In Development, Melissa J. Moisan

Biology and Microbiology Graduate Students Plan B Research Projects

Pancreatic ductal adenocarcinoma (PDAC) is the most frequently mutated (95%) 5exocrine pancreatic cancers. Patients with PDAC are also the least likely to survive more than 5 years with only 8% overall survivability. The median survival for patients with distant metastasis is less than one year. Most pancreatic ductal adenocarcinoma occurs in the pancreatic head, and the remainder can be found within the body (5% to 15%) or tail (10% to 15%) (14). This extremely aggressive cancer has an increasingly large metastatic dissemination rate to surrounding organs such as the liver, lung, and peritoneum, or can be seen as distant metastases …

Investigating The Impacts Of Ammonium Phosphate-Based Fire Retardants On Cyanobacteria (Anabaena) Growth, Gavin Sutter, Brenda Gonzalez Flores, Grace Laskey, Shane Jurak

Humboldt Journal of Microbiology

In recent years the effects of climate change have taken a devastating toll on ecosystems around the world. With high temperatures and extreme droughts, wildfires have become increasingly common. In order to combat these natural disasters wildland firefighters, drop millions of gallons of fire retardant on public lands and forests. These fire retardants consist of between 80%-100% ammonium phosphate which are incredibly effective as fire suppressants yet is more commonly known for its use in fertilizer. Ammonium phosphate fertilizers can lead to stream eutrophication and undesirable environmental impacts. Our research aims to address the effects of fire retardant on growth …

Essential Oils And Their Antimicrobial Effect On Serratia Marcescens, Seren C. Davies-Hughes, Patricia I. Marquez, Henna N. Schulz, Laura S. Sanchez

Humboldt Journal of Microbiology

S. marcescens is a gram-negative, facultatively anaerobic bacterium that is particularly aggressive in its growing capability. It is a concern in medical fields as well as home environments due to its resistance to most antibiotics, high mortality rate, and easy ability to colonize on soap and other fatty substances. Although testing of natural cleansers such as lemon juice, vinegar, and ammonia has been done on S. marcescens and essential oil efficacy has been tested on Escherichia coli and Staphylococcus aureus, no literature has been published on the effect of essential oils on S. marcescens growth. The purpose of this experiment …

Sex-Dependent Effects Of Induced Acute Inflammation On Glucose Homeostasis And Rna Editing Enzymes, Christian A. Rivas

Graduate Theses/Dissertations

The first line of defense against bodily insults, like pathogen invasion, is the innate immune system. Innate immunity sets in motion countless cascades that result in inflammation. Inflammation simultaneously affects multiple biological processes like metabolism and gene expression. Males and females react differently to inflammation. To understand both molecular and physiological sex differences in inflammation, we examined how inflammation affects gene expression and glucose metabolism. Adenosine deaminase acting on RNA (ADAR1) is upregulated by inflammation and catalyzes RNA editing, a process where nucleotides encoded by the genome are modified. ADAR1 also controls the innate immune reaction by decreasing activity of …

Application Of Nitrate To An Anaerobic Subsurface Bioremediation, Cassie Marie Roberts

Masters Theses

"The highly contaminated subsurface matrix of the Baird and McGuire Superfund site is currently threatening the health and safety of the surrounding environment of Holbrook, MA. Contaminants of significant concern due to high concentration are inorganic arsenite and petroleum hydrocarbons, such as naphthalene. Parsons Corporation and the Massachusetts Department of Environmental Protection have implemented a bioremediation pilot to attempt to degrade the hydrocarbons and arsenic with the application of nitrate. The nitrate would act as an electron acceptor for biodegradation of the hydrocarbon contaminants, produce nitrite that would oxidize reduced iron, and iron oxides would sequester arsenic. Preliminary data showed …

Identification Of New Substrates From Pseudomonas Aeruginosa Exos, Adam V. Thota

Master's Theses

Pseudomonas aeruginosa is a gram-negative environmental bacterium that uses its intrinsic and acquired antibiotic resistance to infect patients with compromised epithelium, such as cystic fibrosis and burn wounds, and corneal keratitis. In order to cause disease, most strains of P. aeruginosa use the type three secretion system (T3SS) to disrupt cellular signaling and integrity. However, P. aeruginosa may also secrete exotoxins after invading host cells, which prolongs host cell death and maintains an intracellular niche. Of the T3 secreted effector toxins, ExoS, specifically the ADP-ribosyltransferase activity of ExoS, was shown to delay the death of invaded corneal cells, but it …

Investigating Structural And Biochemical Characteristics Of A Peptidase Required For Staphylococcus Aureus Virulence, Sagar Bhusal

Master's Theses

Staphylococcus aureus is an opportunistic Gram-positive pathogen that transiently colonizes 30% of the population at any given time. Upon breaching host skin or mucosal barriers, S. aureus can infect and cause disease in nearly all host tissues. Once inside the host, S. aureus expresses a plethora of virulence factors, mostly regulated by the Accessory Gene Regulatory (Agr) quorum sensing system, which facilitates the evasion of immune responses or directly promotes pathogenesis. The S. aureus Agr system relies on the production of a small peptide known as an auto-inducing peptide (AIP) to control virulence gene expression in response to cell density. …

Investigating Putative Toxin-Immunity Pairs From A New Class Of Rhs Proteins In Pseudomonas Aeruginosa, Syed Faieq Imam

Master's Theses

Pseudomonas aeruginosa is a gram-negative, opportunistic pathogen that is ubiquitous in nature, especially in human/animal impacted environments. One of the reasons for this is the arsenal of protein systems and toxins that P. aeruginosa utilizes to mold its environment to suit its needs. Recently, we discovered a novel locus in the P. aeruginosa genome, which resembles other loci that are known to mediate interbacterial competition. Our bioinformatic analysis found this locus to be enriched in a rearrangement hotspot (rhs) motif which led us to ad-interim term the three ORFs of the loci as rhsB, rhsC, and rhsI. Furthermore, we have …

Trends In Antibiotic Susceptibility Of Staphylococcus Aureus Isolates In A Pediatric Hospital: An Analysis Of The Impact Of The Sars-Cov-2 Pandemic, Juan Miguel S. Gonzalez Rivero

Honors Undergraduate Theses

Infections caused by the organism Staphylococcus aureus are one of the most common causes for community-associated and healthcare-acquired infections (HAI). Isolates of this bacterium found within the healthcare setting often demonstrate a higher prevalence of antibiotic resistance making these infections difficult to treat. Historically, considerable focus has been placed on methicillin-resistant S. aureus (MRSA), which are strains resistant to β-lactam antibiotics like penicillin, oxacillin and cephalosporins; however, methicillin-sensitive (MSSA) strains may also possess resistance to several first-line antibiotics. Resistance to antibiotics can be acquired through horizontal gene transfer (HGT) by means of mobile genetic elements or by random DNA mutations …

Comparison Of Groundwater Chemistry And Associated Biodiversity Of Sulfidic Karst Habitats In Southcentral Kentucky, Kendall Wheeler

Mahurin Honors College Capstone Experience/Thesis Projects

In most ecosystems, primary production is conducted by plants or photosynthetic microbes; however, extremophilic sulfur-oxidizing bacteria can use hydrogen sulfide gas (H2S) as an electron donor to produce metabolic energy in a type of metabolism called chemoautotrophy. These ecosystems are a prominent feature of some karst landscapes, and two have been observed in the Mammoth Cave system, Sulphur River in Parker Cave and Marianne’s Pass in Mammoth Cave National Park respectively.

Sulfidic water is ubiquitous in southcentral Kentucky and is strongly associated with hydrocarbon deposits. This oil boom of the 1880s in this region predates most environmental regulation and records …

Investigation Of Key Mechanisms Of Contact Dependent Growth Inhibition Systems In Burkholderia Cepacia Complex Species, Zaria K. Elery

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Burkholderia cepacia complex is a group of closely related environmental bacteria that can exacerbate disease in immunocompromised individuals. B. cepacia bacteria are equipped with an arsenal of mechanisms to cooperate and compete for nutrients in various polymicrobial environments. Contact-dependent growth inhibition (CDI) systems are antagonistic mechanisms widespread among proteobacteria. CDI systems consist of Two Partner Secretion pathway proteins that function to deliver the toxic C-terminal portion of the large effector exoprotein (termed ‘BcpA’ in Burkholderia-type CDI systems) to the cytoplasm of a compatible recipient bacterial cell upon direct cell to cell contact. The translocation of BcpA out of the …

Substrate Selection And Effector Gating In The Helicobacter Pylori Cag Type Iv Secretion System, Mackenzie E. Ryan

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Helicobacter pylori is a recognized carcinogen and gastric colonization by strains that harbor the cag type IV secretion system (1) is the strongest known risk factor for stomach malignancy. Gastric adenocarcinoma is the fourth leading cause of cancer-related deaths world-wide ( > 700,000 deaths annually), with H. pylori directly contributing to the development of more than one million new cases of cancer per year accounting for 5.5% of all malignancies. H. pylori exploits cag T4SS activity to alter the mucosal microenvironment by delivering diverse immunostimulatory cargo into target gastric epithelial cells. Currently, the mechanisms by which the cag T4SS …

Receptor Usage And Infection Biology Of Influenza D Virus, Tirth Uprety

Theses and Dissertations--Veterinary Science

Influenza D virus (IDV) utilizes bovines as a primary reservoir with periodical spillover to other hosts. We have previously demonstrated by the traditional hemagglutination assay coupled with sialoglycan microarray and functional assays that IDV can recognize and bind both 9-O-acetylated N-acetylneuraminic acid (Neu5,9Ac₂) and 9-O-acetylated N-glycolylneuraminic acid (Neu5Gc9Ac). Agricultural animals such as cattle can produce both Neu5,9Ac₂ and Neu5Gc9Ac, while humans are genetically unable to synthesize Neu5Gc9Ac. The bifunctional enzyme, glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase (GNE) is a master regulator of de-novo sialic acid synthesis while 9-O-Acetylation of sialic acids is catalyzed by …

Location Of The Fibronectin Binding Domain On The Fibronectin Attachment Protein Of Mycobacterium Avium Subsp. Paratuberculosis, Chrissy Rose Hattery

All Graduate Theses, Dissertations, and Other Capstone Projects

Mycobacterium avium paratuberculosis (MAP) is an acid-fast bacillus that causes a fatal granulomatous ileocolitis called Johne’s Disease that affects primarily ruminants. The impact of MAP infection in the US dairy industry is particularly severe, with up to 70.4% of the herds being infected and annual losses as high as $1.5 billion. MAP is capable of persisting for months in the livestock environment and surviving the pasteurization process. While several vaccines are available, none can prevent infection and treatment with antimycobacterial chemotherapy does not result in a cure. Management and control of MAP infection requires characterization of host-pathogen interaction at the …

Novel Amino Acids Dictate Differences In Sivmac239 And Hiv-2 Rod9 Vpx Cellular Localization, Hunter D. Mayhew

All Graduate Theses, Dissertations, and Other Capstone Projects

Vpx is a protein encoded by Human Immunodeficiency Virus Type 2 (HIV-2) and specific Simian Immunodeficiency Viruses (SIVs) that is essential for successful infection of non-dividing myeloid cells. Vpx facilitates viral replication by trafficking the viral genome into the nucleus of infected cells and targeting the primarily nuclear innate immune protein SAMHD1 for proteasomal degradation. Considering that these activities occur at the nucleus, we hypothesized that Vpx nuclear localization would be tightly correlated with these functions. To assess this, site directed mutagenesis in combination with confocal microscopy or Western Blotting analyses were utilized to evaluate the determinants of nuclear accumulation …

Effectiveness Of Atmospheric Cold Plasma In Inactivating Microorganisms, Nadee Shanika Kaluwahandi

Electronic Theses and Dissertations

In the food processing industry, Cold Plasma (CP) is an emerging green process with a number of potential applications. Cold plasma has mostly been used to reduce microbial counts in foodstuffs and biological materials as well as in different levels of packaging, particularly in cases where there is thermal sensitivity. Recent studies have demonstrated that CP technology is being developed for use in the food and agriculture industries. The primary focus is on the interactions between reactive species and food-borne microbes to inactivate them. The literature review discusses both proven and potential applications for cold plasma in food processing, as …

Exploring The Microbial Composition Of Moonmilk In Wind Cave National Park, Emma Pellegrino

Honors Program Theses

Moonmilk is a white substance mainly composed of calcium carbonate (CaCO3) that is often found in limestone caves. It is one of many mineral composites, or speleothems, in Wind Cave National Park South Dakota and is thought to be formed by microbial activity. This cave system is a complex, isolated environment that serves as an analog for similar domains beyond the Earth. Each site has varying degrees of human exposure, from public tour routes to caverns only occasionally visited by park rangers, making it an ideal place of study for pristine samples in extreme conditions. Wind Cave also varies in …

Antimicrobial Resistance Profile Of Escherichia Coli Isolated From Poultry Litter, M. J. Khong, A. M. Snyder, M. M. Young, N. L. Barbieri, S. L. Weimer

Poultry Science Faculty Publications and Presentations

Antimicrobial resistance is a threat to animal and human health. As a commensal and zoonotic bacterium, Escherichia coli has the potential to be a pathogenic source of antimicrobial resistance. The purpose of this study aimed to investigate the antimicrobial resistance profile of E. coli isolated from litter collected from pens in a broiler chicken experiment. E. coli was isolated from litter samples (n = 68 isolates) of 16 pens housing broilers to d 53 of age. Resistance to 10 antimicrobials was observed by disc diffusion. The presence of 23 antimicrobial and heavy metal resistance genes, O serogroups, and avian pathogenic …

Early-Phase Drive To The Precursor Pool: Chloroviruses Dive Into The Deep End Of Nucleotide Metabolism, David Dunigan, Irina Agarkova, Ahmed Esmael, Sophie Alvarez, James L. Van Etten

Nebraska Center for Virology: Faculty Publications

Viruses face many challenges on their road to successful replication, and they meet those challenges by reprogramming the intracellular environment. Two major issues challenging Paramecium bursaria chlorella virus 1 (PBCV-1, genus Chlorovirus, family Phycodnaviridae) at the level of DNA replication are (i) the host cell has a DNA G+C content of 66%, while the virus is 40%; and (ii) the initial quantity of DNA in the haploid host cell is approximately 50 fg, yet the virus will make approximately 350 fg of DNA within hours of infection to produce approximately 1000 virions per cell. Thus, the quality and quantity of …

Nitrite Cycling In The Primary Nitrite Maxima Of The Eastern Tropical North Pacific, Nicole M. Travis, Colette L. Kelly, Margaret R. Mulholland, Karen L. Casciotti

OES Faculty Publications

The primary nitrite maximum (PNM) is a ubiquitous feature of the upper ocean, where nitrite accumulates in a sharp peak at the base of the euphotic zone. This feature is situated where many chemical and hydrographic properties have strong gradients and the activities of several microbial processes overlap. Near the PNM, four major microbial processes are active in nitrite cycling: ammonia oxidation, nitrite oxidation, nitrate reduction and nitrite uptake. The first two processes are mediated by the nitrifying archaeal/bacterial community, while the second two processes are primarily conducted by phytoplankton. The overlapping spatial habitats and substrate requirements for these microbes …

College Of Natural Sciences 2022 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

This is the 2022 issue of the annual College of Natural Sciences year-end publication.

Contents:
[Page] 2 Dean's message
[Page] 3 Department highlights
[Page] 4 Overview of Bold & Blue Campaign
[Page] 5 Dr. Edward Hogan recognition & endowment
[Page] 6 Career milestones
[Page] 7 Student travel and research
[Page] 8 $11 million COBRE grant
[Page] 9 Professional Science Masters & Research highlights
[Page]10 Outreach highlights throughout the state
[Page] 11 2022 events recap – join us in 2023!
[Page] 12 Updates on our VR initiative
[Page] 14 Overview of awards and recognitions from 2022

Effect Of Soil Transplantation On Fungal Communities During Restoration, Thomas Luehl

All Master's Theses

Ectomycorrhizal fungi are integral parts of natural ecological systems that provide access to nutrients that would otherwise be unavailable by forming symbiotic relationships with plants. Relationships with ectomycorrhizal fungi are known to improve plant growth rate, increase plant resistance to pathogens, and improve survival. Current revegetation practices often ignore this relationship between fungi and plants. During the revegetation of the Interstate 90 Keechelus Lake wildlife overcrossing (Easton, WA), soil from forest sites adjacent to the restoration area were collected and used to inoculate a set of experimental plots to determine whether ectomycorrhizal fungi would become established in the plots and …

The Antibacterial Efficacy Of Silver (I) Cyanoximates Against Streptococcus Mutans Ua159 Biofilm Growth And Infection In Galleria Mellonella Larvae, Jill Hughes

Honors Program Theses

Streptococcus mutans is the known etiological agent of dental caries. S. mutans’ virulence factors, namely biofilm formation and lactic acid fermentation, contribute to its pathogenic behavior within the oral cavity. Biofilms are thick, antibiotically resistant communities of bacteria that are much more difficult to treat than planktonic or free-floating bacteria. Continued misuse of antibiotics against dynamic communities, like biofilms, has led to increased research on non-antibiotic alternatives. Amongst these alternatives, there are silver and silver-based compounds. Silver is commonly incorporated into medicine due to its inhibitory and bactericidal effects and antibacterial properties. Silver (I) cyanoximates have demonstrated promising antibacterial activity …

Contrast Of Smokeless Tobacco And It's Microbiological Footprint In Users And Non-Users, Monayjia Brown, Katie Robbins, Elyse Mckinney, Sydney Snell

Humboldt Journal of Microbiology

Smokeless tobacco products such as vapes have gained significant popularity over the last 20 years (7), and it is clear that the effects of these products are primarily unknown. This study examines how the microbial profiles found in smokeless tobacco products, such as vapes, can be used in forensic science. By linking these profiles to their owners, investigators can identify suspects in cases where traditional evidence is lacking. This information could provide valuable assistance in tracking victims and matching perpetrators or victims to crime scenes. Forensic science involves any evidence found at a crime scene that is examined and analyzed …

Under Ice Photosynthetic Primary Production And Dark Carbon Fixation In A Temperate Freshwater System, Vanessa Cubillos Tellez

Dissertations, Master's Theses and Master's Reports

Ice-covered lakes are vulnerable to environmental change, especially those in the Northern Hemisphere where ice cover is rapidly declining due to global warming. These changes can alter metabolic processes and disrupt carbon cycling driven by primary producers who form the base of the food chain and are key to sustaining ecosystem function. Photosynthetic primary production and dark carbon fixation under the ice in the Keweenaw Waterway, a temperate freshwater system that is ice-covered for ~3 months out of the year, were studied using a carbon isotopic labeling (14C-bicarbonate) technique. Water samples were collected weekly during ice cover and monthly during …

Stem And Pre-Health Students’ Diminishing Online Conversation Volume Regarding Majors And Careers Within The Field: Why Higher Education Should Care, Susan Roh

Electronic Theses and Dissertations

The purpose of this study was to determine the STEM and pre-health online mention volume change regarding STEM and pre-health majors, careers, and universities, with the data collection period encompassing August of 2018 through June of 2021. We evaluated if the mention sentiment shifted between academic year periods. The data gathered for this study was procured in collaboration with Campus Sonar and the social-listening tool of Brandwatch, which allowed for specifications of the data collected. Kruskal-Wallis tests were used to determine the means of the majors, careers, and universities mentions and mean sentiment volumes. Changes in not only online conversation …

Attachment Issues: Microbes, Minerals, And The Persistence Of Soil Organic Matter, Md Shafiul Islam Rion

Graduate Theses, Dissertations, and Problem Reports (ETD)

The remnants of microorganisms are now understood to account for the majority of organic matter in many mineral soils. Despite the significance of this microbial necromass for soil carbon storage, we know relatively little about how the traits of microorganisms interact with soil minerals to determine the stability of microbe derived carbon in soil. Soil minerals differ in their surface area and chemistry potentially influencing microbial attachment, biofilm formation, and the persistence of microbial necromass. To address this knowledge gap, we grew twelve bacterial species from four broad groups of varying cell wall morphology (Gram positive, Gram negative, filamentous actinobacteria, …

From Culture To Metagenomics: A Comprehensive Evaluation Of The Female Reproductive Tract Microbiome In Pregnancy, Jonathan Panzer

Wayne State University Dissertations

The advent of Next Generation Sequencing technologies prompted novel investigations of the microbiome. These revealed both increased diversity of known microbiomes such as those of the gut, oral cavity and vagina, but also bacterial DNA in tissues previously considered sterile such as the blood, liver, brain, and placenta. Thus, previous paradigms of sterility, based primarily on culture data, were called into question. However, interpretation of bacterial DNA signals from low-microbial biomass tissues is complex due to the strong potential for contamination and interference from the surrounding environment. Yet, many new methodologies are being developed to help isolate valid bacterial DNA …

Expanding Our Grasp Of Two-Component Signaling In Clostridioides Difficile, Orlando Berumen Alvarez, Erin B. Purcell

Chemistry & Biochemistry Faculty Publications

The intestinal pathogen Clostridioides difficile encodes roughly 50 TCS, but very few have been characterized in terms of their activating signals or their regulatory roles. A. G. Pannullo, B. R. Zbylicki, and C. D. Ellermeier (J Bacteriol 205:e00164-23, 2023, https://doi.org/10.1128/jb.00164-23) have identified both for the novel C. difficile TCD DraRS. DraRS responds to antibiotics that target lipid-II molecules in the bacterial cell envelope, and regulates the production of a novel glycolipid necessary for bacitracin and daptomycin resistance in C. difficile.

A Characterization Of Key Residues In Class I Viral Fusion Proteins Important For Fusogenic Activity, Hadley E. Neal

Theses and Dissertations--Molecular and Cellular Biochemistry

Viral fusion proteins are critical for viral entry and subsequent infection. Class I fusion proteins are characterized by synthesis as an inactive precursor requiring cleavage by a host cell protease to become fusion competent. Though vaccine and antiviral therapeutic developments often target the fusion protein, questions surrounding cleavage dynamics and protein stability remain. The work presented in this dissertation investigates specific regions of three class I viral fusion proteins in an effort to identify key residues involved in proteolytic processing and membrane fusion.

The trimeric severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) mediates receptor binding, facilitates fusion …