Microbiology Commons^™

Understanding Ubiquitin-Like Signaling At The Host-Pathogen Interface, Danna Eloisa Guzman Gonzalez

University Honors Theses

Research on pathogen intervention and ubiquitin modification has increased over the last few years but a lot is still unknown about ubiquitin-like modifiers (Ubl) and how or if they are modified by pathogens in the same way as Ubiquitin. In this work, two different studies conducted over the course of 2 years are highlighted. The first study focused on purifying and synthesizing four activity based probes in order to study enzymatic activity in the Ubl-modification systems. These probes were reacted with virulence factors isolated from different bacteria and it was concluded that there were unexpected bands formed between some of …

The Influence Of Microorganisms On Human Health, Tiffany Bui

University Honors Theses

The purpose of this thesis is to explore the interplay between the environment, lifestyle, and composition of human microbiomes across different communities, with a specific focus on immune and digestive health. This literature review investigates three distinct types of communities: isolated/traditional, transitional, and urban/industrialized communities, each characterized by unique environments, societal structures, and interactions. These factors contribute to the distinct microbial populations and compositions within each community. It is impossible to avoid contact with microorganisms as they are present in every aspect of our lives, from the air we breathe, the water we drink, the soil we walk on, the …

Characterization Of Folic Acid, 5-Methyltetrahydrofolate And Synthetic Folinic Acid In The High-Affinity Folate Transporters: Impact On Pregnancy And Development, Ana M Palacios, Rachel A Feiner, Robert M Cabrera

Faculty, Staff and Students Publications

Folates are B vitamins that are essential for several molecular, cellular, and biological processes, including nucleotide synthesis, methylation, and methionine cycling. The physiological impacts of these processes on health also extend to cell proliferation, folate deficiency anemia, and reduction of the risk of birth defects during pregnancy. The primary objective of this study was to characterize the binding affinities of different folate forms, folic acid (FA), 5-methyltetrahydrofolate (5MTHF), and folinic acid, to the folate receptors α and β, and to the bovine milk folate binding protein. These three dietary forms of folate are found in enriched grains (FA), various fruits …

​ Soilborne Pathogens Of Strawberry In The Central Coast Region Of California: ​ Survey And Cover Cropping With Wheat For Management Of Macrophomina Phaseolina, Mary Steele

Master's Theses

Surveys of the four major soilborne pathogens of strawberry (Fusarium oxysporum f. sp. fragariae, Macrophomina phaseolina, Phytophthora spp., and Verticillium dahliae) to determine their relative prevalence were conducted in Watsonville-Salinas, CA in 2021 and in Santa Maria, CA in 2022. All four major pathogens were detected at relatively similar prevalence in Watsonville-Salinas, between 22% and 31% of sampled fields. In Santa Maria, M. phaseolina was far more prevalent at 52% of sampled fields, the other three falling between 14% and 17%. Additionally replicated greenhouse and field trials were conducted to evaluate the effects of wheat as …

Development Of Novel Nanocarbon Based Materials And Membranes With Enhanced Biocidal Capabilities For Clean Water Generation, Indrani Gupta

Dissertations

Water scarcity is one of the major challenges facing humanity today, driven by population growth, economic development, and dietary shifts towards more water-intensive animal products. To address this issue, efficient water resource management and recycling of wastewater are essential. However, around 80% of wastewater globally is discharged into water bodies without treatment, posing a risk to ecosystems and human health. Pathogens, or harmful microorganisms, are a primary cause of water impairment and the transmission of waterborne diseases, leading to increased mortality rates. Traditional methods of treating pathogens involve the use of radiation or chemical disinfectants. Nonetheless, these methods have drawbacks, …

The Efficiency Of P27 Cleavage During In Vitro Respiratory Syncytial Virus (Rsv) Infection Is Cell Line And Rsv Subtype Dependent, Wanderson Rezende, Xunyan Ye, Laura S Angelo, Alexandre F Carisey, Vasanthi Avadhanula, Pedro A Piedra

Faculty, Staff and Students Publications

Respiratory syncytial virus (RSV) fusion protein (F) is highly conserved between subtypes A and B (RSV/A and RSV/B). To become fully active, F precursor undergoes enzymatic cleavage to yield F1 and F2 subunits and releases a 27-amino-acid peptide (p27). Virus-cell fusion occurs when RSV F undergoes a conformational change from pre-F to post-F. Previous data show that p27 is detected on RSV F, but questions remain regarding if and how p27 affects the conformation of mature RSV F. Monoclonal antibodies against p27, site Ø (pre-F specific), and site II were used to monitor RSV F conformation by enzyme-linked immunosorbent assay …

Ecology Of Viruses In Marine And Coastal Oxygen-Depleted Waters, Sophie Jurgensen

LSU Doctoral Dissertations

Deoxygenation of marine and coastal waters, both caused and exacerbated by a suite of abiotic and biotic factors, has been documented for more than sixty years. The incidence and severity of low-oxygen areas is predicted to expand globally in the coming decades. Despite their colloquial moniker “dead zones,” low-oxygen areas contain thriving and diverse microorganisms that have significant impacts on global biogeochemical cycles including contributing to positive feedback loops that further expand low-oxygen areas. While the diversity and activity of these microorganisms is beginning to be elucidated, the ecology of their viruses is particularly understudied. In this dissertation, I present …

Effects Of Climate Change On Human Health, Sara El Houzaly, Richa Gupta

Publications and Research

The effects of climate change are evident worldwide as average global land and air temperatures have been rising, glaciers and ice sheets are shrinking with the concomitant rise in sea levels, extreme weather events have become more frequent, and oceans are warming and acidifying. Humanity is facing a big environmental challenge which not only impacts our habitat but will also have ramifications on our health. The present review describes a detailed examination of the scientific evidence proving the relationship between climate change and various fatal human diseases in different geographical regions. Our findings indicate that variations in the patterns of …

The Influence Of Sampling Frequency On Bee Species Richness, Courtney Caccamo

Biology Student Scholarship

As one of Earth’s most valuable pollinators, bees provide important pollination services to wild plant species and crops alike (Winfree 2010). But, in recent years, bee populations appear to be declining due to a variety of anthropogenic drivers (Potts et al. 2010). Quantifying the extent of bee population decline is difficult because there is currently a lack of a standardized protocol for how best to survey bee populations (Tepedino & Portman 2021). One of the commonly used survey methods is pan trapping, which involves leaving out yellow, white, and blue bowls filled with soapy water to passively sample the species …

Considerations For The Use Of Mycorrhizal Fungi Inoculants In Coal Mine Reclamation And Reforestation In Appalachia: A Guide Of Best Practices And Management Recommendations, Cole Hansen Reistrup

Master's Projects and Capstones

Nearly all terrestrial plants form symbiotic relationships with mycorrhizal fungi. These beneficial soil microbes support plant health by increasing plants’ access to nutrients and water, protecting them from pathogens, improving soil properties, and more. A challenge to restoring forests on coal mined land in Appalachia is that mine soils are often degraded in a number of ways, including lacking mycorrhizal fungi, which makes mine soils difficult for trees to grow upon. Substantial improvements to coal mine reforestation success have been made since the development of the Forestry Reclamation Approach in 2005 that provides guidelines for how to create a suitable …

Overexpressing Two Helicobacter Pylori Small Rnas From A Bacterial Pathogenicity-Related Chromosomal Region To Investigate Their Regulation Of Virulence Genes, Roxanne N. Mcpeck, Olivia F. Morgan, Andrea R. Castillo Phd

2023 Symposium

The bacterial pathogen Helicobacter pylori infects the stomachs of approximately 50% of humanity, causing symptomatic disease (e.g., stomach ulcers, gastric cancer, and MALT lymphoma) in 10-15% of the infected. Colonizing the acidic, inhospitable stomach requires H. pylori to tightly regulate gene expression despite lacking many common bacterial genetic regulatory elements. The pathogen may compensate by using abundant non-protein-coding small RNAs (sRNAs) to regulate gene expression, including of infection-intensifying virulence genes. Additionally, severe disease and cancer correlate with infection by H. pylori strains that contain a nonessential chromosomal region, the cytotoxin-associated gene pathogenicity island (cagPAI). This encodes powerful virulence …

Influenza C And D Viruses Demonstrated A Differential Respiratory Tissue Tropism In A Comparative Pathogenesis Study In Guinea Pigs, Chithra C. Sreenivasan, Runxia Liu, Rongyuan Gao, Yicheng Guo, Ben M. Hause, Milton Thomas, Ahsan Naveed, Travis Clement, Dana Rausch, Jane Christopher-Hennings, Eric Nelson, Julian Druce, Miaoyun Zhao, Radhey S. Kaushik, Qingsheng Li, Zizhang Sheng, Dan Dan, Feng Li

Nebraska Center for Virology: Faculty Publications

Influenza C virus (ICV) is increasingly associated with community-acquired pneumonia (CAP) in children and its disease severity is worse than the influenza B virus, but similar to influenza A virus associated CAP. Despite the ubiquitous infection landscape of ICV in humans, little is known about its replication and pathobiology in animals. The goal of this study was to understand the replication kinetics, tissue tropism, and pathogenesis of human ICV (huICV) in comparison to the swine influenza D virus (swIDV) in guinea pigs. Intranasal inoculation of both viruses did not cause clinical signs, however, the infected animals shed virus in nasal …

Exploring The Dynamics Of Bacterial Populations In The Gut Microbiota, Shaikh Obaidullah

Biology and Medicine Through Mathematics Conference

No abstract provided.

Helices In Fluids And Their Applications, Eva M. Strawbridge

Biology and Medicine Through Mathematics Conference

No abstract provided.

Single-Molecule Super-Resolution Imaging Of Geobacter Sulfurreducens Under Anaerobic Conditions, Ziyi Hu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Geobacter sulfurreducens are anaerobic bacteria capable of making electrical contacts with other organisms and extracellular electron acceptors. The challenge of imaging live Geobacter bacteria is maintaining anaerobic conditions during the imaging process. In this thesis, we augment a single-molecule localization microscope (SMLM) with a home-built anaerobic imaging chamber and use constant argon bubbling to maintain oxygen-free imaging conditions. To validate the imaging protocol, we use the transient binding of Nile red to resolve the spherical morphology of lipid-coated glass spheres with nanoscale resolution. However, when imaging Geobacter, the distribution of Nile red localizations is non-uniform, both between different cells …

Adenoviral-Vectored Epigraph Vaccine Elicits Robust, Durable, And Protective Immunity Against H3 Influenza A Virus In Swine, Erika M. Petro-Turnquist, Matthew J. Pekarek, Nicholas Jeanjaquet, Cedric Wooledge, David J. Steffen, Hiep Vu, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

Current methods of vaccination against swine Influenza A Virus (IAV-S) in pigs are infrequently updated, induce strain-specific responses, and have a limited duration of protection. Here, we characterize the onset and duration of adaptive immune responses after vaccination with an adenoviral-vectored Epigraph vaccine. In this longitudinal study we observed robust and durable antibody responses that remained above protective titers six months after vaccination. We further identified stable levels of antigen-specific T cell responses that remained detectable in the absence of antigen stimulation. Antibody isotyping revealed robust class switching from IgM to IgG induced by Epigraph vaccination, while the commercial comparator …

Characterization Of Lps As A Virulence Factor In Burkholderia Cepacia During Plant And Human Infection, Jack Klahr, Elizabeth Danka

Biology Senior Theses

Burkholderia cepacia is a gram-negative bacterium first characterized as the causative agent of sour skin in onion crops. More recently, B. cepacia has become a clinical concern as an opportunistic pathogen that can colonize the upper respiratory tract of cystic fibrosis patients and increase mortality in these patients. Infection is exacerbated by the intrinsic resistance to antibiotics found in this genus of organisms. Additional virulence factors help the bacteria persist in the host during infection. However, few of these factors have been described. In this work, we characterized a putative virulence factor that was first identified through an onion infection …

An Analysis Of The Sensory Characteristics And Microbial Constituents Of Kefir, Katherine Quay Robinson

Honors Theses

Kefir is a fermented beverage produced using sugar water or milk, kefir grains, either water kefir grains or milk kefir grains, respectively, and microbial aggregates consisting of diverse bacteria and yeasts. As kefir and fermented beverages in general are increasing in popularity, research related to optimal sensory characteristics and consumer-approval is vital. Desirable sensory characteristics for kefir beverages include low sour taste/aroma, high sweetness, carbonation, and high viscosity (Surja et al., 2019; Margareth et al., 2020). Production methods of kefir can alter sensory characteristics, but sensory characteristics are likely strongly influenced by the microbial composition of the grains/product. Thus, an …

The Effects Of Aloe Vera On The Human Gut Microbiome, Samantha Leon

Honors Theses

The human gut microbiome is a diverse community of bacteria influenced by multiple factors including host age, geographical location, and diet. This study observed the effects of aloe vera juice on the human gut microbiome. Fecal samples were taken every two weeks over a period of one year; the subject consumed aloe vera juice in alternating cycles of consumption “on” and abstaining “off” with each cycle lasting for eight weeks. The bacterial community in each sample was characterized using 16S rRNA gene sequencing. Sequences were identified and their relative abundances were used to look for patterns distinguishing “on” and “off” …

The Development Of A Primer Payload With Microparticles For Uti Pathogen Identification Using Polythymidine- Modified Lamp Primers In Droplet Lamp, Jonas Otoo

KGI Theses and Dissertations

Nucleic acid amplification tests (NAATs) are among the diagnostic tests with the highest sensitivity and specificity. However, they are more complex to develop than other diagnostic tests such as biochemical tests and lateral flow immunoassay tests. Polymerase chain reaction (PCR) is the gold standard for NAATs. PCR requires thermal cycling to achieve clonal amplification of the target pathogen DNA for diagnosis. Thermal cycling poses a challenge in the development of PCR diagnostics for point-of-care (POC) settings. Loop-mediated isothermal amplification (LAMP) offers an isothermal method for NAATs diagnostics. The advancement of the microfluidics field significantly enhances the development of LAMP diagnostics …

Eco-Interoception: What Plants, Fungi And Protista Have Taught My Body, Sara Riley Dotterer

Art Theses and Dissertations

To me, ecology is the relational, full-body awareness that I am made up of and deeply connected to everything around me; and for better or worse, this is reciprocal. I form ecotones, an ecological transitional zone between two ecosystems, with the world around me. I use this ecotonal lens to blur binaries and dissolve boundaries between me and the world “outside my body.” During my Masters of Fine Arts at Southern Methodist University, I have continuously explored and represented the lives of various more-than-human species outside of my body, including plants, fungi and protista through an ecotonal lens. Although these …

Development Of Recombinant Varicella-Zoster Virus Vaccines Expressing Sars-Cov-2 Antigens, Cody Wilson

Honors Theses

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) continues to cause infections and deaths around the globe. Since its emergence, scientists have worked diligently to discover and produce vaccines to battle the virus. While they successfully created and distributed vaccines, the vaccines are not without flaw. These vaccines do not grant long term immunity, require multiple booster shots, and have not prevented the emergence of viral variants. In this study, the SARS-CoV-2 receptor binding domain (RBD), which is a key part of the spike protein (S), and nucleocapsid (N) genetic sequences were inserted into the live varicella …

Mechanistic Examination Of Protist-Mediated Plant Growth Through The Comparative Development Of Medicago Truncatula, Shane Connolly

University Scholar Projects

Protists are known to increase plant growth through two main mechanisms: the microbial loop and the alteration of the root microbiome. The microbial loop is a nutrient recycling method in which protists provide inorganic nitrogen ions to the plant. Alteration of root microbiome leads to the removal of plant pathogens and shifting communities towards plant growth-promoting bacteria (PGPB). This study aimed to elicit which mechanism could produce the largest boost in shoot weight for Medicago truncatula. A series of microcosm experiments were explored in which M. truncatula was grown with variable microbiome structures to allow for mechanism differentiation. The …

Comparative Analysis Of Rhizosphere And Endosphere Microbiome Of Different Blueberry Species (Vaccinium Sp.), Niladri Bhowmik

Master's Theses

Blueberries are an important agricultural commodity in all over the United States. Due to its health benefits, there is a huge demand globally, thus expanding the industry. Breeding programs are essential to maintain such industries. Challenges that play a role in contemporary breeding programs are various biotic and abiotic stress factors. Studies have shown that microorganisms are recruited by plants to alleviate them during stressful conditions. Though blueberries have been cultivated for about 100 years, how the microbiome has been affected due to this is poorly understood. We hypothesized that interspecific crosses and artificial selection have significantly changed the microbiome …

Causes And Consequences Of Lasr Mutant Selection In Pseudomonas Aeruginosa Populations, Dallas L. Mould

Dartmouth College Ph.D Dissertations

Change is the only constant in life, and these changes, though random in nature, can have consequences. Quorum sensing is heterogeneous in phenotype and prone to negative selection. In P. aeruginosa, the regulator LasR is frequently non-functional in phylogenetically diverse isolates. Through repeated experimental evolution and mathematical modeling, we show that differences in growth enable lasR mutant evolutionary success and this requires a system enabling metabolic choices, known as carbon catabolite repression (or catabolite repression). The differences in catabolite repression between wild type and lasR mutants enable altered metabolite preferences, and the resulting differences in metabolic states enable intraspecies …

Co-Clinical Imaging Metadata Information (Cimi) For Cancer Research To Promote Open Science, Standardization, And Reproducibility In Preclinical Imaging, Stephen M Moore, James D Quirk, Andrew W Lassiter, Richard Laforest, Gregory D Ayers, Cristian T Badea, Andriy Y Fedorov, Paul E Kinahan, Matthew Holbrook, Peder E Z Larson, Renuka Sriram, Thomas L Chenevert, Dariya Malyarenko, John Kurhanewicz, A Mcgarry Houghton, Brian D Ross, Stephen Pickup, James C Gee, Rong Zhou, Seth T Gammon, Henry Charles Manning, Raheleh Roudi, Heike E Daldrup-Link, Michael T Lewis, Daniel L Rubin, Thomas E Yankeelov, Kooresh I Shoghi

Faculty, Staff and Students Publications

Preclinical imaging is a critical component in translational research with significant complexities in workflow and site differences in deployment. Importantly, the National Cancer Institute's (NCI) precision medicine initiative emphasizes the use of translational co-clinical oncology models to address the biological and molecular bases of cancer prevention and treatment. The use of oncology models, such as patient-derived tumor xenografts (PDX) and genetically engineered mouse models (GEMMs), has ushered in an era of co-clinical trials by which preclinical studies can inform clinical trials and protocols, thus bridging the translational divide in cancer research. Similarly, preclinical imaging fills a translational gap as an …

The Response Of Microcystis And The Microbiome To Exogenous Hydrogen Peroxide, Bryan A. Puma

Masters Theses, 2020-current

Microcystis spp. produce prolific annual blooms in freshwater systems worldwide. The success of these blooms depends heavily on the Microcystis spp. overcoming environmental factors such as oxidative stress caused by reactive oxygen species (ROS) like hydrogen peroxide. Most Microcystis genomes do not contain many genes for responding to oxidative stress, including those that encode the enzyme catalase. Other cyanobacteria such as Prochlorococcus that also lack hydrogen peroxide degrading enzymes have been shown to benefit from partnerships with heterotrophic bacteria. Microcystis spp. may also receive similar benefits from heterotrophic bacteria in the phycosphere. To test this hypothesis, we examined the …

Elucidating The Impact Of Sos-Response Timing In On Escherichia Coli Survival Following Treatment With Fluoroquinolone Topoisomerase Inhibitors, Stephanie Schofield

Honors Scholar Theses

Antibiotic treatment failure is a public health crisis, with a 2019 report stating that roughly 35,000 deaths occur in the United States yearly due to bacterial infections that are unresponsive to antibiotics (1). One complication in the treatment of bacterial infection is antibiotic persistence which further compromises our battle to effectively treat infection. Bacterial persisters can exist in clonal bacterial cultures and can tolerate antibiotic treatment by undergoing reversible phenotypic changes. They can survive drug concentrations that their genetically identical kin cannot. Some persisters remain in a slow growing state and are difficult to target with current antibiotics. A specific …

A Critical Assessment Of The Role Of Clpxp-Mediated Proteolysis In The Development And Differentiation Of Chlamydia Trachomatis, Nicholas A. Wood

Theses & Dissertations

Chlamydia trachomatis, an obligate intracellular human pathogen, is the etiological agent of the most commonly reported bacterial sexually transmitted infection and the leading cause of preventable infectious blindness worldwide. In adapting to an intracellular niche, Chlamydia has evolved to eliminate superfluous genes from its chromosome. Despite its highly reduced genome, Chlamydia undergoes a complex developmental cycle in which the bacteria differentiate between two functionally and morphologically distinct forms: the infectious, non-replicative elementary body (EB) and the non-infectious, replicative reticulate body (RB). An EB initiates infection by binding to and inducing uptake into a host cell. Within the cell, the EB …

The Future Is Now In Twisted Coil Polymer Actuators (Tcpa), Ryan Ronquillo

Electronic Theses and Dissertations

This thesis aimed to fabricate and test twisted coiled polymer actuators (TCPA) to understand the mechanical and thermal aspects of this artificial muscle fiber. The purpose of this thesis was to find a linear relationship using the LVDT sensor, fabricating TCPA fibers, and interpreting the data. The project tested whether nylon/polymer could be used as a better artificial muscle fiber.

This research accomplished three goals: (1) designing and fabricating a system capable of creating supercoiled muscle fibers consistently, (2) calibrating the Linear Variable Differential Transformer (LVDT) and Core, and (3) analyzing/interpreting the data of the Twisted Coiled Polymer Actuators (TCPA) …