Microbiology Commons^™

Development Of A Portable Low-Moisture Food Pasteurization Device Using Rf Heating, Eric Jason Ohata

Master's Theses

Bacterial presence in low-moisture foods such as flour, cereals, baby formula, and spices, have become a concern due to sanitizing challenges. The food industry currently focuses on wet food sanitation as opposed to low-moisture foods because of bacteria’s inability to reproduce in low water activity media. Traditionally, food processing RF heating pasteurizes in mass quantities while an equivalent consumer device does not exist the market today. A consumer product would help eliminate food waste by providing an easy way to sanitize food and extend shelf life. The Portable Food Pasteurization (PFP) project is an interdisciplinary project involving the Electrical Engineering, …

The Role Of Med31 And Med12 In Directing Adipogenesis Of Human Adult-Derived Mesenchymal Stem Cells, Joseph Straub

Master's Theses

Selective gene expression is crucial in maintaining the self-renewing and multipotent properties of stem cells. Mediator is a large, evolutionarily conserved, multisubunit protein complex that modulates gene expression by relaying signals from cell type-specific transcription factors to RNA polymerase II. In humans, this complex consists of 30 subunits arranged in four modules: head, middle, tail, and kinase. In our introduction, we show the state of the field of Mediator study with a focus on the critical kinase module. In the following chapters, we used siRNA knockdowns to investigate the roles of the highly-conserved core subunit MED31 and the kinase module …

How Historic Shipwrecks Influence Dispersal Of Deep-Sea Microbiomes, Rachel Moseley

Master's Theses

This thesis investigates how historic shipwrecks potentially shape dispersal of deep-sea microbiomes. Processes impacting dispersal of microbiomes around artificial structures in the ocean and how they connect to other deep-sea habitats is unknown. Dispersal processes are explained for some macroorganisms by theories in ecology, specifically the Theory of Island Biogeography and the Wooden Stepping Stone hypothesis. These have not been investigated for microorganisms, and thus this work will probe if they are applicable to microbial biogeography in this habitat. Experiments were conducted to establish new “island-like” features in near proximity (25-125 m) to wooden-hulled historic shipwrecks in the northern Gulf …

The Response Of Marine Synechococcus To A Landscape Of Environmental Stressors: A Proteomic Exploration, Dana E. Michels

Master's Theses

In the field of marine microbial ecology, many questions remain unanswered with regards to the physiological trade-offs made by phytoplankton to maximize growth (e.g., nutrient acquisition) and minimize loss (e.g., predation defenses). These tradeoffs, which occur at the cellular level, have wide reaching impacts on food web dynamics and global biogeochemical cycles. In the first chapter, we explored the use of a non-canonical amino acid (NCAA) technique, bioorthogonal non-canonical amino-acid tagging (BONCAT), in phytoplankton model systems. This technique has potential to work well in natural systems by enabling isolation of only newly synthesized proteins during an incubation period with the …

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 …

Chga-Depleted Urothelial Amp And Immune Response During Urinary Tract Infection, Theadora Jane Ceccarelli

Master's Theses

Women are 8 times more likely than men to experience a urinary tract infection (UTI) with up to 60% of women reporting a UTI in their lifetime. This significant healthcare burden is caused by the infection of uropathogenic Escherichia coli in the urinary tract. At this time, treatment is limited to antibiotic therapy, which is challenged by antibiotic-resistance. These factors make UTIs an NIH priority and are motivation for our research.CgA is a protein of the granin family co-released with catecholamines from neuroendocrine cells throughout the body. Pro-hormone convertases post-translationally cleave CgA into peptides, like catestatin, which can have antimicrobial …

Assessing The Role Of The Interaction Between Polyamines And Heparan Sulfate In Coxsackievirus B3 Viral Infection, Oreoluwa Omoba

Master's Theses

Non-polioenteroviruses are highly infectious viruses that typically cause mild asymptomatic cases but can cause severe disease such as aseptic meningitis and dilated cardiomyopathy. Coxsackievirus B3 (CVB3) is a member of this group and is prevalent in the United States and Eastern Asia. Viruses like CVB3 rely on the host cell for many molecules in order to replicate. One such set of molecules is the polyamines. Polyamines are small, positively charged molecules that play a role in a multitude of cellular processes including RNA/DNA stabilization, gene expression, translation, and regulating membrane fluidity. Previous studies have shown CVB3 relies on polyamines for …

Elucidating Regulatory Connections Between The Second Messenger Cyclic-Di-Gmp With Biofilm And Motility Phenotypes Of Vibrio Fischeri, Ali Razvi

Master's Theses

The symbiosis between the gram-negative marine bacterium Vibrio fischeri and its host Euprymna Scolopes occurs when the bacteria reaches and colonizes the light organ. This pathway to colonization begins in the outer marine environment and finishes within the deep crypts of the light organ, with states of biofilm formation and dispersal in between. This switch between biofilm formation to dispersal is important as the bacteria transitions from the surface on the light organ into a pore leading to the interior of the light organ. This dispersal is regulated by LAP system which is dependent on the second messenger c-di-GMP. Through …

Study Of Plants Used Against Infections By California Native American Tribes, Maria J. Rojas

Master's Theses

The objectives of this research were to evaluate the antibacterial activity and to determine the chemical composition of a list of medicinal plants used by Native Americans in California. Artemisia californica, Mimulus aurantiacus, Equisetum telmateia, Equisetum hyemale, and Marah fabacea were selected from a list of plants reported as having been used for ailments related to infections by tribes located in California. The extracts obtained through steam distillation from E. telmateia, E. hyemale and M. fabacea were assayed for in vitro antibacterial activity against 16 Gram-negative and 6 Gram-positive bacteria using disk diffusion assays and measuring the diameters of inhibition …

Microplastic Abundance, Distribution And Impacts On Sargassum-Associated Juvenile Fishes In The Gulf Of Mexico, Olivia Lestrade

Master's Theses

Microplastics are a concern in marine environments because they are highly durable, ubiquitous, and can be mistaken for food and ingested by small organisms. Pelagic Sargassum, an important habitat for larval and juvenile stages of many fish species, is found in large surface aggregations, and may provide complex structure in which microplastics become trapped. This could lead to greater risk of microplastic ingestion by fish early life stages associated with Sargassum habitats. To better understand the impacts of microplastics within Sargassum communities, this study examined 1) microplastic concentrations and ingestion by juvenile fishes associated with Sargassum; 2) the microbial …

Analysis Of Biofilm Remediation Capacity For Octenyl Succinic Anhydride (Osa), A Bioactive Food Starch Modifier Compound, Matthew R. Borglin

Master's Theses

Matthew R. Borglin

This thesis demonstrates efficacy of Octenyl Succinic Anhydride (OSA), as a biofilm sanitizer. Biofilms allow bacteria to adhere to solid surfaces with the use of excreted polymeric compounds. For example, surfaces found in food production or processing facilities such as the interior of a raw milk holding tank, are some of the most susceptible to biofilm contamination. When present, biofilms can cause a variety of negative effects, which include; reduction of product shelf life, corrosion, and outbreaks of foodborne illnesses. The close association of biofilms with the majority of foodborne illness cases led the US Environmental Protection …

Analysis And Optimization Of Colorimetric Nanosensors For Rapid Detection Of Microbes In Water, Ruby A. Lang

Master's Theses

Access to safe water is a basic human right recognized by the United Nations General Assembly in 2010 (WHO, 2020). However, a least 2.2 billion people globally still are without safely managed water services meaning they use a drinking water source that can be contaminated with faeces (WHO, 2020). With such a pressing global health issue, it is clear that improvement to water systems is important and required in the Agenda 2030 Sustainable Development Goals (SDGs). However, to improve water systems and prove they are safe water sources, water quality testing must occur. A solution to this issue is the …

Development Of An Attenuated Zika Virus By Editing The 5’ Untranslated Region, E. Ashley Thompson

Master's Theses

Zika Virus (ZIKV) is a mosquito-transmitted flavivirus that usually causes no symptoms to mild febrile in humans, and it has been regarded as an insignificant pathogen to public health. However, recent outbreaks of ZIKV infection have revealed that ZIKV can cause severe neurological effects in adults, such as Guillain-Barre Syndrome (GBS), and in infants whose mothers acquired the virus during pregnancy, causing Congenital Zika Syndrome (CZS). Currently, no approved vaccine is available and there is a critical need to develop an effective and safe vaccine. While most vaccine developmental strategies target the viral prM-E protein of ZIKV, we aimed to …

Elucidating The Molecular Pathways Involved In The Fitness And Water Stress Response Of Pseudomonas Synxantha 2-79 In The Plant Rhizosphere, Clint Henry D. Pablo

Master's Theses

Pseudomonas synxantha 2-79 is a biocontrol agent that represents beneficial indigenous rhizobacteria that are broadly distributed in the Pacific Northwest, USA and flourish in the rhizosphere of commercially grown wheat under surprisingly arid conditions. The molecular adaptation of 2-79-like bacteria to plants growing in dry soils is poorly understood. We hypothesized that the ability of 2-79 to colonize and persist in the rhizosphere of water-stressed plants is underpinned by the formation of hydrating biofilms and the utilization of root exudates that contain plant-derived osmoprotectants called quaternary ammonium compounds (QACs). We tested this hypothesis by identifying waters stress response pathways in …

Zika Virus Inactivates Polyamine Catabolism Via Alternative Splicing To Enhance Infection, Marion Lea Graham

Master's Theses

During viral infection, the virus and host must compete for resources inside the cell. One of these resources is polyamines. Polyamines are small, positively charged molecules that are found in all eukaryotic cells. They play a key role in several cellular functions including growth and proliferation, transcription and translation, and membrane stability. Viruses also rely polyamines for productive replication, utilizing them during DNA/RNa polymerization, nucleic acid packaging, and protein synthesis. in response to a virus infecting a host cell, the host cell will begin to regulate polyamine levels as a way to combat the infection. Polyamine levels are regulated by …

Investigating The Role Of Hypusine In Viral Translation And Infection, Jeremy Joseph Esin

Master's Theses

Polyamines are small, positively charged, molecules found in eukaryotic cells with roles in cellular function and viral infection. in previous work we have shown RNa viruses, including bunyaviruses, to be sensitive to polyamine depletion, but exact mechanisms are unknown. Bunyaviruses are emerging pathogens that cause encephalitis, hemorrhagic fevers, and meningitis. Rift Valley Fever Virus is a bunyavirus that infects both humans and livestock with severe mortality and morbidity. in previous work done with Rift Valley Fever Virus polyamine depleted results in noninfectious interfering particles without affecting the shape or size of the particles. Here, I investigate a specific metabolic pathway …

A Susceptibility Study Of Urinary Isolates To Methenamine Hippurate And Its Metabolites, Nancy Sloan

Master's Theses

Urinary Tract Infection (UTI) is one of the most common bacterial infections in adult women. Treatment is one of the most common reasons for antibiotic prescription. the rise of antibiotic-resistant infections coupled with the shortage of new antibiotics creates an urgent need for alternative non-antibiotic treatments. One alternative is methenamine hippurate (MH), which is a non-antibiotic prophylaxis. It is reported to be active against some common uropathogens including Escherichia coli and Enterococcus species, but its effects on the newly discovered bladder microbiota (urobiome) are undocumented. Given this knowledge gap, this study aimed to evaluate the drug's spectrum of susceptibility on …

Determining Interactions Between Bacteriophage And Urinary Microbiome Lysogens, Michael Bochert

Master's Theses

Bacteriophages (phages) are viruses that infect bacteria. They are the most abundant life forms on earth. It is estimated that there are approximately 10³⁰ phages on the planet (Chibani-Chennoufi et al. 2004). They outnumber their bacterial hosts approximately 10 to 1. Bacteria inhabit most niches on the planet including the human body, where they play critical roles in health and disease. Since phages shape bacterial populations the same way that viruses, such as smallpox and measles, shaped human populations, it is important to understand how they interact with their bacterial hosts. The majority of the phages that we know of …

The Effect Of Historic Shipwrecks On Sediment Microbiomes In The Northern Gulf Of Mexico, Melissa Brock

Master's Theses

Microorganisms are ubiquitously distributed across all aquatic habitats, but it is the environmental conditions of a habitat that determine which microorganisms can thrive in terms of abundance or metabolic activity. Habitats that experience consistent physical and chemical environmental conditions repeatedly favor specific taxonomic groups which may result in a microbial assemblage that is commonly associated with that habitat (i.e., a core microbiome). Core microbiomes have been identified for a variety of natural marine habitats including methane seeps, wood falls, octocoral, and deep-sea sediments. However, it was unknown if the presence of man-made structures on the seafloor, including historic shipwrecks, also …

The Thiol Specific Antioxidant (Tsa1) Gene Is Required For Survival In Macrophages And Oxidative Stress Resistance In Histoplasma Capsulatum, Lauren Kennedy

Master's Theses

Histoplasma capsulatum(Hc) is a pathogenic fungus that causes one of the most common invasive fungal respiratory diseases, Histoplasmosis. Histoplasmaundergoes a dimorphic shift from mold to yeast which is crucial to pathogenesis of the organism.

The thiol specific antioxidant gene, Tsa1,is strongly upregulated in the yeast (pathogenic) morphotype. This data led to the hypothesis that this gene plays a role in protecting Hcfrom host mediated oxidative attack. To characterize Tsa1 function, a knockdown strain (tsa1-RNAi) was created by RNAi gene silencing. Expression of Tsa1in the tsa1-RNAistrain was reduced to 10% that …

The Evolutionary Diversity And Biological Function Of Phenazine Metabolite Biosynthesis In Burkholderia Spp, Samuel Hendry

Master's Theses

Burkholderia encompass a group of ubiquitous Gram-negative bacteria that include numerous saprophytes, as well as several species that cause infections in animals, immunocompromised patients, and plants. Some species of Burkholderia produce colored redox-active secondary metabolites called phenazines (Phz). In the model opportunistic pathogen Pseudomonas aeruginosa, phenazines strongly contribute to the competitiveness, formation of biofilms, and virulence in multiple models of infection. Similar depth of knowledge on the diversity, biosynthesis, and biological functions of phenazines in Burkholderiais missing. This project aimed to bridge this gap in knowledge by focusing on phenazine pathways of B. lata and closely related …

Integrated Aeration For Enhanced Nitrogen Conversion And Removal And The Effect Of Sampling Frequency On Productivity Estimates In Algae-Based Wastewater Treatment Systems, Lauren Parker

Master's Theses

Raceway ponds can be used to cultivate microalgae for purposes such as wastewater treatment and feedstock for animal feeds and biofuels. Besides nitrogen assimilation in biomass, nitrification can be a wastewater treatment mechanism but one that is hindered by the low nighttime dissolved oxygen concentrations (DO) common in wastewater treatment raceways. The large diel difference in pond conditions and changing influent wastewater quality also raises the question of the optimal frequency and timing of grab sample collection, to obtain representative water quality data. Three sets of triplicate pilot raceways (1,000-L, 0.30-m deep, fed primary clarifier effluent) were operated at an …

Development Of A Prolyl Endopeptidase Expression System In Lactobacillus Reuteri To Reduce The Clinical Manifestation Of Celiac Disease, Kara Lynn Jew

Master's Theses

Celiac Disease (CD) is an autoimmune disorder that emerges due to the ingestion of gluten, a protein found in a variety of common grains such as wheat, rye, and barley. Approximately 1 in 100 individuals in the US suffer from CD, making it the most commonly diagnosed gastrointestinal disorder (Ciclitira et. al., 2005). These proline-rich gluten peptides are resistant to proteolysis and accumulate in the duodenum of the small intestine. Once in the duodenum, these peptides illicit an autoimmune response resulting in villous atrophy. Current treatment for CD requires a rigorous adherence to a gluten-free diet. Nevertheless, gluten-containing grains are …

Study Of Paper Microbial Fuel Cells For Use In On-Site Wastewater Testing, William A. Tolmasoff

Master's Theses

This study demonstrated a technique for fabricating simple, low-cost Paper Microbial fuel cells (PMFC’s) in the model of a previous study to, for the first time, produce voltage from wastewater effluent. The PMFC’s were created by stacking and gluing the main components of an MFC together: reservoir layer; anode; cation exchange membrane (CEM); air cathode. A wax printer was used to create the hydrophobic borders of the PMFC’s on filter paper, and graphite paint was applied to the paper to create the anode. The CEM’s considered were filter paper, wax, and Nafion, with Nafion being the most efficient. Finally, the …

See The Forest For The Leaves: Foliar Fungal Community Composition And Volatile Organic Compound Production, Joshua Copeland

Master's Theses

Endophytes are microbes that live within plants without causing detectable illness. These microorganisms can emit volatile organic compounds (VOCs), airborne signaling molecules that can significantly affect plant growth. Despite the prevalence of endophytes and their VOCs, little is known about these factors important to plant health. With this in mind I isolated fungal endophytes from leaves of Populus trichocarpa and Populus fremontii, tree species with economic and environmental uses, to determine if endophyte communities are reserved between the closely related tree species and over seasons. Surface sterilized leaf fragments were plated onto malt extract agar and the resulting fungi were …

Effectiveness Of Windrow Composting Methodology In Killing A Thermo-Tolerant Species Of Salmonella During Mortality Composting, Spencer Gabriel Myers

Master's Theses

In a large agricultural operation, such as the one at Cal Poly San Luis Obispo, disposal of deceased animals is an immense issue. The cost of transporting and rendering every dead animal is inhibitory to the general function of the agricultural operations and their thin budget. Therefore, we propose that composting mortalities could be an economical alternative. Composting is a recognized method for taking animal waste products along with carbon waste and turning it into a pathogen-free, nutrient-rich topsoil. Carcass composting is in fact performed in other countries and states to varying degrees of success. However, the California EPA limits …

The Role Of Polyamines In Enteroviral Attachment, Thomas Mckenzie Kicmal

Master's Theses

Polyamines are small polycationic molecules with flexible carbon chains that are found in all eukaryotic cells. Polyamines are involved in the regulation of many host processes and have been shown to be implicated in viral replication. Depletion of polyamine pools in cells with FDA approved drugs restricts replication of diverse RNA viruses. Viruses can exploit host polyamines to facilitate packaging, transcription, translation, and protease activity but other mechanisms remain largely unknown. Picornaviruses, including Coxsackievirus B3 (CVB3), are sensitive to depletion of polyamines and remain a significant public health threat. We employed CVB3 as a model system to investigate a potential …

Dissecting A Role For Polyamines In Rift Valley Fever Virus Infection, Vincent Mastrodomenico

Master's Theses

Bunyaviruses are emerging viral pathogens that cause encephalitis, hemorrhagic fevers, and meningitis. Rift Valley fever virus is a particularly devastating bunyavirus, infecting both humans and livestock with significant morbidity and mortality. By coordinating several host and viral processes Rift Valley fever virus is able to produce infectious virions. Polyamines are small, positively-charged host-derived molecules that play diverse roles in human cells and in infection. We previously demonstrated that polyamines are crucial for RNA viruses; however, the mechanisms by which polyamines function remain unknown. Here, we investigated polyamines' role in the replication of the Rift Valley fever virus (vaccine strain MP-12). …

A Possible Role Of Clostridium Difficile Association With The Gi Tract In Relapsing Clostridium Difficile Infection, Asiyya Ashraf

Master's Theses

Clostridium difficile infection (CDI), caused by the anaerobic spore-former C. difficile, is a major cause of health-care associated morbidity. CDI occurs in individuals that have a disrupted GI tract microbiota, typically in patients who are on antibiotic therapy. After recovery from an episode of CDI, approximately, 15-30% of patients experience relapse of disease. The mechanism of relapse is not well understood. It is plausible for relapse to occur if C. difficile cells and spores associate with the GI tract mucosa during infection and persist after infection. However, little is known about the association of cells and spores with the GI …

Assessing The Role Of A Putative Peptidase In The Processing And Transport Of Aip In The Agr Quorum Sensing System Of Staphylococcus Aureus, Chance Joseph Cosgriff

Master's Theses

Staphylococcus aureus infections are a global burden on human health. The wide rangeof infectious diseases caused by S. aureus stem from the production of myriad virulence factors that manipulate host immune responses and promote bacterial survival. These virulence traits, coupled with the rise in antibiotic resistance, demonstrate a need for novel therapeutics to control infection. Many current therapeutic initiatives focus on targeting the virulence factors produced by S. aureus or the regulatory systems that control their expression such as the Accessory gene regulatory system, Agr.Initial characterization of a putative S. aureus peptidase MroQ indicates a major role in regulation of …