Life Sciences Commons^™

Investigating Microbe-Plant Symbioses In Space, David Handy

Theses and Dissertations

As life has evolved on Earth, gravity has been a constant around which biological processes have developed, rather than a pressure that has been adapted to. As humanity ventures into space, we remove this constant and can observe a variety of changes in biological systems, such as bone loss in humans, stunted plant growth, or increased virulence in pathogens. The growing body of data shows that life adapts to spaceflight and microgravity in unique ways that, due to our limited understanding, can be difficult to predict. A particularly under-studied area is that of host-microbe interactions. Despite efforts to limit their …

Characterization Of Ato Family Transporters In The Fungal Pathogen Cryptococcus Neoformans, Will Betsill

All Theses

Fungal pathogens are a significant threat to public health as they are becoming increasingly common and more resistant to treatment. Cryptococcus neoformans contributes greatly to this threat annually by causing an estimated 278,000 cases of cryptococcal meningitis resulting in approximately 181,000 deaths globally according to the CDC. C. neoformans is ubiquitous across most of the globe and can be found in such places as in trees or soil. Exposure to this fungus is especially dangerous to individuals who are immunocompromised or immunosuppressed. In these cases, inhalation of spores can lead to infection in the lungs. Once in the lungs, C. …

Adherent-Invasive Escherichia Coli (Aiec) Promotes Mild Colitis In The C57bl/6 Il-10 Ko Mouse Model Of Crohn's Disease, Sarah Sm Zaw

Senior Theses

Crohn's disease (CD) is a chronic inflammatory bowel disease. Interleukin-10 knockout (IL-10 KO) mice are crucial in CD research. Adherent-invasive Escherichia coli (AIEC) is a subgroup of E. coli. In one study, IL-10 KO mice colonized with AIEC developed colitis in the distal colon compared to wild-type (WT) mice. I investigated how AIEC NC101 WT affects colitis severity in IL-10 KO mice of the C57BL/6 genetic background. Similar results in both genotypes would enhance mouse strain accessibility. Germ-free C57BL6 IL-10 KO mice were divided into groups: colonized with AIEC NC101 for 12, 15, or 18 weeks, or kept germ-free. Histopathological …

Microbiological Investigation Of Local Native Clays And Samples From The Scripps Ceramic Studio, Kelly Fuller

Scripps Senior Theses

This study explores the relationship between microorganisms and clay using samples currently being utilized in the Lincoln Ceramics Studio at Scripps College. Clay science spans disciplines, from geology and soil science to industrial material development and artistic practices. Although biological processes have been thought to effect clay properties such as plasticity and malleability, the interplay between microorganisms and clay minerals has not been thoroughly investigated in the scientific community. Drawing from diverse disciplines, this research investigates the microbial ecology of clay bodies to unveil potential innovations in ceramics production. In this experiment, colony-forming unit (CFU) assays were performed in both …

Ribosome Hibernation Factor Induces Antibiotic Persisters Of Mycobacterium Tuberculosis In Neutrophil-Rich Lung Lesions, Jamie Corro

Electronic Theses & Dissertations (2024 - present)

Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, is a prescient global health threat and the leading cause of death by an infectious agent. Treatment of Mtb infection involves administering 2-4 antibiotics for a minimum of 6 months. This extended drug regimen is required to target a subpopulation of persistent bacilli. As their name implies, these bacteria can “persist” by acquiring nonhereditary and transient antibiotic tolerance. Although the precise mechanism is unknown, it’s often attributed to slowing cellular growth and metabolic processes. During zinc deprivation, bacteria can remodel their ribosomes by replacing their zinc-binding paralogues containing the CXXC motif (C+) …

Bloom: A Microbial Self-Portrait, Emily Lauren Mulvaney

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

Investigating Potential Indicators Of Soil Health Through Microbiome Response To Environmental And Anthropogenic Stressors, Austin Cook

Theses and Dissertations

Traditionally, the analysis of soil health has overlooked the biological component of soil due to poor understanding of connections between the microbiome and empirically measured soil health indicators. The purpose of this study was to assess the effects of environmental and anthropogenic stressors on the soil microbiome, with the aim of identifying measurable soil biological indicators. Chosen soils were examined under distinct conditions to evaluate the effect of selected environmental and anthropogenic stressors on the microbiome. Soil biological responses were analyzed via enzymatic response, microbial functional genes, and microbial community. Environmental factors such as soil moisture and organic matter showed …

Characterization Of Protein-Protein Interactions In Quorum-Sensing Receptors From Gram Negative Bacteria, Jessica Schuh

Biological Sciences

Pseudomonas aeruginosa is a bacterium capable of causing disease in immunocompromised individuals and individuals with underlying lung disorders. It controls the expression of a subset of its genes through quorum sensing, which is a cell-cell communication system involved in mediating the transition from individual to group behaviors. Group behaviors are cellular processes undertaken by the cell that are beneficial to the collective, such as biofilm formation – a key component of pathogenesis in the human lung. They rely on the production, accumulation, detection, and response to signal molecules called autoinducers. There are two acyl-homoserine lactone autoinducer quorum sensing systems in …

Minimal Carbon Requirements For Potential Colonizers Of Other Planets, Benjamin Tan

Biological Sciences Undergraduate Honors Theses

The NASA Office of Planetary Protection regulates the safe scientific exploration of other planets. Specifically, the office enacts rules to discourage interplanetary mission practices that would lead to the contamination of Earth-originating microbial life on other planets. Interplanetary contamination jeopardizes the potential to obtain reliable scientific evidence for extraterrestrial life. In coordination with this office, the biosignatures of potential colonizers of other celestials bodies are studied. Several organisms of Earth qualify as potential colonizers of other planets.

This experiment focused on the environment of Mars in particular. Two organisms were tested: Desulfovibrio arcticus and Desulfotalea psychrophila. Both are psychrotolerant or …

The Effect Of Algal Wastewater Treatment Systems On Microbial Communities, Alexis Leach

University Honors Program Senior Projects

In collaboration with the Metropolitan Water Reclamation District of Greater Chicago and Gross-Wen Technologies, I examined the microbial communities in experimental tertiary wastewater treatment systems employing algal phytoremediation. Three algal phytoremediation systems were examined: two vertical conveyor belt systems, known as the 10-foot belt system and the series 4 system, and a third system lacking a converter belt in which planktonic algae grew in a control pond. I used EcoPlates to measure carbon substrate utilization by microorganisms in each system. EcoPlates contain thirty-one different carbon substrates, with a dye that indicates microbial use of each substrate. I conducted a Principal …

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 …

Environmental Toxicants And Human B Cells: Insights From Crispr Editing And Genomic Sequencing, Clayton Allex-Buckner

Browse all Theses and Dissertations

The human immunoglobulin heavy chain gene locus (IGH) has two 3 prime regulatory regions (3’IGHRR), each containing three enhancers (hs3, hs1.2, hs4). In animal models, the 3’IghRR regulates IgH expression and class switch recombination (CSR) to different Ig isotypes. The 3’IGHRR hs1.2 enhancer in humans is polymorphic in that an invariant sequence (IS) can be repeated one to four times in tandem. The hs1.2 polymorphism is of interest due to its association with several human autoimmune disorders and its potential sensitivity to exogenous substances such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD or dioxin). In mouse models, TCDD inhibits the hs1.2 enhancer and 3’IghRR …

Investigation Of Glycoside Hydrolases And Calcium In Cytophaga Hutchinsonii Cellulose Utilization, Choua Kou Vang

All Graduate Theses, Dissertations, and Other Capstone Projects

Cytophaga hutchinsonii is a soil bacterium that can utilize cellulose as a carbon source. The cellulose utilization system of C. hutchinsonii has been predicted to be novel and its endoglucanases could potentially be used in the production of cellulosic based biofuels. These enzymes could be used to process cellulose to glucose or other soluble sugars, which can be further converted to ethanol by yeast fermentation. Current biofuels utilize starches, primarily from corn, which has direct competition with farming space for food crops. This study focuses on observing the growth of C. hutchinsonii knockout mutant strains on cellulose substrate to better …

Characterization Of The Mycobiome Of Rafflesia Seeds: Their Potential Ecological Roles And Applications In Rafflesia Propagation And Conservation, Feruza Karnitskiy

Selected Full-Text Master Theses 2021-

The plant microbiome exerts a profound influence on plant health, growth, and life cycle. This ecosystem comprises diverse microbial communities, such as symbiotic endophytes, mycorrhizal fungi, epiphytes, saprophytes, rhizobia, and pathogens, which inhabit parasitic and non-parasitic plants. Rafflesia speciosa, a holoparasitic plant, is a unique and endangered species that depends on its host Tetrastigma spp. for survival. In this study, fungal metagenomics was conducted to characterize the fungal community—the mycobiome within Rafflesia seeds, and a phylogeny was reconstructed. The ecophysiological characteristics of these fungal genera were also researched in the literature, and their primary ecological trait, whether plant mutualist, saprotroph, …

A Dnak Chaperone System Connects Type Iv Pilus Activity To Polysaccharide Secretion In The Cyanobacterium Nostoc Punctiforme, Heather J. Mcdonald

University of the Pacific Theses and Dissertations

Type IV pili (T4P) systems are widely utilized among bacteria to power and direct surface motility. The production and secretion of a viscous polysaccharide to provide friction and resistance to the extended pilus structure is seen in several species of cyanobacteria including Nostoc punctiforme. The complex coregulation of polysaccharide secretion and T4P motor activity is not fully understood, although studies indicate a consistent relationship between functional motility and intact pathways of polysaccharide secretion and pilus extension in cyanobacteria. Using a combination of protein-protein interaction analysis, cytological studies, and comparative genomics this study proposes a theoretical mechanism for T4P motor influenced …

The Role Of Machine Learning And Network Analyses In Understanding Microbial Composition In An Experimental Prairie, Ali Eastman Oku

Graduate Research Theses & Dissertations

Machine learning and network analyses are powerful modern tools can process and map out connections between large amount of ecological data from complex environmental communities. Random forests, an ensemble machine learning algorithm, are particularly powerful as they can capture complex patterns in data while remaining easily interpretable. These tools are specifically useful in experimental settings where different types of data are collected. The aim of this study was to demonstrate the utility of machine learning models and network analyses at analyzing diverse ecological data from dynamic plant-soil microbial communities in a prairie ecosystem. Our experimental system is an experimental prairie …

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 …

Functional Residues Of Cjpata, Robert Lamont

Theses and Dissertations (Comprehensive)

Antibiotic resistance in pathogenic bacteria continues to challenge clinicians and threaten the lives of infected individuals. For this reason, new classes of antibiotics or new targets for antibiotic therapy are needed to circumvent this global health crisis. In Gram-negative bacteria, the enzymes peptidoglycan O-acetyltransferase A and B (PatA and PatB), are responsible for adding acetyl groups to the C-6 hydroxyl group of N-acetyl muramic acid (MurNAc) in peptidoglycan (PG). These acetyl groups are responsible for inhibiting the activity of lysozyme from host organisms that hydrolyze the β1-4 glycosidic linkage between MurNAc and N-acetylglucosamine (GlcNAc). The acetyl groups …

Biological Remediation Of Fragipan, Corey Hale

Honors College Theses

The fragipan layer in the soil is a naturally occurring subsurface layer that restricts water percolation as well as inhibits root growth. A fragipan layer can be found almost ubiquitously across Southwestern Kentucky. This limits how agriculturalists manage soils in this area. It has been recently discovered by the University of Kentucky that Annual Ryegrass roots produce 3,4 dihydroxyphenylpropionic acid (DHPPA) that reacts with this hardpan to weaken the layer. Certain bacteria, such as Escherichia coli, Lactobacilli, and Bifidobacteria can also synthesize DHPPA through a breakdown process of chlorogenic acid. This reaction typically happens in the human digestive tract. …

Evaluation Of The Selected Nuproxa Feed Additives For Protection Against Lameness And Improving The Wellbeing Of Broilers In The Lameness Challenge Model, Abigail Fanous

Biological Sciences Undergraduate Honors Theses

Bacterial Chondronecrosis with Osteomyelitis (BCO) is a form of bacteria that causes lameness in broiler chickens and is a common concern within the poultry industry. This easily transmissible disease can quickly take over entire livestock of chickens leading to an animal welfare issue. Due to this, it is a pressing issue that must be solved in order to protect the wellbeing of broiler chickens and ensure viable livestock. Nuproxa is a company that specializes in chicken feed in which we used to test different amounts of Panbonis, a dietary supplement, in its effectiveness in protecting broiler chickens against BCO lameness. …

Coastal Stormwater Pond Pollutants And The Potential For Development Of Antimicrobial Resistance In Vibrio And Enterococcus Bacteria, Cassandra L. Horton

Theses and Dissertations

The Southeastern coastal plain is the most rapidly urbanizing region in the United States. Associated landscape changes which increase imperviousness lead to hydrological cycle alterations, increasing runoff of nonpoint source (NPS) pollution. Urban and agricultural NPS runoff is generally discharged into stormwater ponds, which sequester chemical contaminants, nutrients, and microbes to reduce loading into coastal ecosystems. Studies of these ponds have indicated elevated levels of trace metals, antimicrobial compounds, and bacterial contamination (SCSGC 2018).

Interactions of aquatic pathogens Vibrio vulnificus and Enterococcus faecium with trace metals (arsenic, copper, zinc) and clinically relevant antimicrobials (triclosan, ciprofloxacin, oxytetracycline) commonly found in coastal …

Effects Of Mass Death On Community Structure And Ecosystem Function, Abby Kimpton Jones

Theses and Dissertations

Death and decomposition are natural processes that are generally well-understood. However, large events of death, such as mass mortality events (MMEs) are increasing in frequency and their impacts on the ecosystem are largely unknown. These events may have both bottom-up effects from increased nutrient input as well as top-down effects from loss of an ecological functional group by the affected population. Different functional MMEs may result in different top-down effects, creating cascading effects. In Chapter 1, I test the hypothesis that scavenger and herbivore simulated MMEs generate novel bottom-up and top-down effects. Results indicate that MMEs have a significant effect …

Implications Of Antibiotic And Bacteriophage Resistance In Environmentally Isolated E. Coli, Michael Connolly

Honors Theses

The increasing prevalence of antibiotic-resistant bacteria is an emerging problem for humans. Clinical misuse, overuse in agricultural and food settings, and limited numbers of new antibiotics have accelerated the proliferation of antibiotic-resistant bacteria. To confront this threat, scientists must develop new therapeutics that kill these antibiotic-resistant bacteria. In this study, we used Escherichia coli to analyze antibiotic and bacteriophage susceptibility. E. coli is a common, mostly benign, enteric, gram-negative bacteria. We isolated three E. coli strains from the Hans Groot Kill, a stream that runs through Union College’s campus. We sought to assess various E. coli strains’ antibiotic resistance, susceptibility …

Assembly Of The Peripheral Arm Subunits Of Escherichia Coli Complex I And Analysis Of Clinical Mutations, Hind Alkhaldi

Biological Sciences Theses and Dissertations

Respiratory Complex I from E. coli is a proto-type of the mitochondrial enzyme, consisting of a 6-subunit peripheral arm (B-CD-E-F-G-I) and a 7-subunit membrane arm. When subunits E-F-G (N-module), were expressed alone they formed an active complex as determined by co-immunoprecipitation and native gel electrophoresis. When co-expressed with subunits B and CD, only a complex of E-F-G was found. When these five subunits were co-expressed with subunit I and two membrane subunits, A and H, a complex of B-CD-E-F-G-I was membrane-bound, constituting the N- and Q-modules. Assembly of Complex I was also followed by splitting the genes between two plasmids, …

Antibiotic-Resistant Bacteria In Freshwater Crayfish, Colby Finch

Honors Theses

The presence of antibiotic-resistant bacteria is increasing in natural aquatic environments. Alongside this, organisms that live in these ecosystems are increasingly harboring antibiotic-resistant bacteria. In this study, I analyzed the capacity for the crayfish species Procambarus vioscai paynei to harbor antibiotic-resistant bacteria. Crayfish, as well as water and sediment, were sampled from a pond at the University of Mississippi Field Station. The guts of crayfish were plated on TSA agar, as well as agar containing vancomycin, erythromycin, penicillin, tetracycline, or ciprofloxacin. Following incubation, counts of bacteria were determined. Selected bacterial isolates were tested for multiple antibiotic-resistance. Bacterial isolates were also …

A Comparison Of Heterotroph Isolation And Sequencing Methods From Various Cyanobacterial And Algal Microbiomes, Victoria Starks

Honors Theses

Cyanobacteria have provided a vast, new source of natural products to be utilized in drug development. Because of their non-axenic nature, cyanobacteria typically have an abundance of symbiotic heterotrophs living in association with them. These bacteria can play significant roles in the survival of its cyanobacterial host as well as provide the potential production of unique compounds. The possibility of unknown natural products is only increased by the flexible nature of these bacteria, as altering its environmental state can change the activity of biosynthetic pathways and even activate novel production. Our research team’s intent is to isolate cyanobacterial strains from …

To The Window, To The Wall: Improving Environmental Monitoring Protocols, Sarah Jones

Graduate Theses and Dissertations

Detecting microorganisms on environmental surfaces via an environmental monitoring (EM) program is part of a preventive food safety culture. Environmental monitoring should 1) verify that food safety plans are reducing cross-contamination risk from surfaces to food, 2) pinpoint microbial niches, and 3) prevent the transmission of pathogens. Environmental monitoring programs utilize EM tools, such as sponges, to sample food contact and non-food contact surfaces. However, EM tool selection is determined by the individual food firm. This dissertation evaluated and characterized factors influencing EM program effectiveness in the food industry. Specifically, this dissertation focuses on the release of microorganisms from EM …

Analysis And Identification Of Lipolytic Bacterial Species For The Degradation Of Wastewater Lipids, Lindsay C. Smoak

Honors College Theses

The aim of this study was to isolate native bacterial strains from the wastewater treatment facilities of Statesboro, GA to identify their lipolytic activities. Obtained bacterial strains were further assessed via morphological and biochemical methods to determine their enzymatic capabilities. Use of the detergent Tween-20 in growth mediums was the first criteria to assess lipase activity, and these isolates were further investigated to quantitatively measure lipase presence and activity. Lipase protein was precipitated and dialyzed to perform a lipase activity assay, followed by Sodium Dodecyl Sulphate–Polyacrylamide Gel Electrophoresis (SDS-PAGE) to confirm the presence of the lipolytic enzymes. Sanger sequencing was …

Identification, Enumeration, And Diversity Determinations For Fungi Enriched On Phthalates As Sole Carbon Source From Riverine Sediments Using Molecular Methods, Anthony M. Vicidomini

All Capstone Projects

Phthalates are a common chemical compound used as plasticizers in various industries that have been linked to several detrimental effects on health. Due to their widespread use, they have become a common environmental pollutant of soil and water. The persistence and distribution of phthalate esters in the environment has given rise to many microorganisms that are able to incorporate phthalates into various metabolic pathways and degrade them into harmless substances, with fungi being among those that are capable of such degradation of industrial polycyclic aromatic hydrocarbons. In this study, the diversity of fungal communities in response to the presence of …

Microbial Community And Soil Responses To Land Management Practices In Remnant And Restored Tallgrass Prairies, Desirae Marie Klimek

Graduate Research Theses & Dissertations

Critical ecosystem functions, such as decomposition and nutrient cycling, are driven by microbial communities within soil. As such, it is important to examine the effect of restoration practices, such as the presence of native grazers and prescribed burning, on these microbes and the soil they inhabit. The Nachusa Grasslands provides a chronosequence of restored tallgrass prairies ranging in restoration age from 5 to 33 years, as well as remnant prairies, and agricultural fields. These sites were sampled seasonally from 2013-2020 and microbial ribosomal RNA genes were surveyed to characterize soil microbial communities and assess how common restoration practices affect these …