Microbiology Commons^™

Hgs-3 The Influence Of A Tandem Cycling Program In The Community On Physical And Functional Health, Therapeutic Bonds, And Quality Of Life For Individuals And Care Partners Coping With Parkinson’S Disease, Leila Djerdjour, Jennifer L. Trilk

SC Upstate Research Symposium

Purpose Statement: Several studies have shown that aerobic exercise can have a positive impact on alleviating symptoms experienced by individuals with Parkinson's disease (PD). Despite this evidence, the potential benefits of exercise for both PD patients and their care partners (PD dyad) remain unexplored. This research project investigates the effectiveness, therapeutic collaborations, and physical outcomes of a virtual reality (VR) tandem cycling program specifically designed for PD dyads.

Methods: Following approval from the Prisma Health Institutional Review Board, individuals with PD were identified and screened by clinical neurologists. The pre-testing measures for PD dyads (N=9) included emotional and cognitive status …

Materials And Methods Developed For The Recording And Analysis Of Behavior In The Common Marmoset (Callithrix Jacchus)., Christian Wintle

UNO Student Research and Creative Activity Fair

Materials and methods developed for the recording and analysis of behavior in the common marmoset (Callithrix jacchus).

Christian J. Wintle^a, Jordan B. Hernandez^a,b,c, Dobromir Dotov^d, and Jonathan B. Clayton^a,b,e,f,g

^aDepartment of Biology, University of Nebraska at Omaha, Omaha, NE, USA

^bNebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA

^cDepartment of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, NE, USA

^dDepartment of Biomechanics, University of Nebraska at Omaha, Omaha, NE, USA

^eDepartment of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, …

Adaptive Evolution Of Surface Proteins In Microbial Pathogens: Lyme Disease Pathogens (Borreliella Sp.) And Human Immunodeficiency Virus Type 1 (Hiv-1), Li Li

Dissertations, Theses, and Capstone Projects

Cell and virion surface proteins are key to the survival and adaptation of microbial pathogens by enabling them to evade host immune responses and to persist in diverse environments. Pathogens respond to host immune pressures with genetic changes in surface proteins through mechanisms including point mutations, recombination, gene duplication and loss, and lateral gene transfer, resulting in novel antigenic variants and antigenic diversity. This continuous adaptation helps pathogens evade host immunity, leading to chronic infections and recurrent disease outbreaks. Understanding these mechanisms is vital for developing effective strategies to combat infectious diseases.

This dissertation comprises three chapters exploring the adaptive …

A Comparison Of Adenosine Triphosphate With Other Metrics Of Microbial Biomass In A Gradient From The North Atlantic To The Chesapeake Bay, Alexander B. Bochdansky, Amber A. Beecher, Joshua R. Calderon, Alison N. Stouffer, Nyjaee N. Washington

OES Faculty Publications

A new, simplified protocol for determining particulate adenosine triphosphate (ATP) levels allows for the assessment of microbial biomass distribution in aquatic systems at a high temporal and spatial resolution. A comparison of ATP data with related variables, such as particulate carbon, nitrogen, chlorophyll, and turbidity in pelagic samples, yielded significant and strong correlations in a gradient from the tributaries of the Chesapeake Bay (sigma-t = 8) to the open North Atlantic (sigma-t = 29). Correlations varied between ATP and biomass depending on the microscopic method employed. Despite the much greater effort involved, biomass determined by microscopy correlated poorly with other …

Patterns Of Epiphytic Bacterial Growth On Flower Surfaces: Relationships With Flower Longevity And Environmental Factors, Rita Nkem Afagwu

Graduate Theses/Dissertations

Flowers host diverse communities of epiphytic bacteria, which can impact floral functions, pollinator interactions, and overall plant fitness. However, little is known about how the abundance of these bacteria change as flowers age, and how these shifts may correlate with floral longevity. In this study I investigate the change in bacterial abundance across the lifespan of a flower from anthesis (opening of bud to flower) to senescence (wilting of flower) and to explore the potential implications for floral longevity. We tracked the age of the flowers by determining the average age to senescence in flowers of 8 plant species over …

Batch Culture Models Of The Murine Gut Microbiome & The Impact Of Simple Dormancy On Dormancy-Capable Microorganisms Models, Ana C. Mendez

Mathematics Dissertations - Archive

The proposed mathematical biology research utilizes mathematical models to gain insight into biological systems. These systems of ordinary differential equations model diverse topics, ranging from gut microbiomes to harmful algal blooms. A complete stability analysis, supporting phase plane portraits, bifurcation diagrams, and numerical simulations will accompany the models presented. In Chapter 2, the murine gut microbiome is modeled to match laboratory experiments in the literature. In these experiments, mice eat plasmid-carrying “donor” bacteria and naturally carry plasmid-free “resident” bacteria in their gut. The models aim to capture the behavior of plasmids, donor bacteria, and resident bacteria. Chapter 3 explores dormancy …

Investigation Of L-Serine Synthesis And Transport As Stabilizing Feedback Mechanisms Within The Tsetse-Wigglesworthia Symbiosis, Ryan Phillips

Graduate Theses, Dissertations, and Problem Reports (ETD)

Tsetse flies (Glossina morsitans), which are the obligate vectors of Old-World trypanosomes (Trypanosoma spp.) that cause African trypanosomiasis, have a bacteriome that houses the intracellular endosymbiont Wigglesworthia glossinidia. The ancient coevolution of these species has led to the integration of Wigglesworthia metabolism into tsetse physiology and a subsequent reliance on nutrient exchange for maintaining the fitness of both partners. The establishment of this obligate mutualism has facilitated the emergence of feedback mechanisms that stabilize the symbiosis, such as that which involves the exchange of L-serine and B vitamins. The Gammaproteobacteria Wigglesworthia supplement B vitamins lacking …

Co-Divergence Of Lemur Hosts And Gut Microbiomes Across Multiple Evolutionary Scales, Mariah E. Donohue

Theses and Dissertations--Biology

This dissertation bridges micro- and macroevolutionary approaches to understand the co-diversification of animal hosts and their gut microbiomes at different evolutionary timescales. I examined these dynamics using wild lemurs, a diverse Primate clade endemic to the island of Madagascar.

First, I tested the relative effects of host phylogenetic relationships, diet, and habitat in shaping the gut microbiome through deep evolutionary time and across distinct microbial kingdoms. I designed a natural experiment sampling feces from rainforest and dry forest lemur communities with similar phylogenetic assemblages and considerable variation in dietary strategy. Then, I amplified and sequenced two metabarcoding genes, the V4 …

The Sewage Microbiome Dynamics Of Different Serving Neighborhoods In Charleston, Illinois, Sandra Chiamaka Okoye

Masters Theses

The complex microbial ecosystem within sewage systems holds significant implications for environmental and public health. Unlike studies on wastewater treatment plant microbiomes, upstream sewage systems have not been studied widely. This research investigated the dynamic sewage microbiome across diverse serving neighborhoods in Charleston, Illinois, encompassing residential, hospital, industrial, and university areas. Drawing upon recent advancements in microbiome research, the study aimed to unravel the spatial and temporal variations in microbial structures. Three times between June to December 2023 sewage samples were collected from manholes in the areas mentioned above. Community DNA was extracted and sequenced for the V4-V5 region of …

Molecular Investigation Of Tick-Borne Pathogens In Feral Swine (Sus Scrofa) From Seven Us States, Sofiane Aiche

Masters Theses

Feral swine (Sus scrofa) have been proposed as part of the lifecycles of multiple tickborne pathogens (TBP). This is a result of the increase in feral swine populations and increased tick populations and geographic ranges. Few surveys exist on the TBP relevant to human and wildlife of feral swine in the US. The aim of this study is to investigate the prevalence of 10 TBP: Anaplasma spp., Borrelia spp., Cytauxzoon felis, Hepatozoon spp., Babesia spp., Mycoplasma spp., Trypanosoma cruzi, Toxoplasma gondii, Yersinia pestis, and Rickettsia spp. A total of 87 feral swine blood samples …

Social Interactions And Spatial Structure Drive Community Assembly Of Bacterial Biofilm, Matthew C. Bond

Dartmouth College Ph.D Dissertations

Despite the critical nature which microbial communities play in the natural world and human civilization, the breadth of understanding remains shallow. Challenged by scale, high variability between environments, and extensive diversity, microbial ecologists strive to understand connections between a community’s structure and function, as well as the ecological and evolutionary mechanisms underlying observed natural patterning of communities. Biofilms are the predominate mode of growth for microbial communities—characterized by cellular attachment to a surface via a self-produced matrix and heterogeneous structure, often resulting in a primary growth front along the biofilm surface due to differential access to bulk nutrients (cite). This …

Scale And Habitat Effects On Measurement Of Streptomyces Biogeography And Biodiversity, Terilyn A. Stoflet

Cal Poly Humboldt theses and projects

Bacteria in the genus Streptomyces are detected in most soils around the world, as well as on and in seeds, plants, animals, insects and the wind. Currently, more than 700 valid species of Streptomyces have been identified worldwide. Streptomyces produce the majority of antibiotics, antivirals and antifungals, as well as important agricultural bioactive molecules due to their unique genetic capabilities. Their distinct genetic abilities allow them to produce an unlimited amount of biosynthetic gene clusters, or BGC’s. Although many compounds come from Streptomyces, scientists have not discovered the biogeographic patterns of this genus. The biogeography of Streptomyces is a …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Protocol For An Agent-Based Model Of Recombination In Bacteria Playing A Public Goods Game, Isaiah Paolo A. Lee, Omar T. Eldakar, J. Peter Gogarten, Cheryl P. Andam

Biology Faculty Articles

Agent-based models are composed of individual agents coded for traits, such as cooperation and cheating, that interact in a virtual world based on defined rules. Here, we describe the use of an agent-based model of homologous recombination in bacteria playing a public goods game. We describe steps for software installation, setting model parameters, running and testing models, and visualization and statistical analysis. This protocol is useful in analyses of horizontal gene transfer, bacterial sociobiology, and game theory.

For complete details on the use and execution of this protocol, please refer to Lee et al.¹

Breaking Virulent: The Coincidental Evolution Of Virulence Factors In Bacteria., Rhiannon Emmanuelle Cecil

Electronic Theses and Dissertations

Understanding how innocuous organisms can evolve to be pathogenic to humans is of increasing global concern. Further, understanding how existing pathogens may evolved to be more virulent is also vital to our ability to provide healthcare to people afflicted with diseases that promote chronic bacterial infections, such as cystic fibrosis. With the rise of antibiotic resistance in both bacteria and fungi it is paramount that new therapeutics are identified. Understanding what mutations occur that result in increased virulence in microbes can potentially provide new targets for antimicrobial drugs to combat antibiotic resistance. The Coincidental Evolution Hypothesis is a fundamental hypothesis …

Distinguishing Community Assembly Through Functional Redundancy Models., Sandra A. Tsiorintsoa, Sharon Bewick, Matthew Macauley

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Connecting The Nebraska Water Quality Index To The Aquatic Microbial Community Of The North Platte River Basin, Nebraska, Paula R. Guastello

School of Natural Resources: Dissertations, Theses, and Student Research

The Nebraska Water Quality Index, under development by the Nebraska Department of Environment and Energy, summarizes in a single value eight environmental parameters that have been monitored in Nebraska for nearly 20 years. Water quality parameters including those used in the Nebraska Water Quality Index have been shown in previous studies to impact bacterial growth. As such, this index has the potential to correlate with the freshwater microbial community. Here, I relate the Nebraska Water Quality Index to microbial community composition and structure using 16S rRNA gene amplicon sequence data collected from the North Platte River Basin, Nebraska. This index …

Tracing Evolution Of Gene Transfer Agents Using Comparative Genomics, Roman Kogay

Dartmouth College Ph.D Dissertations

The accumulating evidence suggest that viruses and their components can be domesticated by their hosts, equipping them with convenient molecular toolkits for various functions. One of such domesticated system is Gene Transfer Agents (GTAs) that are produced by some bacteria and archaea. GTAs morphologically resemble small phage-like particles and contain random fragments of their host genome. They are produced only by a small fraction of the microbial population and are released through a lysis of the host cell. Bioinformatic analyses suggest that GTAs are especially abundant in the taxonomic class of Alphaproteobacteria, where they are vertically inherited and evolve …

Spatial Structure Of Germination And Seed-Associated Fungi In Tropical Pioneer Seeds, Daniela Varon Garcia

USF Tampa Graduate Theses and Dissertations

Negative density-dependent regulation is the process by which host-specific natural enemies reduce the survival of seeds and seedlings of conspecifics near adult trees, favoring heterospecific recruitment, and ultimately increasing local diversity. Negative density-dependent regulation by fungal pathogens has been consistently reported to promote plant diversity in the tropics, even though they tend to be multi-host and host-specificity is rarely reported. Nevertheless, evidence suggests that host-generalist fungi can have host-specific effects that produce disproportionate negative effects on some plant species but not others, promoting regional diversity. However, such studies have not tested for both host-specificity and distance-dependent effects in fully replicated …

Organic Carbon Decay Mediated By Mesopelagic Microbial Communities, Noah Jonathan Craft

OES Theses and Dissertations

Substantial remineralization of organic carbon occurs in the mesopelagic zone (i.e., the biological pump), the efficiency of which is responsible for the oceans’ capacity to store carbon originally derived from the atmosphere. To better understand how a substrate’s composition influences its degradation by mesopelagic microbial communities, we added treatments made of live algal cells, dead particulate organic carbon and dissolved organic carbon from ¹⁴C-labeled algal cultures to mesopelagic water collected in-situ. Each incubation took place in the laboratory over a period of months, during which PO¹⁴C, DO¹⁴C, ATP, prokaryote abundances and biochemical fractions were measured. …

Past And Ongoing Field-Based Studies Of Myxomycetes, Steven L. Stephenson

Biological Sciences Faculty Publications and Presentations

Evidence from molecular studies indicates that myxomycetes (also called myxogastrids or plasmodial slime molds) have a long evolutionary history, and the oldest known fossil is from the mid-Cretaceous. However, they were not “discovered” until 1654, when a brief description and a woodcut depicting what is almost certainly the common species Lycogala epidendrum was published. First thought to be fungi, myxomycetes were not universally recognized as completely distinct until well into the twentieth century. Biodiversity surveys for the group being carried out over several years are relatively recent, with what is apparently the first example being carried out in the 1930s. …

Characterization Of Antimicrobial Properties Of Excrement And Functional Microbiome Of Black Vultures (Coragyps Atratus), Bridgette Gray

Theses

Black vultures, Coragyps atratus, are obligate scavenging birds that consume and dispose of decaying carcasses and carrion. They fulfill a key ecological niche in the environments in which they live. It has been observed that these vultures sometimes excrete bodily waste onto their legs. This adaptive behavior could help aid them in controlling bacteria and other microbes they encounter while stepping into a carcass to eat. This study directly examined the antimicrobial properties of the excrement of black vultures across various bacterial species utilizing a zone of inhibition test and a nematode species utilizing a survival assay. The black vulture …

Sympatric Soil Microbe Interactions Between Streptomyces And Fusarium Isolates, Lehren A. Olk-Szost

All NMU Master's Theses

Interkingdom interactions between soil bacteria and fungi may play a critical role in occurrence of disease suppressive soils, yet our understanding of these interactions remains limited. Streptomyces are well-known producers of antimicrobial compounds important to medicine and agriculture. Production of these secondary metabolites is often mediated by quorum sensing. Most Streptomyces research occurs in single species experiments, yet new metabolites have been discovered in interspecies co-culture experiments. Interspecies, intergenic, and interkingdom co-culture research will likely reveal many valuable compounds, and strengthen our understanding of complex ecological interactions in soil microbiomes. Interactions between sympatric Streptomyces and Fusarium isolates from disease suppressive …

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 …

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 …

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 …

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 …

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 …

Effect Of Temperature On The Microbiome Of A Laboratory Reared Colony Of Haemaphysalis Longicornis Ticks, Brianna Mitchell

Poster Presentations

Honors research poster.

Haemaphysalis longicornis is a species of tick native to eastern Asia, including eastern China, Japan, eastern Russia, and Korea. To date, it has invaded and has now established its existence in Australia, New Zealand, and several of the Pacific Islands. This species of tick has recently been introduced to the United States, having a confirmed sighting in November 2017 on a sheep farm in New Jersey and since establishing populations in 18 states along the east coast and Appalachia. Based on the existing locations of H. longicornis in its native regions, as well as in the United …

Impacts Of Bacterial Evolution On Host Lethality In Drosophila, Andrew Preston

College of Arts & Sciences Senior Theses

Evolution is the process by which species change their genetic traits, such as the pathogenicity of bacteria, over time in response to changes in their environment. Although the genetic mechanisms underlying many evolutionary processes have been revealed, it is still not well understood how opportunistic pathogens, such as Pseudomonas aeruginosa, become virulent. The overall goal of this thesis is to test the Coincidental Evolution Hypothesis, which proposes that the virulence of opportunistic pathogens evolves coincidentally as a by-product of their interaction with their natural predators. I hypothesized that the virulence of ancestral Pseudomonas aeruginosa changes over time if it co-evolves …