Life Sciences Commons^™

Comparison Of Taxonomy Assignment And Strain Detection In Urobiome Communities Using 16s Rrna Sequencing And Shotgun Metagenomic Sequencing, Delaney Sauer

Master's Theses

Advancements in sequencing technologies have enabled scientists to gain insight into the microbes that inhabit the human body, including the urinary tract. Cataloging the bacteria that inhabit the urinary tract has primarily relied on amplification and sequencing of specific variable regions of the 16S rRNA gene enabling genus-level taxonomic identification. Recently, shotgun metagenomic sequencing has been employed such that bacterial taxonomy as well as the functionality that they encode can be inferred. In this study, we compare taxonomies assigned by 16S sequencing and shotgun metagenomic sequencing of the urinary microbiota (urobiome) of females with and without a clinical diagnosis of …

A Population Level Examination Of The Incredible Fruit Diversity In Astragalus Lentiginosus, Quinn Thomas

Master's Theses

Astragalus lentiginosus is the most taxomically diverse species in the North American flora with over 40 recognized varieties. The incredible diversity within A. lentiginosus, particularly in respect to its fruit morphology, makes it an exceptional model to study adaptation and evolution. However, it remains unknown whether fruit morphology is an adaptation and, if so, the extent to which selection or neutral evolutionary processes shape the striking diversity in this trait. In order to understand the adaptive significance of fruit morphology we must first understand the genetic structure of A. lentiginosus. Varieties of A. lentiginosus vary considerably in their range size …

Hide And Seek: An Exploration Of Antipredator And Predator Avoidance Mechanisms In Orthopodomyia Signifera In Response To Predation From Toxorhynchites Rutilus, Nathaniel Dahlberg

Master's Theses

There have been many observations of larval Orthopodomyia signifera coexisting with the predator Toxorhynchites rutilus. There are three hypotheses that could explain how Or. signifera resists predation from Tx. rutilus. The first hypothesis states that larvae adapt behavioral changes that limit predation. The second hypothesis states thoracic setae serve as a physical defense that prevents Tx. rutilus from grasping Or. signifera. The third hypothesis states Or. signifera possess a chemical defense indicated by aposematic coloration. To test the first hypothesis larval Or. signifera were exposed to conspecific and heterospecific predation cues and their behavior was observed. Both cues …

The Debate On Nil: Progress For Female Collegiate Sports?, Stephanie Andrada

Master's Theses

In this study, seven female collegiate athletes from three different women’s sports teams (basketball, gymnastics, and volleyball) from a mid-major, Division-I college were interviewed. The study analyzed the lived experiences that NIL has on these specific female athletes in these particular women’s sports using a qualitative methodology. Three research questions were posed:

1. In what ways does the commercialization of college sports influence the NIL opportunities for these female athletes?
2. Could NIL perpetuate an uneven playing field for these female athletes in competition for limited resources?
3. To what degree do these female college athletes feel that NIL presents opportunities for equitable …

The Inverse Association Between Prebiotic Consumption And Depression Status In American Adult Females, But Not The Greater Population Or In Males: Nhanes 2015-2018, Cassandra L. Boyd

Master's Theses

It is unknown if a relationship exists between prebiotic intake and depression status. Using 2015-2018 National Health and Nutrition Examination Survey cycles data, adult American estimated mean daily prebiotic intake across demographic groups, gender, and depression status were reported. Additionally, the 10 highest prebiotic content Food and Nutrient Database for Dietary Studies foods were identified. Adults (≥ 18 years) with adequate sleep and at least one day of dietary recall data were included. Participants with excessive alcohol intake, BMI ≤ 18, BMI ≥ 30, or current depression medication use were excluded. The confounding variables were inadequate sleep, unemployment, and age. …

Behavorial Response Of Diving Northern Elephant Seals (Mirounga Angustirostris) When Exposed To Predator Calls, Daphne M. Shen

Master's Theses

Understanding how marine mammals respond to and recover from acoustic stressors is crucial if underwater noise increases. The use of an animal-borne biologger that combines a speaker with a motion sensor allows for the collection of whole-dive and fine-scale data over repeated exposures under identical experimental parameters. This study determined whether northern elephant seals (Mirounga angustirostris), a model for deep-diving marine mammals, exhibited a stereotypical behavioral response when exposed to killer whale whistles, an acoustic stressor. I examined changes in dive characteristics, measured duration of altered response, and observed behavior in response to repeated exposures. When exposed to the playback …

Lactobacillus Metabolite Nc As An Inflammation Inhibitor, Drew Hahnnah Landrowski

Master's Theses

The human body contains a diverse ecosystem of microbes. Commensal bacteria have numerous mutually-beneficial relationships with their host. Not only do they assist in digestion and gut homeostasis, they are critical for development and function of the immune system. As such, hosts and microbes alike have evolved mechanisms to foster symbiosis. Gut barrier function, toll-like receptor signaling, and metabolites are all examples of how hosts interact with microbes to promote this mutually-beneficial relationship. Metabolites from commensal bacteria promote the generation of regulatory T-cells, capable of ameliorating inflammation. A number of inflammatory, allergic, and autoimmune conditions are associated with dysbiosis. Therefore, …

How To Build A Cortex: Coordinated Assembly Of Cortical Septins And Actomyosin In The Leader Bleb, Asia Marie Paguntalan

Master's Theses

In confined spaces, migrating cells can undergo mesenchymal-to-amoeboid transitions by altering their cortical dynamics and adhesion with the environment. Septins frequently associate with cortical actin and non-muscle myosin (NMII), but the functional nature of these interactions remains unclear. Upon non-adhesive confinement and NMII enrichment, fibroblasts can switch to a fast, leader bleb-based mode of motility, characterized by the absence of adhesions and stress fibers and formation of a single, elongated leader bleb. During this transition, cortical actin remodeling and polarized NMII contractility drive leader bleb stabilization by generating long-range cortical flows, in coordination with changes in septin localization and assembly …

Incorporating Sex Chromosomes In Transcriptome Prediction Models And Improving Cross-Population Prediction Performance, Daniel S. Araujo

Master's Theses

Transcriptome prediction models built with data from European-descent individuals are less accurate when applied to different populations because of differences in linkage disequilibrium patterns and allele frequencies. We hypothesized multivariate adaptive shrinkage may improve cross-population transcriptome prediction, as it leverages effect size estimates across different conditions - in this case, different populations. To test this hypothesis, we made transcriptome prediction models for use in transcriptome-wide association studies (TWAS) using different methods (Elastic Net, Matrix eQTL and Multivariate Adaptive Shrinkage in R (MASHR)) and tested their out-of-sample transcriptome prediction accuracy in population-matched and cross-population scenarios. Additionally, to evaluate model applicability in …

Beef Bull Selection And Management Affecting Breeding Season Outcomes For California Cattle Producers On Rangelands, Megan Banwarth

Master's Theses

California’s approximately 660,000 head of beef cattle are highly dependent on range bulls used to produce offspring that can perform across the state’s diverse ecological regions. While knowledge of bull breeding behavior and the technology used to monitor cattle movement and behavior is critical to maximize conception rates and the overall efficiency in natural service sires on rangelands. Bulls need to be functional on rugged coastal landscapes, rolling foothills, deserts, and in high-elevation terrain. Few data exist that indicate factors related to selection, maintenance, and longevity of bulls used in rangeland landscapes. Objectives herein, were to assess factors influencing bull …

The Rise Of Terrorism In Africa And What It Means For U.S. Policymakers, Bridget Mary Hughes

Master's Theses

This thesis utilizes three case studies to measure the rise of terrorism in Africa. This qualitative data leads the reader to one ultimate question: what does the rise in terrorism in Africa mean for the United States (U.S.) and U.S. policymakers, National Security academia, students in National Security, if anything at all? The answer is: if civilian and military compounds are being targeted by these violent extremists, as these three case studies demonstrate, it is my recommendation that U.S. policymakers cease sending troops to the African theater and, instead, allocate funding to the citizens and nonprofits of the countries whom …

Ectotherm Thermoregulation At Fine Scales: Novel Methods Reveal A Link Between The Spatial Distribution Of Temperature And Habitat Quality, Ian Axsom

Master's Theses

Investigating ecological questions at the scale of individual organisms is necessary to understand and predict the biological consequences of environmental conditions. For small organisms this can be challenging because we need tools with the appropriate accuracy and resolution to record and quantify their ecological interactions. Unfortunately, many of our existing tools are only appropriate for medium to large organisms or those that are wide ranging, inhibiting our ability to investigate the ecology of small organisms at fine scales.

In Chapter 1, I tested a novel workflow for recording animal movements at very fine spatial and temporal scales. The workflow combined …

Plant Productivity And Diversity In Coastal Wetlands In Mississippi – Impact Of Hydrological Extremes, Kodi Feldpausch

Master's Theses

Wetlands are highly productive ecosystems that provide important ecosystem services and are threatened by extreme hydrological events. I evaluated how diversion of freshwater like Bonnet Carré Spillway openings in Louisiana, US, affected vegetation productivity and diversity in salt marshes on the neighboring Mississippi Gulf Coast, US. My study area is two estuarine systems that differ in their proximity to the Bonnet Carré Spillway, elevation, and salinity including Hancock County Marshes on the west, and Grand Bay National Estuarine Research Reserve (NERR) on the east in Mississippi. I collected above- and belowground biomass samples in 2020 and 2021, developed linear mixed-effects …

Dietary Protein Intakes, Distribution Patterns, And Quality In Ncaa Divsion 1 Soccer Players, Jun H. Kwon

Master's Theses

Dietary protein is required to support recovery and adaptation following exercise training. While prior research demonstrates that many athletes meet total daily protein needs, intake seems to be predominantly skewed toward the evening meal. An even distribution of protein doses throughout the course of a day is theorized to confer greater skeletal muscle anabolism compared to a skewed pattern of intake. Protein quality is also an important dietary consideration for athletes, with the amino acid leucine being the primary driver of the postprandial anabolic response. The present thesis investigates the protein consumption characteristics among a selected cohort of NCAA Division …

Detection Methods, Occupancy Rates, Management And Conservation For Rodents, Jaran Hopkins

Master's Theses

Chapter 1. Species’ occurrences are dependent on a variety of habitat characteristics, including physical landscape factors and anthropogenic land use and change. Understanding the influence of habitat attributes on species occurrence is essential to successful wildlife and habitat management, specifically in areas with active human use. We tested the influence of vegetation alliance, fragmentation, and human recreation in the form of off-highway vehicles (OHV) in an area of active land management in coastal California, with a focus on the occurrences of six small mammal species. The area is composed of sand dunes subject to natural habitat fragmentation. OHV recreation occurs …

Cataloging And Engineering Temperate Coliphages Of The Human Urinary Microbiome, Elias Crum

Master's Theses

In the US, around 60% of females will be diagnosed with a Urinary Tract Infection (UTI) in their lifetime, and Escherichia coli is the most implicated etiological agent in UTIs. Despite its frequent association with lower urinary tract symptoms, recent studies have found that the urinary microbiome (UMB), the viral, bacterial, and fungal resident members of the urinary tract, of healthy females can also consist of E. coli. While most research has focused on the bacterial constituents of the UMB, bacteriophages, viruses that infect bacteria, are far more abundant. Bacteriophages (phages) of other human microbiomes have been shown to play …

Exploring The Role Of Lactobacillus Jensenii And Lactobacillus Mulieris In The Urogenital Tract, Adriana Daniela Ene

Master's Theses

Lactobacillus is a predominant species of the urogenital tract and it has been found in females with and without lower urinary tract symptoms. The Lactobacillus genus is thought to be beneficial to the host due to its capability to produce hydrogen peroxide, secondary metabolites, and lactic acid. L. jensenii is an organism frequently isolated from the urogenital tract. In March 2020, a new sister taxon of L. jensenii was described, L. mulieris. Shortly thereafter we produced a genomic analysis of all publicly available genomes (n = 43) which reclassified some L. jensenii as L. mulieris. This motivated the in-depth study …

Polyomavirus Jcpyv And Its Role In The Urinary Tract, Rita Lauren Mormando

Master's Theses

Polyomaviruses are the smallest closed-circular supercoiled double-stranded viruses found in the human microbiota. The polyomavirus JC (JCPyV) is most commonly found within the urinary tract, and prior studies estimate that 20-80% of older adults carry JCPyV. In very rare cases, JCPyV leaves the kidneys, causing progressive multifocal leukoencephalopathy. However, the role of JCPyV within the urinary tract remains an open question. In a prior study conducted by our group, the bladder microbiota of females with and without overactive bladder symptoms (OAB) were sequenced. Interestingly, JCPyV was only detected in females with OAB; none of the control (“asymptomatic”) microbiota contained JCPyV. …

Phylogenetic Relationships Among Fishes In The Order Zeiformes Based On Molecular Data From Three Mitochondrial Loci, Lindsay Scarpitta

Master's Theses

The Zeiformes (dories) are mid-water or deep (to 1000 m) marine acanthomorph fishes with a global, circumtropical, and circumtemperate distribution. Some species have a near-worldwide distribution, while others appear to be regional endemics, e.g., near New Zealand. Six families, 16 genera, and 33 species are currently recognized as valid. Relationships among them, however, remain unsettled, especially in light of recent proposals concerning the phylogenetic placement of zeiforms within the Paracanthopterygii rather than allied with beryciforms or percomorphs. The present study uses mtDNA characters to investigate zeiform interrelationships given their revised phylogenetic placement and attendant changes to their close outgroups, carried …

The Impacts Of Framework Mutations On Steady-State Kinetics Of An Aldolase Abzyme, Charles Andrew Mettler

Master's Theses

During affinity maturation, antibodies acquire point mutations that lead to enhanced binding strength to a particular ligand while simultaneously becoming more conformationally restricted as they become increasingly complementary to their ligand’s electrostatic geometry. This property has catalytic potential in transition-state (TS) stabilization whereby kinetic barriers (i.e., the energetic gap between the substrate and its TS) are reduced and reaction rates are enhanced. This basic mechanism is thought to underlie the majority of the rate enhancement observed for enzymes. A key integration of antibody binding specificity and strength with enzymatic catalytic strategy is the development of catalytic antibodies (“abzymes”). Abzymes are …

Interplay Between Human Microbiota And Celiac Disease, John James Colgan

Master's Theses

Celiac disease is an autoimmune disorder of the small intestine in which gluten, an energy-storage protein in wheat and other cereals, elicits an immune response leading to villous atrophy. Despite a strong genetic component, the disease arises sporadically over the lifetime leading us to hypothesize the microbiome might be a trigger. Here, we re-examined 16S data from 3 prior studies examining celiac disease and the microbiome with newer computational tools: the dada2 and PICRUSt 2 pipelines. Our results both confirmed findings of previous studies and generated new data regarding the celiac microbiome of India and Mexico. The datasets were also …

Interrogating Antagonistic Differences Among Pseudomonas Aeruginosa Cdia Alleles, Haotian Yang

Master's Theses

Bacteria are complex social organisms that live within mixed communities where microorganisms compete for limited resources. We studied Contact-Dependent Growth Inhibition (CDI), a particular type of competition mediated by a type 5b, or two-partner, secretion system that is widely spread among Gram-negative bacteria. CdiB and CdiA make up the two-partner secretion system that mediates CDI. CdiB translocates CdiA to the cell surface, and CdiA delivers its C-terminal toxin domain to the target cell. The C-terminal toxin (Tox) domain of CdiA is highly diverse. We studied Tox domains of various Pseudomonas aeruginosa clinical isolates. We found different strains that contain unique …

Integrating Current Analyses Of The Breast Cancer Microbiome, Sidra Sohail

Master's Theses

Breast cancer is the leading cause of cancer death for women in the US. Many cancertypes have significant associations with their resident microbial communities - emerging evidence suggests that breast cancers also interact with the local tissue-associated microbiota. Studies have examined the relationship between breast cancer and its microbiome, however, the studies varied in their approaches used to evaluate these relationships. Microbiome research advances rapidly and analysis pipelines and databases are updated frequently. This dynamic environment makes inter-study comparisons and superficial evaluations challenging as no two studies are using the same standards for evaluation. Researchers have observed the microbiota of …

Role Of Tetraspanins In Sars-Cov-2 Fusion And Entry, Marcos Saul Santiago Figueroa

Master's Theses

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the pandemic the world has been facing in recent years. Even as new countermeasures are developed, there is still much we don’t know in terms of its entry into host cells. Tetraspanins are transmembrane proteins that are near ubiquitous amongst cell types. They fulfill numerous roles, including that of a viral co-receptor. Here, we considered whether tetraspanins, specifically CD9, CD63, and CD81 influence SARS-CoV-2 fusion and entry. Using ACE2-LgBit and tetraspanin overexpressing EVs and HeLa cells, we find that the presence of excess tetraspanins inhibit fusion and entry. However, we …

Cofermentation, Post-Alcoholic, And Post-Malolactic Fermentation Blending Of Malbec, Merlot And Petite Sirah Wines, Armando Arturo Vega-Osorno

Master's Theses

A two-year study was conducted to assess the effects of cofermentation on red wine varietals. During the winemaking process, wines can be made from two or more varieties by picking, crushing and fermenting them together, a practice known as cofermentation. They can also be blended either after the completion of alcoholic fermentation or after malolactic fermentation. In the first year of the study, two grape varieties, Merlot (Mer), and Malbec (Mal) were cofermented. On the second year, a third varietal, Petite Sirah (PS) was also studied. Cofermented wines containing every possible binomial combination of the varietals was made and one …

An Integrated Approach For Controlling Verticillium Wilt Of Strawberry, Jack T. Koster

Master's Theses

Strawberry (Fragaria x ananassa, Duch.) is an important crop in California, with more than 35,000 acres planted in 2018 resulting in a farm gate value of $3.1 billion. In 2020, California strawberry production accounted for more than 85% of national strawberry production and faces serious threats to production due to various soil-borne diseases. One such disease, Verticillium wilt, is caused by the fungal pathogen Verticillium dahliae and is commonly found in temperate zones around the world where strawberries are grown. Due to the phase-out of efficacious fumigants like methyl bromide, alternative disease management methods have become necessary to …

Determination Of Fungicide Resistance In Botrytis Cinerea On Wine Grapes In California's Central Coast Region, Evelyn Alvarez-Mendoza

Master's Theses

Botrytis bunch rot, caused by Botrytis cinerea, is a fungal disease that primarily affects the fruit of wine grapes. Infection of fruit consequently results in reduced yields and wine quality. These factors lead to significant economic losses for growers which prompts the implementation of management practices to control the disease. One objective of this study was to evaluate the level of resistance that populations of B. cinerea in the Central Coast region showed to various chemicals. A fungicide assay was conducted to determine resistant phenotypes to six fungicide active ingredients (pyrimethanil, iprodione, fenhexamid, fludioxonil, trifloxystrobin, boscalid). Thirty-five (2020) and …

Mechanisms Of Substrate Selectivity And Transport By Escherichia Coli Atp- Binding Cassette (Abc) Transporter Metni, Yuchun Chen

Master's Theses

ABC transporters are central in many cellular functions including nutrient uptake, signal transduction membrane assembly, and cellular detoxification. Both structural and functional studies have revealed insights into the high-affinity uptake mechanism of the MetNI methionine ABC transporter. Using the energy from ATP binding and hydrolysis, the MetNI-Q system can import L-Met, D-Met, and other methionine derivatives against concentration gradients. Many mechanistic studies of ABC transporter propose a model in which cognate binding proteins sequester substrates in the periplasm and deliver them to the transporter. In contrast, recent in vivo and crystallographic studies of MetNI-Q suggest that some substrates may be …

Investigation Of Dead Ocean Quahogs (Arctica Islandica) Shells On The Mid-Atlantic Bight Continental Shelf, Alyssa Leclaire

Master's Theses

Ocean quahogs, Arctica islandica, are a long-lived, widely dispersed, biomass dominate in the Mid-Atlantic; therefore, quahog shells are valuable resources for studying climate change over time. Recently, dead ocean quahog shells were discovered south and inshore of the present biogeographic range of this animal. The presence of ocean quahog shells outside the current range is presumably a consequence of past regressions and transgressions of the Cold Pool, the bottom-trapped, cool body of water that allows boreal animals to live at lower latitudes. Dead ocean quahog shells were collected offshore of the DelMarVa Peninsula then radiocarbon-dated, evaluated for taphonomic condition, …

Effects Of Shoreline Development And Freshwater Discharge On Nekton Assemblage And Trophic Structure In A Northern Gulf Of Mexico Estuary, Glenn Schumacher

Master's Theses

Coastal salt marshes support a diversity of nekton and facilitate critical ecosystem functions but are threatened by shoreline development and climate change. Therefore, coastal ecosystem managers have begun incentivizing the use of living shorelines (LS), erosion control structures incorporating native plantings, to mitigate ecological consequences of marsh loss. However, post-restoration climate changes may shift habitat templates and negate positive effects of ecosystem restoration. I evaluated the ecology nekton along LS, natural marshes, hardened shorelines and greyed shorelines within Biloxi Bay, Mississippi, during a high freshwater discharge (HFD) period by comparing nekton assemblage (using species richness, Shannon-Wiener diversity, and relative abundance), …