Mincer, Tracy

Genomics has been revolutionized by improved sequencing technologies, allowing for the detailed exploration of microbial dark matter and complex microscopic ecosystems. The bottleneck in genomic workflows has shifted from high-throughput sequencing to data analysis. This dissertation developed the Florida Center for Coastal and Human Health Shotgun Metagenomics Workflow (FCHsm) that is easy to use and tailor to unique datasets. This work acts as the beta-testing for the workflow, as it analyzes disparate biomes (environmental and host microbiomes) at varying sequencing depths (shallow and deep). FCHsm was used to resolve molecular dynamics and mine trans-kingdom metagenomes for secondary metabolic biosynthetic gene clusters (BGCs) in two marine environments— Indian River Lagoon toxic harmful algal blooms (IRL HABs) and the medicinal Leiodermatium sponge holobiont.
First, an in silico mock dataset was analyzed to benchmark the FCHsm workflow. Sourmash, coupled with the Genome Taxonomy Database, outcompeted the other taxonomic profilers by accurately predicting the size of the mock metagenome (450 genomes) and recalling the highest number of species (82 %) and strains (44 %). Nonpareil calculated the sequencing effort needed for 100 % coverage for all the datasets and correctly estimated the 75 Gbp of sequencing needed for almost 100 % coverage of the mock metagenomes (99.5 %). Next, the trans-kingdom metagenomes of the IRL were explored, and potential HAB biomarkers were identified.

Sediments are the ultimate resting place of plastics in the ocean, providing information on plastics that have escaped from the waste stream through freshwater input, marinas, and agricultural runoff. Sediment samples taken as part of a previous study in the Indian River Lagoon, Florida, may shed light on the speculation of microplastics in this environment. These samples were taken in four seasons (2 wet and 2 dry) during 2016, 2017, and 2018 in Harbor Branch, Jensen Beach, Fort Pierce, and Vero Beach. Plastic particles were extracted from the sediments with >95% efficiency through density separation, filtration, and scanned using infrared spectroscopy. Analysis identified plastics as small as 30 μm, the most common polymers individuated being ~100μm. A preliminary overview of the study has revealed the presence of microplastics in the majority of the sediments analyzed. Future in depth analysies of these samples is planned to determine the polymers present.

SARS-CoV-2, commonly referred to by the disease it causes, COVID-19, took the world by surprise in late 2019 and triggered a multi-year-long pandemic. Helped by its initial airborne infectivity, the virus accumulated mutations causing the disease to become even more infectious and lethal. This led to variants that struck the globe in waves, outcompeting their predecessors and leading to yet more mutations. However, this trend ended with the emergence of Omicron, the present dominant variant, which exhibits greater infectivity but lessened lethality. Notably, the same mutations have repeatedly emerged, evolving from independent lineages all around the planet. This paper aims to identify and compare these mutations, and evaluate their influence on the variants that they inhabit. Using this information, this paper predicts characteristics of future SARS-CoV-2 variants by speculating what changes Omicron may undergo.

SARS-CoV-2 is a viral pathogen that causes a disease termed coronavirus disease 2019. In December of 2019 the virus spread all over the world, causing a global pandemic. The disease mostly affects the respiratory system and common symptoms include fever, dry cough, labored breathing, and others. Among the other symptoms something noteworthy was found; COVID-19 caused olfactory and gustatory dysfunction in some affected individuals. The mechanisms relating to olfactory and gustatory dysfunction can shed light on the pathology of SARS-CoV-2 and how it uses the body to proliferate. This thesis will explore the prevalence, diagnosis, and prognosis of olfactory and gustatory dysfunction, as well as a potential route into the brain due to SARS-CoV-2 infection.

The dwindling population of the Florida manatee faces greater threats every year. With the addition of a domoic acid (DA) producing algal bloom of Pseudo-nitzschia, in the Indian River Lagoon (IRL), they may have yet another threat. This study uses prior literature to compare and contrast the neuroanatomy of the California Sea Lion, Zalophus californianus, and the Florida Manatee, Trichechus manatus, to predict the effects of DA toxicosis in manatees. It also investigates the possible effects of this kind of harmful algal bloom (HAB) in the IRL and for the people living near it. This study demonstrates, based on DA research in sea lions, that manatees could have decreased survivability due to DA induced hippocampal lesion development causing perseveration behaviors and loss of memory and goal directed behaviors. As well as decreased survivability to cold stress syndrome due to increased levels of gamma glutamyl transferase (GGT) .

Coloboma and CHARGE Syndrome are rare congenital conditions that arise in about 1 in 10,000 children. Coloboma is a defect in the eyes. CHARGE Syndrome involves Coloboma, Heart defects, Atresia choanae (also known as choanal atresia), Restricted growth and development, Genital abnormalities, and Ear abnormalities. This thesis aims to spread awareness about the medical and physical complications that come with these conditions and the impacts they have on individuals. This thesis not only meticulously studies and characterizes the mutations and symptoms involved in Coloboma and CHARGE Syndrome, but also provides insight on treatment and possibilities of a cure.

This past year has seen an exponential increase in the amount of polystyrene foam products utilized for convenience purposes. Home food delivery services, takeout, and packaging from the surplus of online shopping are major contributors to the overall presence of polystyrene foam products polluting the environment. Expanded Polystyrene (EPS), is made from petroleum, like most common plastics. However, polystyrene (PS) foam comprises over 90% air which makes it difficult to recycle due to its lightweight and bulky nature. The polystyrene foam is therefore discarded with trash or littered in the environment. The foam products become lost in the environment and make their way to rivers and the ocean to begin the decomposition process which is sped up by UV irradiation. The microplastics and nanoplastics resulting from breaking down PS products will subsequentially impact the wildlife with effects that were made clear in various studies that have been conducted.