Biology Commons^™

Insights To Protein Pathogenicity From The Lens Of Protein Evolution, Janelle Nunez-Castilla

FIU Electronic Theses and Dissertations

As protein sequences evolve, differences in selective constraints may lead to outcomes ranging from sequence conservation to structural and functional divergence. Evolutionary protein family analysis can illuminate which protein regions are likely to diverge or remain conserved in sequence, structure, and function. Moreover, nonsynonymous mutations in pathogens may result in the emergence of protein regions that affect the behavior of pathogenic proteins within a host and host response. I aimed to gain insight on pathogenic proteins from cancer and viruses using an evolutionary perspective. First, I examined p53, a conformationally flexible, multifunctional protein mutated in ~50% of human cancers. Multifunctional …

Understanding Exosomal Extracellular Vesicles And Morphine In The Neuropathology Of Human Immunodeficiency Virus And Differential Zika Virus Strain-Associated Pathology, Allen Caobi

FIU Electronic Theses and Dissertations

Exosomal Extracellular Vesicles (xEVs), integral to intercellular communication and regulation of immune responses, have functional effects based on their contents, which they transport to neighboring cells. However, in the context of infection, EV cargo can be modulated, by either infected or uninfected cells. We hypothesize that CNS-associated neuropathology, is partially, due to the cargo transported by the exosomes. We theorize that the cargo released from infected cell-derived xEVs may either facilitate or inhibit viral neuropathogenicity. Here we investigated xEVs in the case of two neurotropic viruses, Zika virus (ZIKV) and Human Immunodeficiency Virus (HIV). The hallmark characteristic of ZIKV-infection is …

An Investigation To Corroborate Volatile And Biological Profiles Of Human Odor For Forensic Subject Identification, Chantrell J.G. Frazier

FIU Electronic Theses and Dissertations

Hands are an integral part in transferring complex microbial communities to and from our surroundings. As a result, hands are significant in provenance investigations as specific microbiota can be deposited on everyday objects through touch interactions. Skin microbiome, including bacteria, fungi, and viruses, are unique to each person, and this ‘uniqueness’ can be exploited and applied to forensic identification. Skin microbiota and volatile organic compounds (VOCs) are closely related due to specific bacteria breaking down non-volatile organic compounds to volatile organic compounds that are characteristically present in human scent. However, analyses of microbiota from touch interactions have proven to be …

A Multi-Taxa Metagenomic Evaluation Of The Everglades Soil Microbiome And The Impact Of Salinity On Community Structure And Biogeochemical Cycles With A Soil Forensic Application, Deidra Christina Jordan

FIU Electronic Theses and Dissertations

Coastal wetlands, such as the Everglades, are increasingly being exposed to stressors that have the potential to modify their existing ecological processes because of global climate change. Their soil microbiomes include a population of organisms that are important for biogeochemical cycling, but continual stresses can disturb the community's composition, causing functional changes. The Everglades features wetlands with varied salinity levels, implying that they contain microbial communities with a variety of salt tolerances and microbial functions. Therefore, it's critical to track the effects of stresses on these populations in both freshwater and brackish marshes. The study addressed this by first constructing …

The Evolution Of Bioluminescence Across The Shrimp Family Sergestidae: A Genomic Skimming And Phylogenetic Approach, Charles G. Golighty Iii

FIU Electronic Theses and Dissertations

The family Sergestidae provide a unique system for studying the evolution of bioluminescence, with species possessing one of three distinct forms of photophores. This study capitalizes on molecular data to construct a genus-level phylogeny of sergestid shrimp. “Genome skimming” was implemented, capturing mitochondrial genomic data across 19 species. Additional individuals were incorporated through Sanger sequencing of four partial gene regions. The -sergestes group of genera was recovered as non-monophyletic, with the -sergia group of genera being recovered as monophyletic. Ancestral state reconstructions of light organ type indicate the organs of Pesta photophore is the ancestral state for the …

Exploring Epigenetics As A Tool For Population Assessment And Conservation In Large Marine Predators, Andria Paige Beal

FIU Electronic Theses and Dissertations

Worldwide, many large marine predator populations are in decline. These populations can be difficult to study due to the extensive home ranges and migration patterns often exhibited by these species. Molecular tools are therefore necessary to measure specific parameters on these populations that would otherwise be nearly impossible to obtain. This dissertation pioneers the use of environmental epigenetic approaches for that purpose, and specifically the epigenetic modification known as DNA methylation, using sharks and small cetaceans as model organisms. This work is organized into five chapters. Chapter I is an introductory chapter that lays out the fundamentals of environmental epigenetics …

Conservation Of South Florida Orchid Mycorrhizal Fungi, Ellen Garcia

FIU Electronic Theses and Dissertations

Starting in the late 1800’s orchids were heavily poached, leaving many species to reach critically low numbers. Coupled with habitat loss and urbanization many orchid populations were extirpated in southern Florida. Due to lack of endosperm, orchid seeds are reliant on specific mycorrhizal fungi to obtain nutrients to enable growth and development resulting in very low germination rates in nature. The obligate relationship on mycorrhizal fungi complicates orchid re-establishment. The research project aims are (1) to evaluate the correlation between phenotypic traits and optimal growing conditions in various micro-climate, and (2) to assess the range of mycorrhizal fungi community in …

Epigenetic Mechanisms As Drivers Of Environmental Responses In Stony Corals, Javier A. Rodriguez Casariego

FIU Electronic Theses and Dissertations

The current pace of anthropogenic global change is imposing unprecedented conditions to biological systems. Coral reef ecosystems are particularly sensitive to the rapid increase in thermal anomalies and the changes in water chemistry caused by global change. However, although their decline has been documented worldwide, there are signs suggesting that stony corals harbor greater phenotypic plasticity than previously expected, sparking the interest in the study acquired non-genetic modifications (e.g., epigenome, microbiome) potentially increasing their resilience to global change, and constituting one of the main targets for intervention.

Epigenetics constitutes an exciting frontier to understand how the environment influences the regulation …

Invasion Ecology And Response To Fire Of The Nonnative Fern Lygodium Microphyllum In The South Florida Everglades, Nicole Sebesta

FIU Electronic Theses and Dissertations

Lygodium microphyllum (Old World Climbing Fern (OWCF)) is a climbing fern native to tropical and subtropical regions of Australia, Asia, and Africa. First introduced to Florida as an ornamental in the 1960s, the fern has become a serious invasive in numerous Florida habitats, severely degrading native herbaceous and woody vegetation and altering fire behavior. One area with the greatest increase in OWCF cover is the sawgrass marsh of southern Everglades National Park (ENP), where prescribed fire is used for both maintenance of sawgrass marshes and management of OWCF infestations. However, the efficacy of OWCF control using fire in this habitat …

Uncharacterized Isosporoid Parasite In The Florida Grasshopper Sparrow (Ammodramus Savannarum Floridanus), Matthew S. Morris

FIU Electronic Theses and Dissertations

A novel and potentially fatal isosporoid parasite was discovered within a captive population of Florida Grasshopper Sparrows, kept at the Rare Species Conservatory in Loxahatchee, Florida. The purpose of this thesis was to (1) to ascertain the prevalence of the Isospora sp. in the captive population of FGSPs; (2) to show that the pathogen can cause both morbidity and mortality in the FGSP; (3) to use population modeling as a management tool to show the potential effects of the disease on the wild population; and (4) recommend mitigation and management strategies informed by our research. Overall, histopathology and necropsy reports …

Density Dynamics Of Endosymbiotic Wolbachia Bacteria In The Drosophila Host, Zinat Sharmin

FIU Electronic Theses and Dissertations

Wolbachia pipientis is one of the most widespread bacterial endosymbionts, infecting mites, crustaceans, and filarial nematodes as well as about half of all insect species. These bacteria cause many neglected human diseases that include African river blindness and lymphatic filariasis affecting over 100 million people worldwide. Interestingly, Wolbachia also suppress the transmission of viruses such as Dengue, Chikungunya, and Zika. In most reported cases, Wolbachia antiviral activity is a density-dependent effect, with high Wolbachia density conferring the strongest viral suppression. However, little is currently known about how Wolbachia load is controlled within the insect host. A small number of studies …

Functional Regionalization In The Fly Eye As An Adaptation To Habitat Structure, Carlos A. Ruiz

FIU Electronic Theses and Dissertations

With over 150,000 described species, flies constitute one of the most species-rich groups of animals on earth, and have managed to colonize almost every corner of it. Part of their success comes from their amazing flying skills, which are strongly tied to their visual capabilities. To navigate fast and accurately through their habitats, they must be able to process the inordinate amounts of visual information necessary to sort obstacles, avoid predators and remain on course. Surprisingly, despite their tiny brains, flies have no problem in processing all that information to generate correcting maneuvers in just about 30 ms. To this …

Growth Of Diatom Fistulifera Alcalina In Bacterial Co-Culture And Comparative Mitogenomics Of Fistulifera Species, Erwin David Berthold

FIU Electronic Theses and Dissertations

Diatoms are excellent biological models of growth and intracellular oil generation. The productivity and compounds of diatoms, especially oils, support aquatic food chains and human medical and industrial needs. The qualities that made diatoms prolific producers, specifically diatom physiological features such as growth rates with intracellular lipid storage in alkaline environments, are however poorly understood. Another physiological aspect that remains unexplored is the effects of bacteria on the growth and lipid production of alkaliphilic diatoms. More studies, especially co-cultures, are needed for advances in diatom biology and strain performance for the algal biotechnological field. Besides physiology, diatom genetics using next-generation …

Carbon Storage Of Restored Mangrove Forests In Biscayne Bay, Florida, Daniel Chomin-Virden

FIU Electronic Theses and Dissertations

Space-for-time substitution was used to evaluate the rate of carbon storage in three carbon pools (aboveground, belowground, and soil organic carbon) across four restored mangrove forests in Biscayne Bay, Florida, USA. The restored forests ranged in age from 8 to 20 years. Diameter at breast height was used to estimate aboveground biomass. Belowground biomass and soil carbon were determined using 15 cm soil cores. Time to equivalence was calculated for the sites by reference to geographically proximate natural mangrove forests. Time to equivalence in aboveground and belowground biomass were 50.4 and 13.6 years, respectively. Soil organic carbon and total carbon …

A Comparative Genomics Exploration Of Inter-Partner Metabolic Signaling In The Coral-Algal Symbiosis, Katherine E. Dougan

FIU Electronic Theses and Dissertations

At the foundation of coral reef ecosystems is the symbiosis between the coral host and its microbial community, particularly its photoautotrophic algae from the family Symbiodiniaceae. As a symbiosis centered around nutritional exchange, determining the mechanisms involved in the maintenance of this cooperative exchange is central to understanding how it breaks down. As the nutritional transfer primarily consists of sugars, this work first focuses on the cnidarian insulin signaling pathway, an evolutionarily important metazoan pathway involved in diverse functions, most notably metabolism. This dissertation unveiled 360 putative cnidarian insulin-like peptides (cnILPs) from existing transcriptomic datasets, where they were previously missed …

Connections In The Underworld: A Morphological And Molecular Study Of Diversity And Connectivity Among Anchialine Shrimp., Robert Eugene Ditter

FIU Electronic Theses and Dissertations

This research investigates the distribution and population structure of crustaceans, endemic to anchialine systems in the tropical western Atlantic focusing on cave-dwelling shrimp from the family Barbouriidae. Taxonomic and molecular tools (genetic and genomic) are utilized to examine population dynamics and the presence of phenotypic hypervariation (PhyV) of the critically endangered species Barbouria cubensis (von Martens, 1872). The presence of PhyV and its geographic distribution is investigated among anchialine populations of B. cubensis from 34 sites on Abaco, Eleuthera, and San Salvador, Bahamas. Examination of 54 informative morphological characters revealed PhyV present in nearly 90% (n=463) of specimens with no …

Investigating The Population Dynamics Of An Avian Apex Predator Across An Urban Gradient, Donna Marain

FIU Electronic Theses and Dissertations

Predators are often the focus of conservation efforts. They can be useful sentinel species, umbrella species, and flagship species. Predators can also be the first guild lost when ecosystems are under stress, especially from anthropogenic land-use change. Avian predators (raptors) can be an exception to this trend, filling the role of apex predators across the urban gradient. South Florida contains the Everglades ecosystem and one of the fastest growing human populations in the country. In the current study, I investigated the population dynamics of South Florida’s most abundant hawk: the Red-shouldered Hawk (Buteo lineatus, RSHA) across the urban …

Back From The Brink?: Rebounding And Remnant Amphibian Populations In A Pathogen Enzootic Environment, Alexander D. Shepack

FIU Electronic Theses and Dissertations

The Anthropocene epoch has been marred by a global biodiversity crisis and the advent of Earth’s sixth mass extinction. Amphibians, the most threatened vertebrate taxa, have become the poster children for this sixth mass extinction. The pathogenic fungus Batrachochytrium dendrobatidis has been blamed for many of declines and extinctions seen in amphibians. The now panglobal Bd causes the disease chytridiomycosis in a large number of amphibian species and has been linked to population crashes in Central and South America, Australia, Europe, and the United States. Now enzootic around the world, amphibian populations continue to confront Bd in a long-term battle …

Exploration Of The Role Of Microbiome Structure, Metabolism, And Modification In Black Band Disease Etiology, Patricia Waikel

FIU Electronic Theses and Dissertations

The coral microbiome plays an integral role in coral health. Modification of the microbiome is thought to alter susceptibility to disease. Black Band Disease (BBD), is polymicrobial, mat forming, and affects reef building coral globally. Dominated by the cyanobacterium Roseofilum reptotaenium, it has been noted to increase in virulence with increasing temperatures, making BBD of particular concern in the face of climate change-induced warming seas. The active sulfur cycle of BBD makes dimethylsulfoniopropionate (DMSP), a widely available source of sulfur in the marine environment, of particular interest in the study of BBD. Traditional infection studies require field collection and …

Phylogenetic And Transcriptomic Analyses Of Vision In Two Cave Adapted Crustaceans, Asellus Aquaticus (Isopoda: Asellidae) And Niphargus Hrabei (Amphipoda: Niphargidae)., Jorge L. Perez Moreno

FIU Electronic Theses and Dissertations

The unique characteristics of aquatic caves and of their predominantly crustacean biodiversity nominate them as ideal study subjects for evolutionary biology. The present dissertation capitalizes on a perfect natural experiment, the Molnar Janos thermal cave system in Budapest, Hungary. This intricate freshwater cave system and the immediately adjacent Malom Lake present the ideal opportunity to address questions of colonization, adaptation, and evolution. Despite marked environmental differences between the cave and surface waters, both localities are inhabited by natural populations of two emerging model cave species, the isopod Asellus aquaticus and the amphipod Niphargus hrabei. In the present dissertation, I …

Understanding, Quantifying, And Reducing Bias In Fisheries-Independent Visual Surveys, James Kilfoil

FIU Electronic Theses and Dissertations

Understanding spatiotemporal changes in populations is vital for conservation managers to assess current recovery efforts, determine future conservation priorities, and forms the basis to explore complex ecological questions. In fisheries, these data have traditionally been collected using fisheries-independent surveys that rely on extractive sampling practices (e.g., longlines, gillnets, trawls). However, with the growing availability of low-cost, high-definition cameras, researchers are increasingly using visual surveys as a non-invasive alternative. Camera surveys have a number of advantages including their archivable data, and offer insights into species habitat use and behavior. However, the use of cameras has a number of inherent biases. Understanding, …

The Metabolic Ecology Of Tropical Amphibians Across An Elevational Gradient In The Andes Of Southeastern Peru, Michael R. Britton

FIU Electronic Theses and Dissertations

Metabolism is a fundamental biological process that determines the rate at which organisms process energy and materials, and determines the availability of resources for growth, maintenance and reproduction. Metabolic rates scale across levels of organization from cells to whole organisms and affect population, community, and ecosystem processes. Anthropogenic climate change and other environmental changes are predicted to have major impacts on the energetics of organisms that will be mediated through metabolic physiology. Tropical ectotherms, such as amphibians, may be among the most vulnerable to metabolic impacts of climate change as a result of being ectothermic, having high thermal sensitivity, and …

Characterizing Elasmobranch Species Diversity, Occurrence And Catches In Small-Scale Fisheries Of The Caribbean, Camila Cáceres

FIU Electronic Theses and Dissertations

Although 95% of fishers are artisanal, little is known about the magnitude of their catches and impacts on marine ecosystems at a global scale. I used a rapid assessment framework to study elasmobranch occurrence, elasmobranch fisheries, and use in coastal small-scale fisheries in the Caribbean, combining observational data and fisher’s knowledge. A total of 800 Baited Remote Underwater Videos were deployed in addition to 660 interview surveys that were collected in Colombia, Guadeloupe, Martinique, Tobago and the Florida Keys. In Colombia, I compared elasmobranch and teleost species richness and relative abundance within four coral reef habitats, where species targeted by …

The Genetics Of Olfactory And Visually Guided Attractive Behaviors In Aedes Aegypti Mosquito, Joshua Ibukun Raji

FIU Electronic Theses and Dissertations

Mosquitoes detect their hosts and seek suitable resources crucial for survival by integrating chemosensory, thermal, and visual cues. The diversity of the cues involved in mosquito attractive behaviors has made the design of behavioral control strategies a challenge. The genetic basis of mosquito attractive behaviors can now be determined using genome editing. The contribution of the IR8a chemosensory pathway was uncovered by disrupting the IR8a co- receptor in Aedes aegypti using CRISPR/Cas9. Ir8a mutant female mosquitoes are not attracted to lactic acid, a behaviorally active component of human sweat, and lack odor-evoked responses to acidic volatiles. The loss of Ir8a …

Mechanisms For The Persistence Of The Coral Holobiont In The Warming Oceans Of The Anthropocene, Daniel G. Merselis

FIU Electronic Theses and Dissertations

Coral Reefs are rapidly deteriorating in response to an onslaught of human-mediated stressors. Just one stressor alone, climate change, may extirpate coral reef ecosystems within a human lifetime, threatening societal and ecological catastrophe. Reef-derived ecosystem services are crucial for sustenance, coastal protection, and economic prosperity in over 100 countries. Near-term human decisions will determine whether reef-corals, the ecosystems they engineer, the 25% of marine biodiversity they support, and the human communities that depend upon them can be protected. My dissertation aims to characterize the potential for corals' adaptive mechanisms to facilitate their continued survival- information which will only represent hope …

Evolutionary Expansions And Neofunctionalization Of Ionotropic Glutamate Receptors In Cnidaria, Ellen G. Dow

FIU Electronic Theses and Dissertations

Reef ecosystems are composed of a variety of organisms, transient species of fish and invertebrates, microscopic bacteria and viruses, and structural organisms that build the living foundation, coral. Sessile cnidarians, corals and anemones, interpret dynamic environments of organisms and abiotic factors through a molecular interface. Recognition of foreign molecules occurs through innate immunity via receptors identifying conserved molecular patterns. Similarly, chemosensory receptors monitor the environment through specific ligands. Chemosensory receptors include ionotropic glutamate receptors (iGluRs), transmembrane ion channels involved in chemical sensing and neural signal transduction. Recently, an iGluR homolog was implicated in cnidarian immunological resistance to recurrent infections of …

Developing A Meta-Population Framework For Caribbean Spiny Lobster (Panulirus Argus) Stocks, Nan Yao

FIU Electronic Theses and Dissertations

The Caribbean spiny lobster (Panulirus argus) provides many ecological and economic benefits to the Southeast United States, as well as many South American and Caribbean countries. However, limited knowledge on the recruitment dynamics of this valuable species has long been an issue for the fishery management. Panulirus argus has a pelagic larval stage called the phyllosoma. During the larval stage, a phyllosoma can drift with currents from six to nine months. This long pelagic life stage leads to the hypothesis that P. argus stocks in the Caribbean are demographically open. Evidences from biophysical modeling and genetic analysis have …

Role Of Withaferin A As A Neuroprotectant Against Beta Amyloid Induced Toxicity And Associated Mechanism, Sneham Tiwari

FIU Electronic Theses and Dissertations

Neurological disorders are the biggest concern globally and ageing contributes in worsening the disease scenarios. In AD or AD like diseases, there is abnormal accumulation of extracellular amyloid beta produced due to abnormal processing of the transmembrane amyloid precursor protein, by β and γ-secretases. It spreads in the cortical and limbic regions of the brain leading to neuronal toxicity, impairment in memory and neurological functions. Aβ deposition in the CNS is common in aging HIV patients. Neurotoxic protein Tat, results in increased Aβ in combination with drugs of abuse cocaine. We examined the role of Withaferin A, against Aβ induced …

Florida's Pillar Coral (Dendrogyra Cylindrus): The Roles Of The Holobiont Partners In Bleaching, Recovery, And Disease Processes, Cynthia Fairbank Lewis

FIU Electronic Theses and Dissertations

The iconic pillar coral, Dendrogyra cylindrus, is one of five Caribbean species listed in 2014 under the US Federal Endangered Species Act because of its extreme low abundance and continued decline in US waters. Until recently, little was known about the demographics or genetic diversity of Florida’s D. cylindrus population. This study represents the first time two holobiont partners (coral animal and associated photosynthetic algal endosymbionts) have been closely examined, spatially and temporally, in this little-studied species. The aim was to explore the influences of coral animal genotypes, mutualistic photosynthetic algal strains, and hyperthermal stress on bleaching and …

Factors Affecting Green Turtle Foraging Ecology Across Multiple Spatial Scales, Elizabeth Rose Whitman

FIU Electronic Theses and Dissertations

The hierarchical levels at which resource selection occurs can have important consequences for individual and population energy budgets and structure the impacts of a forager on its ecosystem. Assessing factors affecting resource selection of large marine herbivores across scales is important because of their potentially large impacts on seagrass community dynamics and historical and current changes in their population sizes and those of their potential predators. I explored the factors (predation risk, resource abundance, quality and identity) affecting resource use of large marine herbivores (green turtles, Chelonia mydas) from the scale of habitat patches to forage species within patches. …