Biology Commons^™

Understanding The Impacts Of Current And Future Environmental Variation On Central African Amphibian Biodiversity, Courtney A. Miller

University of New Orleans Theses and Dissertations

Global climate change is projected to impact multiple levels of biodiversity by imposing strong selection pressures on existing populations, triggering shifts in species distributions, and reorganizing entire communities. The Lower Guineo-Congolian region in central Africa, a reservoir for amphibian diversity, is predicted to be severely affected by future climate change through rising temperatures and greater variability in rainfall. Geospatial modelling can be used to assess how environmental variation shapes patterns of biological variation – from the genomic to the community level – and use these associations to predict patterns of biological change across space and time. The overall goal of …

The Splice Is Not Right: Splice-Site-Creating Mutations In Cancer Genomes, Reyka Glencora Jayasinghe

Arts & Sciences Electronic Theses and Dissertations

Accurate interpretation of cancer mutations in individual tumors is a prerequisite for precision medicine. Large-scale sequencing studies, such as The Cancer Genome Atlas (TCGA) project, have worked to address the functional consequences of genomic mutations, with the larger goal of determining the underlying mechanisms of cancer initiation and progression. Many studies have focused on characterizing non-synonymous somatic mutations that alter amino acid sequence, as well as splice disrupting mutations at splice donors and acceptors. Current annotation methods typically classify mutations as disruptors of splicing if they fall on the consensus intronic dinucleotide splice donor, GT, the splice acceptor, AG. Splice …

Physella Acuta, Comparative Immunology And Evolutionary Aspects Of Gastropod Immune Function, Jonathan H. Schultz

Biology ETDs

Gastropod immunobiology has benefitted from investigations focused on the planorbid snail Biomphalaria glabrata, intermediate host for the human parasite Schistosoma mansoni. Though such concentrated efforts have elucidated fascinating aspects of invertebrate immunity, they have not provided full knowledge regarding the evolution of immune function among other gastropod species. This dissertation presents the importance of making strategic choices regarding which organisms to select for comparative immunology. Herein, the choice was made to investigate the immunobiology of Physella acuta, a freshwater snail species of the Physidae, a sister family to Planorbidae to which B. glabrata belongs. Benefiting greatly from …

Diversification Across A Dynamic Landscape: Phylogeography And Riverscape Genetics Of Speckled Dace (Rhinichthys Osculus) In Western North America, Steven Michael Mussmann

Graduate Theses and Dissertations

Evolution occurs at various spatial and temporal scales. For example, speciation may occur in historic time, whereas localized adaptation is more contemporary. Each is required to identify and manage biodiversity. However, the relative abundance of Speckled Dace (Rhinichthys osculus), a small cyprinid fish in western North America (WNA) and the study species for this dissertation, establishes it an atypical conservation target, particularly when contrasted with the profusion of narrowly endemic forms it displays. Yet, the juxtaposition of ubiquity versus endemism provides an ideal model against which to test hypotheses regarding the geomorphic evolution of WNA. More specifically, it also allows …

Microbial Ecology Of South Florida Surface Waters: Examining The Potential For Anthropogenic Influences, Chase P. Donnelly

HCNSO Student Theses and Dissertations

South Florida contains one of the largest subtropical wetlands in the world, and yet not much is known about the microbes that live in these surface waters. These microbes play an important role in chemical cycling and maintaining good water quality for both human and ecosystem health. The hydrology of Florida’s surface waters is tightly regulated with the use of canal and levee systems run by the US Army Corps of Engineers and The South Florida Water Management District. These canals run through the Everglades, agriculture, and urban environments to control water levels in Lake Okeechobee, the Water Conservation Areas, …

Investigating The Interaction Of Monoamines And Diel Rhythmicity On Anti-Predator Behavior In An Orb-Weaving Spider, Larinioides Cornutus (Araneae: Araneae), Rebecca Wilson

Electronic Theses and Dissertations

Circadian rhythms are ubiquitous among organisms, influencing a wide array of physiological processes and behaviors including aggression. While many neurophysiological mechanisms are involved in the regulation of aggressive behaviors, relatively few studies have investigated the underlying components involved in the interplay between circadian rhythms and aggression. Spiders are an ideal model system for studying circadian regulation of aggression as they are ecologically both predators and prey. Recent studies have revealed a nocturnal orb- weaving spider Larinioides cornutus exhibits a diel and circadian rhythm in anti-predator behavior (i.e. boldness) that can be manipulated by administration of octopamine (OA) and serotonin (5- …

Expression Of Line-1 In Human Somatic Tissues And The Factors Correlated With Line- 1 Expression, G. M. Jonaid

UNLV Theses, Dissertations, Professional Papers, and Capstones

Despite the long-held assumption that transposons are normally only expressed in the germline, recently we discovered that full length or partial transcripts of LINE1 are frequently found in the somatic cells. However, the extent of variation in LINE1 levels across different tissues and different individuals, and the genes and pathways that are co-expressed with LINE1 are unknown. Co-expressed genes may be candidate genes that are functioning in transposon silencing. Here, we report the extent of variation in L1HS expression levels across cancer tissues and healthy tissues collected for The Cancer Genome Atlas (TCGA). L1HS is overexpressed in most of the …

Genomic Signatures Of Adaptive Evolution, Jessica Weber

Biology ETDs

Comparative genomics has revolutionized virtually all fields of biology including the study of evolution. In this dissertation, I used next-generation sequencing to explore the evolutionary histories and adaptive evolution of a diverse set of taxa. Comparisons ranged across time scales, from population-level genetic diversity studies to questions spanning the deepest branches of the metazoan lineage. Whole genome sequencing of 50 unrelated Korean individuals revealed that Koreans have a distinct genetic history from the Chinese and Japanese populations. Our Korean-specific variome database was used to identify novel disease-causing variants in the Korean population, highlighting the value of high-quality ethnic variation databases …

Systematics And Diversification Of The Pantropical Avian Order Coraciiformes, Jenna Merle Mccullough

Biology ETDs

How and why species diversify is a central theme of evolutionary biology. Species-rich, morphologically diverse, pantropical clades provide rare opportunities to explore questions about drivers of diversification in the tropics. Here, we present the first complete species tree of Coraciiformes (6 families, ~177 species of kingfishers, motmots, bee-eaters, and allies), produced with thousands of ultraconserved elements. We recovered a well-supported tree which shows that there are two clades within Coraciiformes: 1) bee-eaters sister to rollers + ground- rollers and 2) todies sister to motmots + kingfishers. We estimated the biogeographical history of the group, explored bill shape evolution with a …

Off-Target Based Drug Repurposing Using Systems Pharmacology, Brent M. Kuenzi

USF Tampa Graduate Theses and Dissertations

The goal of this study was to identify novel drug repurposing opportunities in cancer by utilizing the off-target profiles of clinically relevant kinase inhibitors. This was based on the observation that the global target profiles of compounds are largely ignored and that many compounds have activity that cannot be explained by their cognate target alone. Additionally, by utilizing clinically relevant compounds, any results would hold a high potential for eventual clinical implementation. We utilized a systems pharmacology approach utilizing cell viability-based drug screening to identify compounds with beneficial off-target activity and then using chemical and phosphoproteomics in order to elucidate …

Determining The Relationship Between Aging And Oxidative Stress In A Drosophila Melanogaster P38 Kb Framework, Aleksandra J. Majewski

Theses and Dissertations

Aging is inevitable for all organisms and can be characterized by degeneration of tissue, adecrease in motor function, and impaired stress response. In humans, it is often accompanied by an increased propensity for age related diseases. While all adults experience biological aging (senescence) not all adults experience age-associated disease. Thus, we claim these are not normal prospects of aging. Although the implications of aging are well understood, the molecular underpinnings for these processes remain elusive. As advances in medical science have been successful at prolonging lifespan, they concurrently extend the amount of time spend in diseased states. If we wish …

Multi-Omics Portraits Of Cancer, Kuan-Lin Huang

Arts & Sciences Electronic Theses and Dissertations

Precision oncology demands accurate portrayal of a disease at all molecular levels. However, current large-scale studies of omics are often isolated by data types. I have been developing computational tools to conduct integrative analyses of omics data, identifying unique molecular etiology in each tumor. Particularly, this dissertation presents the following contributions to the computational omics of cancer: (1) uncovering the predisposition landscape in 33 cancers and how germline genome collaborates with somatic alterations in oncogenesis; (2) pioneering methods to combine genomic and proteomic data to identify treatment opportunities; and (3) revealing selective phosphorylation of kinase-substrate pairs. These findings advance our …

Schistosomiasis In The Wild: A Transcriptomics Perspective On Field-Derived Biomphalaria Pfeifferi And Schistosoma Mansoni, And Their Interactions, Sarah K. Buddenborg

Biology ETDs

Schistosomiasis, caused by trematodes in the genus Schistosoma, is a widespread neglected tropical disease with the species S. mansoni infecting over 100 million people. We aimed to better understand the snail host and parasite responses during intramolluscan stages of infection by performing dual RNA-Seq on field-collected snails with natural infections from western Kenya. We collected uninfected Biomphalaria pfeifferi, B. pfeifferi with a patent cercariae-producing S. mansoni infection, and B. pfeifferi exposed to field-collected S. mansoni at 1 and 3d (days post infection).

We first created a high-quality B. pfeifferi transcriptome to identify the snail response to S. mansoni infection. …

Evolution Of Voltage-Gated Ion Channels, Kevin Gregory Bennett, Kevin Bennett

Master of Science in Integrative Biology Theses

Voltage-gated Ion Channels (VICs) form a superfamily of energy-independent membrane transporters that facilitate the transfer of charged sodium, calcium, and potassium ions across the cell membrane (Hodgkin & Huxley 1952). The channels contain a selective ion-conducting pore along with several other structural and gating features that come together to form a functional hetero- or homotetramer. A comprehensive phylogenetic study of all available proteins aimed at finding unknown distribution and illuminating evolutionary paths would be immensely useful in understanding relationships of structure, function, and organismal distribution. This phylogenetic analysis of VICs will be immensely useful in characterizing functional and structural distribution, …

Determination Of Adamts13 Susceptibility In Type Iia Von Willebrand Disease, Monica Buselli

Dissertations, Masters Theses, Capstones, and Culminating Projects

von Willebrand Disease (vWD) is a bleeding disorder caused by a deficiency in von Willebrand Factor (vWF), a large glycoprotein that assists in coagulation. Specifically, large vWF multimers in the blood stream are key components in starting the coagulation cascade. vWF is cleaved by the metalloprotease ADAMTS13, regulating the multimers size, which hinders vWF’s ability to function properly. The three main types of vWD —Type I, II, and III— are not well defined, and as a result are all similarly treated with plasma-derived vWF replacement therapy. Plasma-derived vWF is a treatment that does not cure the problem but relieves the …

Changes In The Microbial Community Of Lubomirskia Baicalensis Affected By Red Sponge Disease, Colin Rorex

Electronic Theses and Dissertations

Lake Baikal is the oldest known lake and a unique ecosystem, home to several species of fresh water sponge. A disease outbreak affecting the dominant species, Lubormirskia baialensis, was recently reported. The cause of the disease has not been determined but one of the current hypothesis is that the increase in methane concentration is correlated to the disease outbreak. This pilot study characterized the microbiomes of sick and healthy sponges through the use of 16S rRNA sequencing. Sick sponge microbiomes shared a conserved group of taxa while the healthy sponge microbiomes had greater diversity. Indicator species analysis identified two significant …

Newall Glacier Nucleic Acid Analysis, Shannon Turner

Honors Projects

The Newall Glacier is located in Antarctica between Mount Newall and Mount Weyant, at approximately 77°30′S, 162°50′E. Having existed for millions of years, and being rarely touched by human populations, glaciers are a major source of information on climate and life in the past. During the past 5 decades, a multi-country team of scientists have collaborated to drill into many of Antarctica’s glaciers and ice fields, removing ice cores for scientific investigation. The ice core section chosen for this project was drilled from the Newall Glacier in 1988 and its depth was from 100.670 to 101.000 m. The purpose of …

Characterization Of Two Cyclic Di-Gmp Phosphodiesterases Hypothesized To Regulate Virulence In Streptomyces Scabies, Madison Flasco

Undergraduate Honors Thesis Projects

Common scab is a devastating disease that affects the marketability of potatoes. The disease results in raised and pitted lesions seen on the surface of the potato and is caused by the soil pathogen, Streptomyces scabies. The S. scabies genome has two cyclic-di-GMP phosphodiesterases, RmdA and RmdB, both regulators of morphology and development. These proteins break down the ubiquitous second messenger molecule cyclic di-GMP, a molecule in charge of cell cycle progression and virulence. Both proteins contain diguanylate cyclase domains and phosphodiesterase domains, GGDEF and EAL, respectively, while RmdA contains an additional PAS_4 domain. Despite similar domain configurations, the two …

The Dissemination, Regulatory Role, And Evolution Of Mycobacterial Inteins, Danielle Skye Kelley

Legacy Theses & Dissertations (2009 - 2024)

Inteins are intervening protein elements, capable of coordinating escape from a host protein through a self-catalyzed mechanism, called protein splicing. This results in free intein and a mature host protein product. Inteins are also mobile elements and many contain homing endonucleases that enable the targeting to ectopic sites and invasion of novel niches. Inteins have been found across all three domains of life and are often present in replication, recombination, and repair proteins. However, it is unclear if the observed distribution is simply a factor of endonuclease preference or if inteins have been selectively maintained due to an adaptation that …

Photosynthetic Activity Under Low Light, Danijela Lonco

Williams Honors College, Honors Research Projects

Are bacteria capable of undergoing oxygenic photosynthesis under low-light conditions inside of caves? Inside of an Australian cave, Chlorophyll f was recently discovered. This chlorophyll pigment was found to demonstrate the capability for photosynthesis, suggesting that Chlorophyll f extends the spectrum of usable light needed for oxygenic photosynthesis (Lars, 2015). Due to the findings in this study, a team went to Carlsbad Caverns to see if there were any bacteria capable of undergoing oxygenic photosynthesis under low light.

The Effects Of The Red Tide Producing Dinoflagellate, Karenia Brevis, And Associated Brevetoxins On Viability And Sublethal Stress Responses In Scleractinian Coral: A Potential Regional Stressor To Coral Reefs, David A. Reynolds

UNF Graduate Theses and Dissertations

Coral cover is in decline on a global scale, with increased mortality events being attributed to a number of global and regional stressors. While the impacts of global stressors (e.g. sea surface temperature rise, ocean acidification) are well documented, there is growing interest in identifying and understanding the impacts of regional stressors. The reason for this change in focus is that regional stressors can often work in combination, sometimes synergistically, with global stressors and that stressors on a regional scale tend to be more easily mitigated by management practices. One regional stressor that impacts a myriad of marine organisms in …

Transcriptome Analysis Of Root Development In Wheat Triticum Aestivum Using High Throughtput Sequencing Technologies, Ghana Challa

Electronic Theses and Dissertations

Root provides plant water, nutrients and anchorage from soil. Most our knowledge of molecular mechanisms of root development is from the dicot model plant Arabidopsis, but very few studies have done in monocot crop systems like rice, maize, and wheat. We are studying very short root (VSR) phenotype in wheat, and lack of a sequenced reference genome in wheat prompted us to sequence and assemble the root transcriptome of the reference cultivar Chinese Spring (CS). A root transcriptome was assembled from the sequenced reads generated from root tip and the mature root tissues of CS. Approximately 169 million reads were …