Biology Commons^™

Understanding The Role Of Cereblon In Hematopoiesis Through Structural And Functional Analyses, Afua Adutwumwa Akuffo

USF Tampa Graduate Theses and Dissertations

The discovery and implementation of immunomodulatory drugs (IMiD®s) has revolutionized the treatment of many hematological malignancies due to the plethora of IMiD®-induced clinical responses that include anti-angiogenesis, anti-inflammation, and anti-tumor effects, as well as enhanced erythropoiesis, immune modulation and improved metabolism. More ground-breaking was the identification of cereblon as the target of IMiD®s. Upon binding to thalidomide and other immunomodulatory drugs, the E3 ligase substrate receptor cereblon (CRBN) promotes proteosomal destruction of neo-substrates by engaging the DDB1-CUL4A-Roc1-RBX1 E3-ubiquitin ligase in human cells but not in mouse cells suggesting that sequence variations in CRBN may cause its inactivation. Therapeutically, CRBN engagers …

Investigating Mechanisms Of Immune Suppression Secondary To An Inflammatory Microenvironment, Wendy Michelle Kandell

USF Tampa Graduate Theses and Dissertations

The immune system plays a dynamic role in cancer progression. The theory of immunoediting suggests that the relationship between the tumor cell and the immune cell is one that is in flux: initially highly active and responsive to tumor antigen to one that has escaped immune responsiveness. Once the tumor has formed and effectively “escaped”, there are multiple mechanisms that work against a conventional immune response. The tumor cell clones that have escaped the elimination phase are those that are less immunogenic. These clones downregulate MHC, have increased apoptosis through DAMP-driven mechanisms, and suppressive cell phenotypes are driven through cytokine-driven …

Spatiotemporal Changes Of Microbial Community Assemblages And Functions In The Subsurface, Madison C. Davis

USF Tampa Graduate Theses and Dissertations

The subsurface hosts diverse microbial community assemblages and functions. These communities play an important role in biogeochemical cycling and groundwater purification. Many physicochemical factors affect microbial communities and can cause short-term or long-term perturbations. Subsurface microbes are susceptible to anthropogenic changes in the environment, which can be caused by nutrient inputs or municipal groundwater extraction. Despite the importance of the subsurface microbiome, these microbial communities are poorly characterized. This dissertation describes the characterization of spatiotemporal drivers of subsurface microbial communities through a variety of techniques that include eDNA analyses, bioinformatics, hydrochemical analyses, stable isotope geochemistry, and multivariate statistics. Three coastal …

The Role Of Apkcs And Apkc Inhibitors In Cell Proliferation And Invasion In Breast And Ovarian Cancer, Tracess B. Smalley

USF Tampa Graduate Theses and Dissertations

Research has demonstrated that the atypical protein kinase C-zeta (PKC-ζ) is a component of many dysregulated pathways in breast and ovarian cancer, including cellular proliferation, survival, and cell cycle upregulation. Breast and ovarian cancers affect women every day and are second and fifth leading cause of cancer death. Women who seek treatments are commonly met with invasive surgeries or chemotherapy. Protein kinase C (PKC) is a family of serine and threonine phosphorylating kinases that have been shown to modulate and transduce signaling cascades that play roles in the development and survival of cancers. Atypical PKC (aPKC), have been heavily suggested …

Isotope-Based Methods For Evaluating Fish Trophic Geographies, Julie L. Vecchio

USF Tampa Graduate Theses and Dissertations

Data on the movement and diets of fish during a variety of life stages are important inputs to fisheries stock assessments and marine ecosystem models. Stable isotopes may provide previously inaccessible information on movement and diet of a variety of managed and forage fish species. Here I used several novel means of interpretation for stable isotope data to infer diets and movements of several important fisheries species over both short (weeks to months) and long (lifetime) timescales. To calculate a constant partitioning offset (CPO) between the δ¹⁵N of muscle and of liver tissue, I conducted a literature search …

Targeting Cancer-Anorexia Cachexia Syndrome And Septic Inflammatory-Based Atrophy With R/S 1,3 Butanediol Acetoacetate Diester, Andrew P. Koutnik

USF Tampa Graduate Theses and Dissertations

Cancer anorexia cachexia syndrome (CACS) is a distinct atrophy disease negatively influencing multiple aspects of clinical care and patient quality of life. Although it directly causes 20% of all cancer-related deaths, there are currently no model systems that encompass the entire multifaceted syndrome, nor are there any effective therapeutic treatments. Here, we show that the VM-M3 mouse model of systemic metastasis demonstrates a novel, immunocompetent, logistically feasible, repeatable phenotype with progressive tumor growth, spontaneous metastatic spread, and the full multifaceted CACS with expected sex dimorphisms across tissue wasting. We also demonstrate that the ubiquitin proteasomal degradation pathway was significantly upregulated …

Temporal Variability Of Polycyclic Aromatic Hydrocarbons In Deep-Sea Cephalopods Of The Northern Gulf Of Mexico, Isabel C. Romero, Heather L. Judkins, Michael Vecchione

USF St. Petersburg Campus Faculty Publications

As part of the effort to understand the effects of the Deepwater Horizon Oil Spill (DWHOS), we analyzed tissue from five species of midwater oceanic cephalopods in the northern Gulf of Mexico (GoM) during three time periods, including one period sampled fortuitously just before the spill (2010), and two periods sampled after the spill (2011 and 2015–2016). The species, Japetella diaphana, Abralia redfieldi, Histioteuthis corona, Leachia atlantica, and Onychoteuthis banksii were collected in three geographic areas in the GoM (east, south and southeast of the Macondo wellhead). Results indicate a shift in the composition of polycyclic aromatic hydrocarbons (PAHs) in …

First Genome Sequence Of The Gunnison’S Prairie Dog (Cynomys Gunnisoni), A Keystone Species And Player In The Transmission Of Sylvatic Plague, Mirian T. N. Tsuchiya, Rebecca B. Dikow, Loren Cassin-Sackett

Integrative Biology Faculty and Staff Publications

Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America’s grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators. An additional keystone role lies in their extreme susceptibility to sylvatic plague (caused by Yersinia pestis), which results in periodic population extinctions, thereby generating spatiotemporal heterogeneity in both …

Molecular Tools For Coral Reef Restoration: Beyond Biomarker Discovery, John Everett Parkinson, Andrew C. Baker, Iliana B. Baums, Sarah W. Davies, Andréa G. Grottoli, Sheila A. Kitchen, Mikhail V. Matz, Margaret W. Miller, Andrew A. Shantz, Carly D. Kenkel

Integrative Biology Faculty and Staff Publications

As coral reefs continue to decline due to climate change and other stressors, scientists have proposed adopting genomic tools, such as biomarkers, to aid in the conservation and restoration of these threatened ecosystems. Biomarkers are easily measured indicators of biological processes that can be used to predict or diagnose health, resilience, and other key performance metrics. The ultimate goal of developing biomarkers is to determine the conservation value and utility of a given coral colony, including the host animal, its algal symbionts, and their microbial partners. However, this goal remains distant because most efforts have not yet moved beyond the …

Diversity And Abundance Of Dragonflies And Damselflies In Tampa Bay, Florida, Meredith A. Krause, Thomas Koster, Bryan N. Macneill, Daniel J. Zydek, Nicholas T. Ogburn, Jonathan Sharpin, Robert Shell, Marc J. Lajeunesse

Integrative Biology Faculty and Staff Publications

Little is known about the community of dragonflies and damselflies in Tampa Bay, Florida, USA. To address this gap, we conducted 2 longitudinal surveys of adult odonates in a natural floodplain of the Hillsborough River in 2013 and 2017. Along with abundance and species diversity, we also measured intraspecific variation in body size, sexual dimorphism, wing-cell asymmetry, and water mite ectoparasitism. Our first weekly survey from Oct 2013 to Oct 2014 sampled 327 adults (230 female, 97 male) from 8 dragonfly species, with the eastern pondhawk (Erythemis simplicicollis Say; Odonata: Libellulidae) representing 79% of captures, followed by the second …

Transmission Of West Nile And Five Other Temperate Mosquito-Borne Viruses Peaks At Temperatures Between 23°C And 26°C, Marta S. Shocket, Anna B. Verwillow, Mailo G. Numazu, Hani Slamani, Jeremy M. Cohen, Fadoua El Moustaid, Jason Rohr, Leah R. Johnson, Erin A. Mordecai

Integrative Biology Faculty and Staff Publications

The temperature-dependence of many important mosquito-borne diseases has never been quantified. These relationships are critical for understanding current distributions and predicting future shifts from climate change. We used trait-based models to characterize temperature-dependent transmission of 10 vector–pathogen pairs of mosquitoes (Culex pipiens, Cx. quinquefascsiatus, Cx. tarsalis, and others) and viruses (West Nile, Eastern and Western Equine Encephalitis, St. Louis Encephalitis, Sindbis, and Rift Valley Fever viruses), most with substantial transmission in temperate regions. Transmission is optimized at intermediate temperatures (23–26°C) and often has wider thermal breadths (due to cooler lower thermal limits) compared to pathogens with …

Phylogeny Of Terrestrial Isopods Based On The Complete Mitochondrial Genomes, Subvert The Monophyly Of Oniscidea, Rui Zhang, Ruru Chen, Jianmei An, Carlos A. Santamaria

Integrative Biology Faculty and Staff Publications

Background: Oniscidea is the only truly terrestrial taxon within the Crustacea, and vital to soil formation. However, the monophyly of suborder Oniscidea has been in dispute since 1995, with different studies disagreeing on whether the coastal Ligiidae are included within the suborder. To clarify the phylogenetic hypothesis of suborder Oniscidea, we sequenced the complete mitochondrial genomes of Ligia exotica (Roux, 1828) and Mongoloniscus sinensis (Dollfus, 1901).

Results: Like most metazoan, the complete mitogenomes of two species with circular double strands. The structure and characters of mitogenomes of these two species are analyzed. The constructed phylogenetic analyses show that Oniscidea is …

Investigating Among-Individual Growth Heterogeneity In Longleaf Pine: Advancing Dendrochronological Approaches, Jamie E. Munn

USF Tampa Graduate Theses and Dissertations

Within a population, individuals frequently differ in the rate at which they grow, and this rate can be impacted by both genetic differences and abiotic factors. Often, dendrochronology is used to elucidate growth trends based on climate or other factors. This dissertation explores new statistical approaches to dendrochronological research.

First, I created a chronology for a population of longleaf pine (Pinus palustris P. Mill.) individuals in a southwest Florida sandhill community. I then used generalized linear mixed models to investigate the effects of fire frequency, year, tree age and size, and elevation on variation in radial growth heterogeneity. I then …

The Adaptations Of The Sulfur-Oxidizing, Gammaproteobacterium "Candidatus Endoriftia Persephone", Endosymbiont Of The Giant Tubeworm Riftia Pachyptila, To Hydrothermal Vent Habitat Heterogeneity, Juliana M. Leonard

USF Tampa Graduate Theses and Dissertations

The siboglinid tubeworm Riftia pachyptila is a dominant member of the deep-sea megafauna where seawater and hydrothermal vent (HTV) effluent interface and mix. It is one of the fastest growing invertebrates on land or in the sea. It does not have a digestive tract (e.g. mouth, gut, or anus), and is completely dependent on its sulfur-oxidizing endosymbiont, the Gammaproteobacterium “Candidatus Endoriftia persephone” for its nutritional requirements. This association was the first and is the most well studied among chemolithoautotrophic symbioses. “Ca. E. persephone” is a chemolithoautotrophic bacterium that oxidizes sulfide as an electron donor for energy, reduces oxygen as a …

Understanding The Influence Of The Cancer Microenvironment On Metabolism And Metastasis, Shonagh Russell

USF Tampa Graduate Theses and Dissertations

Cancer is a complex and heterogeneous disease. Not only is there considerable variability between different cancer types, but there is enormous variability between and within patients who have the same type of cancer. Within tumors, there are multiple cell types, including cancer cells, stromal cells, and immune cells. The tumor microenvironment often induces the healthy cells to become pro-tumorigenic. Cell metabolism is exquisitely sensitive to changes in the tumor microenvironment and can be measured to infer the aggressiveness of cancer and predict response to therapy. In this dissertation, we aim to understand how the microenvironment, specifically low pH, affects the …

Modeling Of Interaction Of Ions With Ether- And Ester-Linked Phospholipids, Matthew W. Saunders

USF Tampa Graduate Theses and Dissertations

Phospholipids are present in all parts of cells and are used in many signalling and struc- tural roles. As structural molecules they act as the main component of cellular membranes. Bilayer properties are heavily influenced by the structure of their component polar lipids, and different lipids are found in different organisms. A distinguishing feature of Archaeal plasma membranes is that their phospholipids contain ether-links, as opposed to bacterial and eukaryotic plasma membranes where phospholipids primarily contain ester-links. In our work we examine the effects of salt on bilayer structure in the case of both ester- and ether-linked lipid bilayers. We …

The Distribution And Biogeochemistry Of Subtropical Intertidal Microbial Mats, Bert D. Anderson

USF Tampa Graduate Theses and Dissertations

Microbial mats have played an important role in the carbon (C) and nutrient cycles since the Archean Eon and modern mats are important contributors to the biogeochemistry of intertidal wetlands. Microbial mats are flat assemblages of microbes that are currently found in many unvegetated habitats globally. Intertidal salt pans are a common habitat for microbial mats, however little is known about the distribution of microbial mats within the intertidal landscape. Understanding the spatial distribution of microbial mats is critical to developing quantitative estimates of the impacts of microbial mats on their ecosystems. We photographically measured the presence and density of …

Functional Characterization Of The Ovarian Tumor Domain Deubiquitinating Enzyme 6b, Jasmin M. D'Andrea

USF Tampa Graduate Theses and Dissertations

The posttranslational modification ubiquitination is major regulatory mechanism used throughout cell signaling pathways such as cell cycle regulation and the DNA damage response. As such, the E3 ligases and their deubiquitinating enzyme counterparts, which conjugate and deconjugate ubiquitin to and from protein substrates respectively, must be tightly regulated to prevent aberrant cellular behaviors that could lead to diseases such as cancer.

Of the five families of deubiquitinating enzymes, the Ovarian Tumor Domain (OTU) family is fairly unique and under-studied; many of its family members hold a linkage specificity to certain ubiquitin chains and a number of them have been implicated …

Measuring Flowering Phenology And Its Consequences: A Systematic Review, Samantha M. Mangum

USF Tampa Graduate Theses and Dissertations

Despite growing interest in flowering phenology among ecologists, as reflected by an increase in the number of papers, there is little information on how studies typically measure and describe a plant’s flowering phenology. The focus of this study was the literature on flowering phenology and the approaches researchers have taken to quantify flowering phenology. Initially, a comprehensive description of the breath of literature on flowering phenology was produced. From there, I described the current research on flowering phenology: the year that the studies were published, the locations of the studies, and the particular biomes where the studies were performed. The …

Enhancing Immunotherapeutic Interventions For Treatment Of Chronic Lymphocytic Leukemia, Kamira K. Maharaj

USF Tampa Graduate Theses and Dissertations

Chronic lymphocytic leukemia (CLL) is the most common leukemia in developed countries. It is characterized by the accumulation of CD5+ B lymphocytes in the peripheral blood, bone marrow, and lymphoid tissues of affected patients. Patients experience lymphadenopathy, fatigue, and are severely immunocompromised. Management of disease and symptoms is possible with chemo-immunotherapy for higher risk patients; however, CLL remains incurable unless bone marrow transplant is performed. Identification of novel targets and optimization of current therapeutics is therefore still necessary. The new targeted therapies are at the forefront of development for CLL treatment, but it remains challenging to maximize their efficacies while …

Species Abundance, Spatial And Vertical Distributionsof Large Heteropods (Pterotracheidae And Carinariidae)In The Northern Gulf Of Mexico, Kristine A. Clark

USF Tampa Graduate Theses and Dissertations

A description of species abundance, richness and distribution, and eye size of heteropod molluscs from the families Pterotracheidae and Carinariidae in the oligotrophic ecosystem of the northern Gulf of Mexico (GOM) is described based on discrete-depth sampling protocols. The collections were comprised from two midwater sampling programs conducted sequentially after the 2010 Deepwater Horizon oil spill (DWHOS): the Offshore Nekton Sampling and Analysis Program (ONSAP, 2011) and the Deep Pelagic Nekton Dynamics of the Gulf of Mexico (DEEPEND, 2015-2018). Study materials from DEEPEND were collected during the initial five cruises of 2015-2017. These programs collected over 3,495 heteropods in two …

Investigating Student Conceptual Understanding Of Structure And Function By Using Formative Assessment And Automated Scoring Models, Kelli Patrice Carter

USF Tampa Graduate Theses and Dissertations

There has been a call from the national community of biologists and biology educators to increase biological literacy of undergraduate students, including understanding and application of core concepts. The structure and function relationship is a core concept identified by the wider biology community and by physiology faculty. Understanding of the core concept structure and function across multiple levels of organization may promote biological literacy. My research focused on the development of formative written assessment tools to provide insight into student understanding of structure and function in anatomy and physiology.

In chapter two I developed automated scoring tools to facilitate the …

Complex Tripartite Hydro Politics Of River Ganges, Muttaki Bin Kamal

USF Tampa Graduate Theses and Dissertations

This paper studies if the Flagship Namami Gange program of Cleaning the river Ganges in India aligns with the transcendental discourse on the river. Web contents as Facebook, YouTube and Twitter along with Indian English daily newspaper reports are used here as the source of data. The study shows that the program aligns with the transcendental discourse on river Ganges as the Mother Goddess and reaching out to her devotees.

Multiscale Model Of Regional Population Decline In Little Brown Bats Due To White-Nose Syndrome, Andrew M. Kramer, Claire S. Teitelbaum, Ashton Griffin, John M. Drake

Integrative Biology Faculty and Staff Publications

1. The introduced fungal pathogen Pseudogymnoascus destructans is causing decline of several species of bats in North America, with some even at risk of extinction or extirpation. The severity of the epidemic of white-nose syndrome caused by P. destructans has prompted investigation of the transmission and virulence of infection at multiple scales, but linking these scales is necessary to quantify the mechanisms of transmission and assess population-scale declines.
2. We built a model connecting within-hibernaculum disease dynamics of little brown bats to regional-scale dispersal, reproduction, and disease spread, including multiple plausible mechanisms of transmission.
3. We parameterized the model using the approach of …

A Ctenophore (Comb Jelly) Employs Vortex Rebound Dynamics And Outperforms Other Gelatinous Swimmers, Brad J. Gemmell, Sean P. Colin, John H. Costello, Kelly R. Sutherland

Integrative Biology Faculty and Staff Publications

Gelatinous zooplankton exhibit a wide range of propulsive swimming modes. One of the most energetically efficient is the rowing behaviour exhibited by many species of schyphomedusae, which employ vortex interactions to achieve this result. Ctenophores (comb jellies) typically use a slow swimming, cilia-based mode of propulsion. However, species within the genus Ocyropsis have developed an additional propulsive strategy of rowing the lobes, which are normally used for feeding, in order to rapidly escape from predators. In this study, we used high-speed digital particle image velocimetry to examine the kinematics and fluid dynamics of this rarely studied propulsive mechanism. This mechanism …

4dee—What's Next? Designing Instruction And Assessing Student Learning, Luanna Prevost, Amanda E. Sorensen, Jennifer H. Doherty, Diane Ebert-May, Bob Pohlad

Integrative Biology Faculty and Staff Publications

No abstract provided.

Multiscale Model Of Regional Population Decline In Little Brown Bats Due To White-Nose Syndrome, Andrew M. Kramer, Claire S. Teitelbaum, Ashton Griffin, John M. Drake

Integrative Biology Faculty and Staff Publications

1. The introduced fungal pathogen Pseudogymnoascus destructans is causing decline of several species of bats in North America, with some even at risk of extinction or extirpation. The severity of the epidemic of white-nose syndrome caused by P. destructans has prompted investigation of the transmission and virulence of infection at multiple scales, but linking these scales is necessary to quantify the mechanisms of transmission and assess population-scale declines.
2. We built a model connecting within-hibernaculum disease dynamics of little brown bats to regional-scale dispersal, reproduction, and disease spread, including multiple plausible mechanisms of transmission.
3. We parameterized the model using the approach of …

The Caricomp Network Of Caribbean Marine Laboratories (1985–2007): History, Key Findings, And Lessons Learned, Jorge Cortes, Hazel A. Oxenford, Brigitta I. Van Tussenbroek, Eric Jordan-Dahlgren, Aldo Croquer, Carolina Bastidas, John C. Ogden

Integrative Biology Faculty and Staff Publications

Caribbean Coastal Marine Productivity (CARICOMP) was a basin-wide cooperative, international network of marine laboratories established in 1985. Recognizing major trends of change in coastal ecosystems and the importance of the linkages among them, our goal was to monitor synoptically with standardized methods the physical environment and to document trends in measures of the structure and functioning of coral reefs, seagrasses and mangroves. Between 1985 and 1993, the CARICOMP Steering Committee established a data management center and wrote a methods manual. Marine laboratories joined the program by appointing a Site Director and signing an agreement specifying the cost sharing and responsibilities …

Comparison Of Dna Methylation In Vibrio Vulnificus Cells Grown In Human Serum With Those Grown In Seawater, James W. Conrad, Valerie J. Harwood

Integrative Biology Faculty and Staff Publications

The chromosomal methylation statuses of the highly virulent Vibrio vulnificus strain CMCP6 grown in human serum and in seawater are compared here. Growth in seawater resulted in ∼4 times as much methylation as that in human serum, primarily N⁴-methylcytosines.

Through The Eyes Of Faculty: Using Personas As A Tool For Learner-Centered Professional Development, Patricia Zagallo, Jill Mccourt, Robert Idsardi, Michelle K. Smith, Mark Urban-Lurain, Tessa C. Andrews, Kevin Haudek, Jennifer K. Knight, John Merrill, Ross Nehm, Luanna B. Prevost, Paula P. Lemons

Integrative Biology Faculty and Staff Publications

College science instructors need continuous professional development (PD) to meet the call to evidence-based practice. New PD efforts need to focus on the nuanced blend of factors that influence instructors’ teaching practices. We used persona methodology to describe the diversity among instructors who were participating in a long-term PD initiative. Persona methodology originates from ethnography. It takes data from product users and compiles those data in the form of fictional characters. Personas facilitate user-centered design. We identified four personas among our participants: Emma the Expert views herself as the subject-matter expert in the classroom and values her hard-earned excellence in …