Biology Commons^™

Engaging Students In A Genetics Course-Based Undergraduate Research Experience Utilizing Caenorhabditis Elegans In Hybrid Learning To Explore Human Disease Gene Variants, Natalie Forte, Virginia Veasey, Bethany Christie, Amira Carter, Marli Hanks, Alan Holderfield, Taylor Houston, Anil Challa, Ashley Turner

Research, Publications & Creative Work

Genetic analysis in model systems using bioinformatic approaches provides a rich context for a concrete and conceptual understanding of gene structure and function. With the intent to engage students in research and explore disease biology utilizing the nematode Caenorhabditis elegans model, we developed a semester-long course-based undergraduate research experience (CURE) in a hybrid (online/in-person) learning environment—the gene-editing and evolutionary nematode exploration CURE (GENE-CURE). Using a combination of bioinformatic and molecular genetic tools, students performed structure-function analysis of disease-associated variants of uncertain significance (VUS) in human orthologs. With the aid of a series of workshop-style research sessions, students worked in teams …

Enzyme Kinetics Of Deoxyuridine Triphosphatase From Western Corn Rootworm, Carlos Riera‑Ruiz, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

Objective The Western corn rootworm (WCR), Diabrotica virgifera virgifera, is a highly adaptable insect pest that has evolved resistance to a variety of control strategies, including insecticides. Therefore, it is interesting to examine how housekeeping proteins in WCR have been changed under WCR-controlling strategies. In this study, we focused on one of such proteins in WCR, a ubiquitous enzyme 5’-triphosphate nucleotidohydrolase (dUTPase). In the thymidine synthetic pathway, dUTPase hydrolyzes deoxyuridine triphosphate (dUTP) and supplies the substrate, deoxyuridine monophosphate, for the thymidylate synthase (TS). It decreases the cellular content of uracil, reducing uracil misincorporation into DNA. Suppressing the dUTPase activity, …

Uncovering The Determinants Of Compositionally Distinct, Coexisting Biomolecular Condensates, Andrew Zijia Lin

Arts & Sciences Graduate Student Theses and Dissertations

Biomolecular condensates form via the phase transitions of proteins and nucleic acids. What is unclear is how unique condensates achieve compositional specificity. Of particular interest is the ability of distinct condensates to have shared and distinct components. This is readily apparent in the multinucleate filamentous fungi Ashbya gossypii, where condensates share a common cytoplasm. In Ashbya, the RNA-binding protein Whi3 forms condensates with CLN3, BNI1, and SPA2. These RNAs are responsible for initiating the cell cycle, forming actin cables, and directing polarized cell growth respectively. However in vivo observations have shown that certain Whi3-RNA condensates are capable of mixing while …

Phenological Activities Of Desert Bees Track Rainfall More Than Temperature And Predict Temporal Abundance Trends Over 16 Years, Jade Elijah Mclaughlin

Biology ETDs

Phenology, the timing of recurrent biological events, is a key mechanism by which species adapt or acclimatize to variable environmental conditions, including those influenced by climate change. Measurable traits, including the onset and end of activity, peak activity, and duration, characterize the phenology of life events, and could be significant predictors of trends in population abundance or stability in a changing climate. Bees provide critical pollination services, and understanding the covariates of bee phenological traits can refine predictions on the vulnerabilities of bees and their services to climate change. We paired 16 years of monthly bee survey data (2002-2019) with …

Association Of Human Leukocyte Antigen (Hla) Alleles With Atopic Dermatitis In The Uae Population, Suhib Ziad Abu Jwayed

Thesis/ Dissertation Defenses

In the face of the increasing global prevalence of Atopic Dermatitis (AD), a chronic inflammatory skin condition, this thesis seeks to elucidate the genetic underpinnings of AD within the UAE population. Previous literature has underscored the ethnic-specific involvement of HLA genetic variations, especially within HLA-A and HLA-DRB1 genes, in the pathogenesis of various skin diseases, including AD. Leveraging this knowledge, our research specifically aimed to investigate the association between these HLA variants and AD in the UAE. Utilizing a comparative approach, the frequencies of HLA-A and HLA-DRB1 variants were assessed in AD patients vis-à-vis a control group. Our data, based …

Shell Pnw, Victoria B. Martinez Bruno, Amy C. Hirons Dr.

Hirons Field Techniques

No abstract provided.

Blue Runner (Caranx Crysos) Neurocranium, Delaney Deinlein, Gabriel Droz, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

Neurocranium from approximately 30 cm total length (TL) Blue Runner (Caranx crysos), collected from Dania Pier in 2023 by Charles Klinger.

Mimicking Biofilms: Photosynthetic Assessments Of C. Reinhardtii In 3 Physical Forms, John Michael Roesgen

Biology ETDs

Oxygenic photosynthesis supports the majority of life on Earth through the capture of energy from sunlight and the assimilation of CO₂ into basic building blocks of cells. Microalgae are fast growing and account for about half of global photosynthesis. In addition, they can be cultivated and their metabolism can be redirected to generate additional useful products ranging from biofuels to pharmaceuticals. However, the efficiency of metabolite production is severely impacted by the slow diffusion of CO₂ through water and the high energetic costs of harvesting microalgae from liquid cultures. Microalgae grow in open water, but they also form …

Anti-Cancer Activity Of Rhus Coriaria (Sumac) Against 5-Fluorouracil-Resistant Colorectal Cancer Cells, Zohra Nausheen Nizami

Thesis/ Dissertation Defenses

Colorectal cancer (CRC) is the second leading cause of cancer-related death, both worldwide and in UAE. 5-fluorouracil (5-FU), a pyrimidine analogue, is a chemotherapeutic agent that is an integral component of chemotherapy regimens for CRC treatment. However, 5-FU resistance (intrinsic and/or acquired) inhibits their clinical efficacy. In recent years, there has been a growing popularity for plantbased cancer therapeutics, specifically using phytochemical compounds. Rhus coriaria (Sumac) is a Mediterranean plant whose fruits are used as a spice and medicinal herb. Extracts of Rhus coriaria fruits have been reported to exhibit anticancer activity against breast and CRC cancers. In the present …

Population Structure And Genetic Diversity Of The Socotra Cormorant (Phalacrocorax Nigrogularis), Noura Mabkhout Almansoori

Thesis/ Dissertation Defenses

The Socotra cormorants (Phalacrocorax nigrogularis) are regional endemic seabirds restricted to the Arabian Gulf, Gulf of Oman, and the Arabian Sea. This species is classified as vulnerable by the IUCN Red List. However, no population genetic study has been conducted on P. nigrogularis in their range, and population structure, gene flow and connectivity between colonies is unknown. Likewise, genetic diversity of this species has not yet been characterized. Thus, the aim of this thesis was to fill these gaps by inferring population structure, assessing gene flow and genetic diversity of Socotra cormorant colonies in their known distribution range. For this …

Catfish Neurocranium, Fiona Smith, Juliana Ottens, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Modulation Of Chronic Allergic Contact Dermatitis Through B Cells Reprogramming, Sara Saeed Alhmoudi

Thesis/ Dissertation Defenses

Allergic contact dermatitis (ACD) is a common inflammatory disease caused by contact with an allergen and is a T-cell mediated type IV hypersensitivity reaction. Short chain fatty acids (SCFAs) showed the ability to modulate immune cells in case of inflammation. Pentanoate is one of the abundant SCFA that showed therapeutic ability by inducing IL-10 secretion in lymphocytes. IL-10 producing regulatory B cells have shown to decrease different inflammatory responses; however, overall role of B cells in ACD is not well studied. This project aims to explore the role of B cells during chronic ACD and their modulation with the SCFA …

T-Bet And Eomes Are Required For Mature Nk Cell Homeostasis And Function, Pamela Wong

Arts & Sciences Graduate Student Theses and Dissertations

Natural Killer (NK) cells are innate lymphocytes known for their role in recognizing and killing virus-infected or tumor cells without prior sensitization. NK cells express a variety of inhibitory and activating receptors that control their effector functions. Once activated by target cells, cytokines, or activating receptor ligation, NK cells are capable of potent IFN-γ secretion in addition to direct cytotoxicity mediated by perforin and granzymes. Because of their anti-tumor function, NK cells are currently utilized in promising immunotherapy approaches. NK cells develop in the bone marrow and arise from the common lymphoid progenitor, which also gives rise to T, B, …

Trna Methyltransferases Mediate Acinetobacter Baumannii Pathobiology, Jenna Mcguffey

Arts & Sciences Graduate Student Theses and Dissertations

Bacterial pathogens commonly encounter hostile conditions, including disinfectants, antimicrobials, and the host immune system. To be successful, they must adapt through dynamic and complex regulatory mechanisms, such as post-transcriptional modifications on a variety of molecules, including tRNA. In recent years, this tRNA “epitranscriptome” has been increasingly appreciated as an under-researched mechanism for bacterial stress responses. These modifications can impact the translation efficiency of a cohort of stress response factors whose transcripts are enriched for the corresponding codons. However, the variety and roles of tRNA modification enzymes in human pathogens is still largely unknown. The Gram-negative pathogen Acinetobacter baumannii is currently …

Shining A Light Through A Multiomic Lens On Germline Variants: Patterns And Functional Implications Across Cancer Types, Fernanda Martins Rodrigues

Arts & Sciences Graduate Student Theses and Dissertations

The landscape of cancer research has undergone a profound transformation, transcending traditional tissue-centric viewpoints to embrace a more intricate understanding of cellular origins and molecular drivers. It has become evident that genes and variants implicated in specific cancers extend their influence across a spectrum of cancer types. Our prior work, encompassing an >10K cases from The Cancer Genome Atlas (TCGA) and more than >1K pediatric cases, illuminated the intricate web of germline predisposition variants and genes spanning 33 cancer types. These findings not only contributed to the refinement of guidelines for rare germline variant detection but also enriched the clinical …

Uncovering The Genetic Basis Underlying The Pseudomonas Syringae Pv. Tomato Strain Dc3000’S Response To Iaa And Its Role In Regulating Ptodc3000 Biology, Joshua Michael Brian Johnson

Arts & Sciences Graduate Student Theses and Dissertations

Indole-3-acetic acid (IAA) is a molecule ubiquitous to the environment and is known to be produced across all three domains of life. It is most well-known for its role as an important plant hormone (an auxin) and until recently, its roles in other organisms have not been explored. It is well established that bacteria, and pathogens in particular, need to sense and respond to environmental signals. One model organism for studying plant pathogen interactions that is known to both produce and respond to IAA is Pseudomonas syringae pv. tomato strain DC3000 (PtoDC3000). Many plant metabolites have been explored as potential …

Effect Of Ploidy On Salinity And Temperature Tolerance In Early Life Stages Of The Eastern Oyster (Crassostrea Virginica), Christian Boudreaux, Jessica Pruett, Alexz Carpenter, Kristie Willett, Deborah Gochfeld

Honors Theses

The U.S. Gulf of Mexico contains the largest remaining wild oyster fishery in the world, but populations have declined in recent decades. A growing interest in off-bottom aquaculture that relies on triploid eastern oysters (Crassostrea virginica) has emerged in the Gulf region, yet these faster growing oysters suffer high mortality as adults during low salinity events (< 5 ppt) in warmer summer months. The combined effects of salinity and temperature stressors on early life stages of triploid oysters are unknown. Early life stages are particularly crucial to understand because triploid oysters do not occur naturally and must be reared in hatchery settings, requiring appropriate water conditions to yield the greatest survival and growth. Thus, we tested the effects of different temperatures (28oC and 32oC) and salinities (5, 10, and 15 ppt) on diploid and triploid oysters at three critical production stages: veliger, pediveliger, and spat. Veliger survival was significantly lower for triploids relative to diploid oysters at all experimental conditions, but triploid veligers had faster growth than diploids at 32oC and 15 ppt. Pediveliger settlement was not affected by ploidy type and only reduced at high temperature (32oC) and the lowest salinity (5 ppt). Diploid spat showed highest survival at 28oC and 15 ppt, while triploids survived best at 32oC and 15 ppt. Triploid spat attained greater shell height compared to diploids in our 6-day exposures, but growth decreased for both ploidies at lower salinities. At the salinity and temperature levels examined, diploid early life stages performed best at 28oC and 15 ppt, whereas triploids were more successful at 32oC and 15 ppt. A broader understanding of the combined effects of environmental stressors will improve the success of hatchery production yields and the resulting economic and environmental benefits of the oyster industry.

Book Review: Kings, Conquerors, Psychopaths: From Alexander To Hitler To The Corporation, Tim Bakken

Genocide Studies and Prevention: An International Journal

The book Kings, Conquerors, Psychopaths is a survey of a vast amount of human wrongdoing. It lays bare the motivations of aggressors who wish to subjugate nations or groups of people and corporate executives and government bureaucrats who make discretionary decisions that harm people. Along with cataloging mass killings by despots and soldiers, the book includes stories about Ponzi-schemers and the deaths of automobile drivers and passengers who were killed by vehicle defects known to the manufacturer. The book posits that “[p]owerful, elite forces are trying to force us backward toward a non-democratic state, one where power, wealth, and prerogative …

Atlantic Cutlassfish (Trichiurus Lepturus), Gabriela R. Ridings Ms., David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Minimization Of Diet For Optimum Consumption Using Linear Programming, Nita Ngozi Ezekwem, Aditi Ghosh

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Msis-Kondrashov: Does Humanizing Scientists Increase Student Science Identity And Quantitative Skills?, Rachel Hartnett

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Integrating Quantitative Skills Into Biology Courses, Kathleen Hoffman, Sarah Leupen, Hannah Pie, Michelle Starz-Gaiano, Patricia Turner, Tory Williams

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Targeting Bet Proteins Downregulates Mir-33a To Promote Synergy With Pim Inhibitors In Cmml, Christopher T. Letson

USF Tampa Graduate Theses and Dissertations

Chronic Myelomonocytic Leukemia (CMML) is a rare myeloid malignancy with a dismal prognosis and no therapeutic options which are capable of altering the natural course of the disease. There remains a significant need for novel therapies that are able to meaningfully improve patient outcomes. In this study we explore the effectiveness of Bromodomain and Extra-Terminal domain protein inhibitor (BETi) combinations in CMML. Preclinical studies in myeloid neoplasms have demonstrated efficacy of BETi. However, BETi demonstrate poor single agent activity in clinical trials. Several studies suggest that combinations with other anti-cancer inhibitors may enhance the efficacy of BETi. To nominate BETi …

Green Synthesized Silver Nanoparticles-Based Sensing For Monitoring Water Pollution: An Updated Review, Muhamad Allan Serunting, Muhammad Ali Zulfikar, Henry Setiyanto, Dian Ayu Setyorini, Vienna Saraswaty

Karbala International Journal of Modern Science

Water is a basic human need and has been heavily contaminated. Therefore, it becomes a concern to remove the pollutant and monitor its quality. The removal methods include precipitation, filtration, adsorption, and photodegradation. Meanwhile, the monitoring can be done by measuring and analyzing the contaminant using spectrophotometry and chromatography. Nevertheless, those methods usually need a complicated preparation, and are expensive. Thus, a simple method is necessary to overcome these drawbacks by developing a sensor. In recent years, the sensor performance has been enhanced by using nanomaterials, such as silver nanoparticles (AgNPs). AgNPs can be synthesized using plant extracts through a …

Synthesis And Characterization Of Zirconium Oxide Nanoparticles Using Z. Officinale And S. Aromaticum Plant Extracts For Antibacterial Application, M. J. Tuama, M. F. A. Alias

Karbala International Journal of Modern Science

Abstract The dramatic rise in bacterial infections and increased resistance to conventional antibiotics has led to the exploration of biologically derived nanomaterials to counteract bacterial activity. Nanotechnology, which deals with materials at the atomic or molecular level, is a promising way to achieve this goal. Zirconium oxide nanoparticles (ZrO2NPs) have shown strong antibacterial effects due to the increased surface-to-volume ratio at the nanoscale. This study focused on the production of ZrO2NPs in an environmentally friendly manner, which included extracts from Zingiber officinale (ginger), where G-ZrO2NPs were produced, and Syzygium aromaticum (clove), which produced S-ZrO2NPs. Various techniques were used, such as …

Brain Metastasis-Associated Fibroblasts Secrete Fucosylated Pvr/Cd155 That Induces Breast Cancer Invasion, Emma Adhikari

USF Tampa Graduate Theses and Dissertations

Breast cancer (BC) continues to be the most diagnosed cancer and the second leading cause of cancer deaths in women worldwide. High mortality, in most cancers, is due to metastasis; BC is the most common source of one of the deadliest forms of metastasis–brain metastasis (BM) in female. Patients with triple negative breast cancer (TNBC) exhibit the highest incidence of BM and poorest survival outcomes upon diagnosis with BM. The prognosis of breast cancer brain metastasis (BCBM) remains poor because the blood–brain barrier (BBB) prevents the uptake of drug substances, including chemotherapeutic agents, targeted agents, and toxins, from the brain. …

Genomic Diversity And Carbohydrate Utilisation In Human-Associated Bifidobacterial Isolates, Ortensia Catalano Gonzaga

ORBioM (Open Research BioSciences Meeting)

Bifidobacteria are beneficial commensals of the human gastrointestinal tract and their presence in the gut has been associated with positive health effects on the host. They account for a vast proportion of the infant gut microbiota, when the infant is fed on a milk-based diet, with their number progressively decreasing in adult and elderly. The gut microbiota and associated metabolic activities significantly impact on human health by promoting appropriate development of the infant immune system and contributing to the maintenance of the intestinal homeostasis. In recent years it has become clear that microbial colonization of the gut immediately following birth …

Monocytes And Macrophages Promote Increased Tissue Factor-Factor Viia-Dependent Procoagulant Activity In Response To The Sars-Cov-2 Spike Protein, James Harte

ORBioM (Open Research BioSciences Meeting)

Background

Venous thromboembolism (VTE) is a high-incidence complication of severe SARS-CoV-2-associated COVID-19. Recently, abnormal tissue factor expression has been linked to thromboembolic events in patients with COVID-19. Monocytes and macrophages are the predominant source of tissue factor in peripheral circulation, which suggests a potential pathomechanistic interplay between SARS-CoV-2 and the monocyte-macrophage axis. However, the link between monocytes and macrophages and the thromboembolic risk associated with COVID-19 is largely unaddressed.

Aims

In this study, we investigated changes in monocyte/macrophage procoagulant activity in response to the SARS-CoV-2 spike protein.

Methods

Immortalised human-derived monocytes and differentiated macrophages were treated with the SARS-CoV-2 spike …

Doxorubicin-Induced Modulation Of Tgf-Β Signaling Cascade In Mouse Fibroblasts: Insights Into Cardiotoxicity Mechanisms, Conner Patricelli, Parker Lehmann, Julia Thom Oxford, Xinzhu Pu

Biology Faculty Publications and Presentations

Doxorubicin (DOX)-induced cardiotoxicity has been widely observed, yet the specific impact on cardiac fibroblasts is not fully understood. Additionally, the modulation of the transforming growth factor beta (TGF-β) signaling pathway by DOX remains to be fully elucidated. This study investigated DOX’s ability to modulate the expression of genes and proteins involved in the TGF-β signaling cascade in mouse fibroblasts from two sources by assessing the impact of DOX treatment on TGF-β inducible expression of pivotal genes and proteins within fibroblasts. Mouse embryonic fibroblasts (NIH3T3) and mouse primary cardiac fibroblasts (CFs) were treated with DOX in the presence of TGF-β1 to …

Individual And Population Age Impact Social Behavior And Network Structure In A Long-Lived Insect, P. A. Cook, R. A. Costello, Vincent A. Formica, E. D. Brodie Iii

Biology Faculty Works

Social behaviors vary among individuals, and social networks vary among groups. Understanding the causes of such variation is important for predicting or altering ecological processes such as infectious disease outbreaks. Here, we ask whether age contributes to variation in social behavior at multiple levels of organization: within individuals over time, among individuals of different ages, among local social environments, and among populations. We used experimental manipulations of captive populations and a longitudinal dataset to test whether social behavior is associated with age across these levels in a long-lived insect, the forked fungus beetle (Bolitotherus cornutus). In cross-sectional analyses, …