Biology Commons^™

Application Of The Method Cell Biology, Terry Shackleford

San Jose - Lonergan Chair in Catholic Philosophy

Summer 2024, Application of the Method Cell Biology

Students in the Fall 2023 semester "Mechanisms of Disease Course" were given a practical assignment that in turn allowed for discussion on gathering data on orphan diseases and covering what the disease is, how the disease progresses, who is affected by the disease, and what is the effect of the disease on their life.

Overcoming Microenvironmentally Mediated Resistance In Targetable Non-Small Cell Lung Cancer, Bina Desai

USF Tampa Graduate Theses and Dissertations

The introduction of targeted therapies has resulted in immense success in treating lung cancer patients, where many patients experience long-term remission. Yet, the tumors relapse into an advanced state of disease, and ultimately, treatment failure. This can be ascribed to incomplete eradication of tumor cells by targeted therapies, which enables the residual tumor cells to propagate resistant tumors and cause subsequent relapse in patients. Therapy sensitivity is influenced not only by cell-intrinsic mechanisms but also by inputs from the stromal microenvironment. Despite widespread recognition of the stromal microenvironment's role in modulating therapy sensitivity, its contribution to therapeutic responses in vivo …

Neuronal Injury Model Divulges Differences In Dendrite And Axonal Function And Regeneration In Adults, Lauren S. Vaughn, Jinyoung Lee

Faculty Publications

No abstract provided.

Terrestrial Salinization Impacts On Growth And Behavior Of A Common Detritivore Armadillidium Vulgare (Isopoda), Danielle Harmoney Orcutt

Master's Theses

Climate change and human activities are changing the nutritional landscape by increasing the availability of some essential elements and decreasing others. Sodium (Na) is an essential element in heterotrophs, which is required for water regulation, nerve function, and muscle function. Heterotrophs can acquire Na through diet and environment, often experiencing limited availability of Na due to plants concentrating Na 10-100 times less than heterotrophs need. The Sodium Subsidy-Stress (SSS) hypothesis posits that organismal performance follows a hump-shaped curve of a physiological response, where Na acts as a subsidy, increasing organismal performance such as growth until an optimal threshold is reached, …

Unraveling The Role Of Hid-1: Insights Into Sgii Regulation, Breanna L. Sellers

Electronic Theses and Dissertations

The regulated secretory pathway is important for the secretion of hormones and neuropeptides from large dense core vesicles (LDCVs). Dysregulation of the biogenesis of LDCVs can result in metabolic and neurological diseases. Recent studies have suggested that the peripheral membrane protein HID-1 plays a role in the sorting and storage of granins which contribute to LDCV biogenesis. To further understand how HID-1 influences the regulation of granins, we investigated potential HID-1 interactors. We determined that while HID-1 is likely functioning in the same pathway as USP25, a deubiquitinating enzyme (DUB), the cause of reduced cellular SgII levels is likely not …

Population Genetic Diversity In Two Biological Systems, Alyson Emery

Electronic Theses and Dissertations

Population genetic analysis can be used to answer questions about population structure and composition in many biological systems. Recent improvements to sequencing technologies have made population genetic studies more accessible than ever before. Many of the same techniques can be applied to different biological systems, but some analyses may differ depending on how genetically divergent the populations in question are. Here, we describe two unique projects using next-generation genome sequencing, each looking at population structure at different levels of genetic divergence: the first involved determining interspecific population structure between two species of hybridizing field cricket using a novel sequencing method, …

Akt Disruption Leads To Non-Canonical Apical Constriction In Drosophila Embryos, Vincent Brown

Electronic Theses and Dissertations

The Akt/mTOR pathway (Akt pathway) has largely been examined in terms of its role as the primary nutrient sensing pathway due to its ability to recognize nutrient availability within a cell, particularly amino acids and glucose. Among its nutrient sensing characteristics, this pathway also contributes to a large variety of other cell functions such as cell growth, proliferation, protein synthesis, and cell survival via anti-apoptotic signaling. Although many aspects of this pathway have been carefully studied, the extent to which it regulates embryonic development remains unclear. Here, I examine Akt function in the early Drosophila embryo and demonstrate that Akt …

Division I Collegiate Baseball Pitching Performance In Relation To Forearm Kinematics And Kinetics, Christopher W. Watson

Master's Theses

This thesis investigates physical and anthropometric factors influenced by forearm rotation biases associated with supination and pronation on pitch characteristics among Division I college baseball pitchers. The study involved twenty-two participants who underwent comprehensive physical assessments, including measures of forearm strength, range of motion, and grip strength, as well as finger and hand length measurements. Ball flight metrics were collected during intrasquad scrimmages using advanced radar tracking technology. Results revealed significant relationships between distinct physical biases of strength in pronation and supination, pinch strength, anthropometrics such as middle finger length, and specific pitch characteristics. This study lays the groundwork for …

Turkey Tail Mushroom (Trametes Versicolor): An Edible Macrofungi With Immense Medicinal Properties, Olaide Olaide Ajibola, Cirilo Nolasco-Hipolito, Octavio Carvajal-Zarrabal, Shanti F. Salleh, Gbadebo C. Adeyinka, Stephen A. Adefegha, Mirja K. Ahmmed, Kazi Sumaiya, Raymond Thomas

Biology Publications

Macrofungi, commonly known as mushrooms, are not only considered functional foods for supplying essential nutritional ingredients but also a good source of physiologically beneficial medicines. Trametes versicolor, referred to as turkey tail’s Mushroom or Yun Zhi in China, is an edible mushroom that has extensive historical usage in conventional and traditional Chinese medicine. This mushroom contains an abundance of physiologically bioactive compounds, most notably β-glucan polysaccharides, which are responsible for antioxidant, neuroprotection, hypolipidemic effects, immune-modulating effects, and anticancer effects. Trametes versicolor has also been revealed to have wound healing, antidiabetic, antimicrobial, antifibrotic, neurotrophic, and …

Poly(U) Polymerases Have Complex Roles In Modulating The Small Rnaome And Transcriptome Of C. Elegans, Leanne Helen Kelley

Dissertations - ALL

A continuously growing body of work has shown that RNA regulation is an essential aspect of germline development across metazoans. However, another layer of regulation exists “above” this: post-transcriptional modifications to RNAs can alter their function and affect biological activity. Poly(U) polymerases (PUPs) add uridines to the 3’ end of RNA molecules, a process called uridylation, or U-tailing. Previous research has identified the importance of PUPs in C. elegans development, and this work here aims to elucidate the function of PUPs at the molecular level. Using pup-1, pup-2, pup-3, and pup-4 deletion mutants in small RNA-seq, long-read …

Anatolian Medicinal Plants As Potential Antiviral Agents: Bridging Traditional Knowledge And Modern Science In The Fight Against Covid-19 And Related Viral Infections, Engi̇n Ti̇lkat, Israt Jahan, Ayşe Hoşer, Alevcan Kaplan, Oğuzhan Özdemi̇r, Ahmet Onay

Turkish Journal of Biology

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the worldwide coronavirus illness 2019 (COVID-19), often known as the coronavirus pandemic. Since December 2020 however, COVID-19 vaccines have been extensively administered in numerous countries. In addition to new antiviral medications, the treatment regimen also encompasses symptom management. In spite of sustained research efforts, the outbreak remains uncontrolled, with affected patients still lacking proper treatment. Consequently, this review serves as a valuable asset for researchers and practitioners aiming to delve into the yet unexplored potential of Anatolian flora in the fight against COVID-19 and other viral infections. Numerous …

Expressions Of The Satellite Repeat Hsat5 And Transposable Elements Are Implicated In Disease Progression And Survival In Glioma, Sila Naz Köse, Tutku Yaraş, Ahmet Bursali, Yavuz Oktay, Ci̇hangi̇r Yandim, Gökhan Karakülah

Turkish Journal of Biology

The glioma genome encompasses a complex array of dysregulatory events, presenting a formidable challenge in managing this devastating disease. Despite the widespread distribution of repeat and transposable elements across the human genome, their involvement in glioma's molecular pathology and patient survival remains largely unexplored. In this study, we analysed the expression levels of satellite repeats and transposons along with genes in low-grade glioma (LGG) and high-grade glioma (HGG). Endogenous transposable elements LTR5 and HERV_a-int exhibited higher expression in HGG patients, along with immune response-related genes. Altogether, 16 transposable elements were associated with slower progression of disease in LGG patients. Conversely, …

Exploring The Impact Of Diabetes On Aging: Insights From Tert And Col1a1 Methylation, Jessica Nathania Liamry, Farizky Martriano Humardani, Giovani Chandra, Lisa Thalia Mulyanata, Tjie Kok, Fenny Irawati, Hikmawan Wahyu Sulistomo, Christoph Reichetzeder, Sulistyo Emantoko Dwi Putra

Turkish Journal of Biology

Background/aim: Aging, a multifaceted biological process, leading to diminished physical performance, especially in older adults with diabetes, where a mismatch between biological and chronological age is noticeable. Numerous studies have demonstrated that diabetes accelerates aging at both cellular and organ levels. Notable aging markers are TERT, related to telomere length, and COL1A1, a key component of skin collagen. Additionally, age-related methylation increases, as revealed through methylation analysis, illuminate aspects of aging. However, the detailed interplay between aging and diabetes, particularly regarding methylation, remains underexplored and warrants further study to elucidate their biological links.Materials and methods: In this research, we elucidate …

Bud14 Function Is Crucial For Spindle Pole Body Size Maintenance, Sevi̇lay Müni̇re Gi̇rgi̇n, Ayşe Koca Çaydaşi

Turkish Journal of Biology

Background/aimSpindle Pole Bodies (SPB), functional equivalent of centrosomes in yeast, duplicate through generation of a new SPB next to the old one. Yet, SPBs are dynamic structures that can grow and exchange, and mechanisms that regulate SPB size remain largely unknown. This study aims to elucidate the role of Bud14 in SPB size maintenance in Saccharomyces cerevisiae.Materials and methodsWe employed quantitative fluorescence microscopy to assess the relative and absolute amounts of SPB structural proteins at SPBs of wildtype cells and in cells lacking BUD14 (bud14∆). Quantifications were performed using asynchronous cell cultures as well as cultures synchronously progressing through the …

Defining Evolution: Exploring Students’ Conceptions Of Evolution In Introductory Biology Courses, Jeremy L. Hsu, Meredith A. Dorner, Kate M. Hill

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background

Understanding evolution is an important part of undergraduate biology education. Despite its importance, however, students often struggle to understand evolution, often holding preconceived notions of what evolution is. Here, we investigate how students in both majors and non-majors introductory biology define and conceive of evolution at the start of the semester for a two-year college and a four-year university near each other. We analyze open-ended responses to an in-class activity on the first day of the semester that asked students to define evolution, generating insight into how students are thinking of evolution prior to any formal instruction on evolution …

Molecular Docking, Pharmacological Profiling, And Molecular Dynamics Simulation Of Potential Antihyperuricemic Agent From Secondary Metabolites Of Dillenia Philippinensis Rolfe (Dilleniaceae), Louie Rince C. Suyo, John P. Paulin, Nicole Clarence Louise L. Gapaz, Markus Brent S. Arevalo, Vince Tyrell P. Yongco, Librado A. Santiago

Karbala International Journal of Modern Science

Crystal accumulation in the joints due to increased serum uric acid (sUA) may lead to an inflammatory condition called gout. Increased sUA is caused by the excessive reabsorption of the urate anion transporter-1 (URAT-1). Therefore, URAT-1 inhibition will promote uric acid excretion and reduce the risk of having gout. Dillenia philippinensis Rolfe, often known as katmon, is an endemic plant in the Philippines with bioactive compounds associated with several therapeutic benefits. The present study represents the first scientific inquiry into the antihyperuricemic potential of compounds isolated from D. philippinensis. This study aimed to assess the interaction of URAT-1 with …

Two Draft Genome Assemblies Of Staphylococcus Aureus Strains Isolated From A Cheek Swab Of A Healthy Female Participant, Alex Kula, Sandra Jablonska, Lexi Avalos, Tyler Jensen, Helen Appleberry, Catherine Putonti

Biology: Faculty Publications and Other Works

Staphylococcus aureus is an opportunistic pathogen often commensal within the nasal and oral cavities. Here we present the genomes of S. aureus O139-S and O139-NS, both isolated from the cheek swab of a healthy female participant. While found in the same sample, the two strains displayed distinct colony morphologies.

Draft Genomes Of Klebsiella Aerogenes, Klebsiella Huaxiensis, And Klebsiella Michiganensis Isolates From The Urinary Tract, Alex Kula, Muna Arman, Helen Appleberry, Alan J. Wolfe, Catherine Putonti

Biology: Faculty Publications and Other Works

Several Klebsiella spp. can be the cause of urinary tract infections. Here we present the draft genome assemblies for four urinary isolates of three Klebsiella spp.: Klebsiella aerogenes UMB7541, Klebsiella michiganensis UMB11142 and UMB11423, and Klebsiella huaxiensis UMB11391 to further explore the genetic diversity of Klebsiella in the urinary tract.

Evolutionary Patterns Of Anolis Lizard Skulls: An Investigation In Geometric Morphometrics And An Educational Exploration Of Structure And Function, Katherine Beyer Starr

Master's Theses

This study explores the evolutionary patterns of Anolis lizard skulls and integrates findings into a curriculum focused on elucidating the structure and function of a lizard's head. The first objective was to develop an understanding of how the evolutionary patterns, of an extraordinary group of lizards (Anolis) compares to their relatives. Most of the prior research on Anolis morphology has focused on the post-cranium because of its significance towards subdivision of the arboreal habitat. But the group’s remarkable diversity in head shape has been seriously under-investigated. By performing geometric morphometric analysis of skull shape across a large sample of anoles …

Draft Genomes Of Neisseria Perflava Umb0578, Proteus Mirabilis Umb8339, And Enterococcus Faecalis Umb7967 Isolated From Urine Samples, Alex Kula, Ali Khan, Megan Martinez, Jevan Terry, Helen Appleberry, Alan J. Wolfe, Catherine Putonti

Biology: Faculty Publications and Other Works

The urinary tract of females harbors a variety of microorganisms, both for those with and without symptoms. Here, we present the draft genome sequences of three isolates from urine samples—Neisseria perflava UMB0578, Proteus mirabilis UMB8339, and Enterococcus faecalis UMB7967.

Draft Genomes Of One Staphylococcus Haemolyticus And Five Staphylococcus Lugdunensis Strains Isolated From Catheterized Urine Samples Of Females, Helen Appleberry, Haaris Anjum, Taleah Cage, Kayla Jarm, Haashir Khan, Lizzie Proctor, Junelle Saroca, Alan J. Wolfe, Catherine Putonti, Alex Kula

Biology: Faculty Publications and Other Works

Although Staphylococcus haemolyticus and Staphylococcus lugdunensis are members of the normal human flora, they also can cause infection. Here, we present the draft genomes of five strains of S. lugdunensis and one strain of S. haemolyticus isolated from transurethral catheterized urine samples from different females experiencing lower urinary tract symptoms.

Illuminating The Twilight Zone: In-Situ Imaging Facilitates Discovery Of Mesopelagic Plankton Dynamics And Community Structure, Alexander Barth

Theses and Dissertations

Ocean ecosystems provide both food and regulation of climate. Much of ocean ecosystem functioning occurs through processes in the pelagic, where plankton are the dominant organisms. While plankton have been researched for several centuries, recent advances in technology are greatly improving the ability to better understand plankton and how their communities are structured. Specifically, in-situ imaging allows oceanographers and plankton ecologists to better sample fragile taxa and record organisms’ true traits at high frequencies. These tools can facilitate investigation into new topics in plankton ecology and better understand critically understudied habitats, like the mesopelagic of open-ocean systems. However, in-situ imaging …

Sleep Restores An Optimal Computational Regime In Cortical Networks, Yifan Xu

Arts & Sciences Graduate Student Theses and Dissertations

Computation within the brain necessitates consistency and robustness, as no complex system can function effectively without these fundamental attributes. However, maintaining this robustness requires active efforts due to the inevitable perturbations (Turrigiano & Nelson, 2004). To unlock the unifying principle of how brain works, it is essential to identify an optimal set point that the system strives to maintain and restore, ensuring stability and functionality. Our lab recently demonstrated that cortical dynamics are homeostatically organized around criticality (Ma et al., 2019), a computational regime that optimizes information processing, such as information capacity and dynamic range (Shew & Plenz, 2013). This …

The Experience Of Homelessness And Its Effects On Gut Eubiosis, Kamerin Villagomez

University Honors Theses

Microorganisms which populate the human gastrointestinal tract (GIT) have a profound effect on overall human health. The relationship between host health and eubiosis, or balance, of the GIT microbiome is symbiotic and can have reciprocal relationships with quality of sleep, quality of diet, stress and mental health, and the experience of pain. These specific aspects of health are unique in populations experiencing homelessness due to the multi-dimensional and complex nature of their lived experience. Very few studies explore populations experiencing homelessness, with even fewer investigating the intersection between this population and the human GIT microbiome. It is important to do …

Effects Of Mmp14 Overexpression On Cardiac And Ovarian Connective Tissue And Myocyte Size In Pregnant And Post-Partum Mice, Emily Catherine Walliser

Theses and Dissertations

The main protein component of extracellular matrix is collagen, which fills spaces and supports cells. In the heart, collagen provides the scaffolding for cardiomyocytes and aids in contractile forces. In the ovary, collagen gives follicles their structural support. MMP14 or membrane type 1 matrix metalloproteinase is a membrane bound proteinase that cleaves extracellular matrix proteins, including collagen I and III. Recent studies have shown that overexpression of MMP14 influences collagen content in the heart, and elevated MMP14 has also been linked to ovarian cancer. In the current study, we investigate the effects of overexpression of a human MMP14 (hMMP14) transgene …

Estuarine Microbial Community Composition And Efficiency Changes In Response To Vibrio Parahaemolyticus Exposure, Sarah Mulligan

Theses and Dissertations

Vibrio parahaemolyticus is a pathogenic bacterium whose full impact on natural estuarine phytoplankton communities has not been fully resolved. The primary goal of this research was to test how the addition of V. parahaemolyticus to a natural estuarine microbial community would impact the other microbes present. We hypothesized V. parahaemolyticus exposure would reduce phytoplankton biomass and alter the composition of phytoplankton and bacterial communities. Experimental bioassays (60h) were used to assess the effects of the presence of V. parahaemolyticus . Samples for measurements of chemotaxonomic photopigment concentrations, 16S sequencing-based community composition, photosynthetic efficiency, cell density, and V. parahaemolyticus abundance were …

Understanding The Role Of Host Derived Interleukin 1 Alpha In Breast Cancer Progression, Manikanda Raja Keerthi Raja

Theses and Dissertations

In breast cancer research, Interleukin-1 alpha (IL1α) remains a lesser-explored frontier, while its counterpart, Interleukin-1 beta, has garnered extensive scrutiny and understanding. To address this knowledge gap, our investigation leveraged the MMTVdriven HER2+ orthotopic model in Wildtype (WT) and IL1α-/- mice. Our approach demonstrated tumor regression in IL1α-/- mice at the 2-week timepoint, while WT tumors grew exponentially. At 2 weeks, IL1α-/- mice exhibited an immune "hot" microenvironment with increased CD45+ immune cells, particularly CD11b+ myeloid, and CD8+ T cells. CD8+ cells in IL1α-/- mice showed enhanced anti-tumor cytokine production and proliferative capability, with …

Histories Of Stress: A Life Course Approach To Population Health In Late Medieval And Early Modern Berlin, Emily Brennan

Theses and Dissertations

Given our current climate crisis and urban population increases, researchers are increasingly interested in the health outcomes at the intersection of climate change and urbanization. Since climate change and urbanization affects human health in a variety of ways, more work is needed in diverse cultural contexts to understand temporal and geographic variations of such phenomena more fully. Using skeletal individuals from 13^th – 18^th century Berlin (n = 387), this project analyses demographic and health trends from the founding of the city in the late medieval period (c. 1200 – 1500) to the early modern period, when the …

The Effects Of High Fat Diet On Lipid Deposition In Skeletal Muscle, Alexander Huss

Theses and Dissertations

By the year 2030, almost 50% of adults in the United States are expected to be obese. Obesity has been shown to increase the risk of several chronic metabolic diseases, several cancers, and is associated with impaired skeletal muscle function and metabolism. Despite this, little it is known about the role of altered muscle lipid homeostasis, lipid droplet dynamics, and lipid droplet-mitochondrial interactions in contributing to muscle dysfunction in obesity. Therefore, we sought to investigate the impact of high-fat diet induced obesity on overall skeletal muscle lipid deposition, intramyocellular lipid droplet content and morphology, and lipid droplet-mitochondrial contact. Male C57/BL6 …

Investigating The Presence Of Bacterial Phytoplasma Disease In Grasses Of Central Texas And Their Associated Hemiptera, Danielle Rios

Masters Theses (Archived)

No abstract provided.