Digital Commons Network^™

The Role Of The Poly-N Repeat In The Plasmodium Falciparum Histone Acetyltransferase Protein, Pfgcn5, Kely Johana Rubiano Cardona

Arts & Sciences Graduate Student Theses and Dissertations

P. falciparum possesses the most AT-rich genome sequenced to date, with long AAT repeats coding for asparagines (N) in intragenic regions. As a result, nearly a quarter of its proteome is composed of proteins with poly-N repeats. Since the discovery of its genome, the function of these repeats has remained as one of the biggest mysteries in the biology of this parasite. Furthermore, it has long been known that proteins with N-rich domains aggregate easily, particularly during heat stress (HS). Given that the hallmark of this disease is recurrent febrile episodes, it is not well understood how the parasite survives …

Computational And Mathematical Modeling Of Microbial Community And Host Responses To Microbiota-Directed Complementary Foods Administered To Children With Acute Malnutrition., Steven J. Hartman

Arts & Sciences Graduate Student Theses and Dissertations

Globally, millions of children suffer from undernutrition, with stunting affecting 150 million and wasting nearly 50 million under five years old. Current interventions have shown limited effectiveness in mitigating long-term consequences such as stunted growth, cognitive deficits, and immune dysfunction. Through this body of work, I investigated the efficacy of a microbiota- directed complementary food (MDCF-2) as a next generation therapeutic food to combat childhood stunting. Across two randomized controlled trials involving Bangladeshi children with either moderate acute malnutrition or post-severe acute malnutrition, MDCF-2 significantly outperformed standard ready-to-use supplementary foods (RUSF), leading to significantly improved ponderal and sustained linear growth …

Low-Tech Seed Enhancement Technology Could Improve Seedling Establishment Of Longleaf Pine Understory Perennial Forbs, Madeline E. Schmuck, Michael C. Disilvestro, Danny J. Gustafson

Journal of the South Carolina Academy of Science

Reintroducing native plants into restoration and revegetation projects could increase plant species diversity, increase floral resources for pollinators, and positively affect trophic-level interactions in the community. Direct seeding in restoration projects has generally had poor success rates due to biotic and abiotic factors, leading to significant seed wastage of the already insufficient native seed supply. Seed balls (aka seed aggregates, seed bombs, and seed pellets) are a low-cost, low-tech seed enhancement technology. The seeds are encased in a soil and clay matrix, providing good seed-soil contact, controlling seed planting depth, nutrients, and protection from seed predators. We conducted a greenhouse …

Abundance, Distribution, And Shoaling Of Driftfishes And Allies (Scombriformes: Stromateoidei) In The Pelagic Gulf Of Mexico, Juliet Tretler

All HCAS Student Capstones, Theses, and Dissertations

The suborder Stromateoidei contains 80 species of mesopelagic fishes in five families distributed throughout temperate and tropical seas worldwide, including the Gulf of Mexico (Gulf hereafter). Mesopelagic fishes, especially those that spatially aggregate, serve as important forage items for commercially, recreationally, and ecologically important species of fish, marine mammals, and seabirds. However, knowledge of the ecology and trophic importance of stromateoid fishes in the Gulf is extremely limited. This study provides quantitative information on the species composition, abundance, distribution, and biomass contribution of the stromateoid species to the Gulf deep-pelagic fish assemblage, with comparison to “archetypal” mesopelagic fish families (e.g., …

Kabasura Kudineer Choornam, A Medicinal Polyherbal Formulation, Modulates Human Macrophage Polarization And Phagocytic Function, Asli Korkmaz, Duygu Ünüvar, Si̇nem Günalp, Derya Göksu Helvaci, Duygu Sağ

Turkish Journal of Biology

Background/aim: Kabasura kudineer choornam (KKC) is a polyherbal formulation of 15 ingredients. It has antiinflammatory and antimicrobial properties and are effective in managing the symptoms of H1N1 swine flu and COVID-19. However, its mechanism of action is not fully understood. In this study, we examined the effect of KKC on the polarization and function of primary human macrophages.

Materials and methods: Human monocyte-derived macrophages (M0 macrophages) pretreated with KKC extract were polarized into M1, M2a, or M2c subtypes. The expression of the M1/M2 polarization markers was analyzed using qPCR, flow cytometry, and ELISA, and the phagocytosis capacity of …

Different Hypoxic Response Of Human Cavii And Caenorhabditis Elegans Homologous Genes Cah-3, Cah-4, Cah-5, Sümeyye Aydoğan Türkoğlu, Aysu Bozkurt, Fatma Poyrazli, Derya Okuyan

Turkish Journal of Biology

Background/aim: A number of carbonic anhydrase (CA) family proteins have been implicated in cancer. They contribute to the hypoxic microenvironment. CAVII is often downregulated in colorectal carcinoma and it has been associated with increased tumor size, node metastasis, and adverse clinical outcomes. In this study, we aimed to investigate the effect of hypoxia on CAVII protein in human colon cancer and prostate cancer cells. In addition, the regulation of CAH genes in Caenorhabditis elegans was examined. These are homologous to CAVII in humans.

Materials and methods: CAVII expression was analyzed in different cell lines such as human colon cancer (SW480 …

Mir-9-5p Alleviates The Development Of Abdominal Aortic Aneurysm By Regulating The Differentiation Of Cd4+Il-10+T Cells Via Targeting The Crosstalk Between Nrf2 And Nf-Κb Signaling Pathways, Hongfu Liu, Jinyi Zhang, Lubin Li, Benxiang Yu, Chunlei Zhang, Wenqiang Niu, Yawen Cheng, Hengyang Dong, Yukun Zhang, Xinlin Luo, Yanlian Xiong, Yueming Wang

Turkish Journal of Biology

Background: Abdominal aortic aneurysm (AAA), a gradual segmental dilatation of the abdominal aorta, is associated with a high mortality rate. The pathophysiological molecular mechanisms underlying AAA remain unclear. In recent years, changes in miRNA levels have been reported to be involved in the development and treatment of AAA. This study aimed to investigate the potential targets and underlying mechanisms of miR-9-5p in attenuating AAA progression by modulating the inflammatory response.

Materials and methods: Biochemical kits were used to measure the levels of inflammatory factors, antioxidant enzyme activity, and serum oxidative stress in normal and AAA model mice. miR-9-5p overexpression was …

Lactic Acid Bacteria Alleviate Neuronal Excitotoxicity And Extend Caenorhabditis Elegans Lifespan, Bao Le, Thi Nhat Hong Nguyen, Seung-Hwan Yang

Turkish Journal of Biology

Aim: Neuronal cell death plays a critical role in the development of neurological disorders associated with aging. This study aimed to evaluate the beneficial effects of heat-killed lactic acid bacteria (hkLAB) on neuroblastoma cells and Caenorhabditis elegans.

Materials and methods: We pretreated heat-killed Lactobacillus fermentum CNU384 (hkCNU384), L. brevis CNU386 (hkCNU386), L. helveticus CNU395 (hkCNU395), and L. paracasei CNU396 (hkCNU396) at a concentration of 10⁹ CFU/mL to investigate their neuroprotective effects on glutamate-induced SH-SY5Y cells and their impact on the lifespan of 6-hydroxydopamine (6-OHDA)-induced C. elegans.

Results: Our findings indicate that hkCNU395 and hkCNU396 protected against glutamate-induced cell death …

Understanding The Effects Of Genetic Variation On Maize And Pennycress Root System Architectures And Their Interaction With Nitrogen, Alexander Euway Liu

Arts & Sciences Graduate Student Theses and Dissertations

Roots are a critical yet hidden part of plants, providing physical support and access to resources such as nutrients and water. The development of a plant’s root system across time and space is referred to as root system architecture, which influences the effectiveness of resource capture. In modern agriculture, applications of nitrogen fertilizers are critical to maintain high yield. However, up to 70% of applied nitrogen is not utilized by the plant and escapes into waterways and the atmosphere, causing environmental harm. Efficient nitrogen uptake is limited by the ability of the plant to access and absorb nitrogen through its …

Thionine Modulates Tau Phosphorylation In An Alzheimer’S Disease Cell Culture Model, Seda Önder, Kevser Bi̇beroğlu, Özden Tacal

Turkish Journal of Biology

Background/aim: Tau protein, which is crucial for sustaining the cytoskeletal network by assisting microtubule construction, contributes significantly to the pathophysiology of Alzheimer’s disease (AD). The hyperphosphorylation of tau causes it to detach from microtubules (MTs), leading to the formation of neurofibrillary tangles (NFTs) in neurons, which ultimately results in cell death. Thionine (TH), a cationic phenothiazine-structured compound, has been the topic of extensive research due to its interesting physicochemical properties. It is a common biological dye, especially useful in histology due to its strong affinity for biological membranes. Furthermore, TH serves as a photosensitizer in phototherapy. It has a phenothiazine …

Chelidonium Majus L.-Containing Gel May Improve Diabetic Wound Healing By Modulating Mmp-2, Mmp-9, And Collagen Levels, Kaan Kaltalioğlu, Eli̇f Naz Gürsoy, Barbaros Balabanli, Zeki̇ Aytaç, Şule Coşkun Cevher

Turkish Journal of Biology

Background/aim: Delayed wound healing in diabetic patients is a significant complication that reduces quality of life, prompting the continuous investigation of new therapeutic agents. This study designed to explore the dose-dependent effects of different parts of Chelidonium majus L. (CM), a medicinal plant traditionally used for skin disorders, on diabetic skin wounds.

Materials and methods: In diabetic rats, full-thickness excisional wounds were formed. CM-containing gels (aerial parts at 3%, 6%, 9% and root at 0.5%, 1%, 1.5%) were developed and applied to the wounds. After the treatment period, the rats were sacrificed, and wound healing activity was assessed macroscopically, histopathologically, …

Examining Associations Between Street Vegetation And Child Firearm Violence At Microgeographic Locations In 3 Us Cities: A Case-Control Study, Zihan Lin, Gregory A. Wellenius, Jonathan Jay

Biological, Geological, and Environmental Faculty Publications

Background: Firearm violence is a leading cause of death among U.S. children under age 18. Urban vegetation, a vital component of the living environment, has been found to influence firearm violence, yet the relationship between different types of street vegetation and firearm violence with children as the victim at the microgeographic scale remains unclear.

Methods: We analyzed 2316 child firearm assault incidents from Los Angeles, New York City, and Philadelphia from 2015 to 2021. Using a spatial case-control approach, we matched assault locations with control locations within 1-km. For each location, we applied deep learning algorithms to Google Street View …

Lysosomes As Gatekeepers: How Lic1-Mediated Trafficking Regulates Angiogenesis And Vascular Morphogenesis, Dymonn Johnson

Arts & Sciences Graduate Student Theses and Dissertations

Dynein cytoplasmic 1 light intermediate chain 1 (LIC1, DYNC1LI1) is a core subunit of the dynein motor complex that plays a critical role in cytoplasmic cargo trafficking, including Rab-mediated endosomal recycling and lysosomal degradation. LIC1 interacts with various cargo adaptors, such as RILPL1 and RILPL2, to regulate these processes, and defects in this gene are predicted to impair dynein motor function, Rab binding, and lysosomal trafficking. Here, we identified a dync1li1 zebrafish mutant with a premature stop codon at the exon 12/13 splice acceptor site, that exhibits increased angiogenesis. In vitro, LIC1-deficient human endothelial cells show elevated cell surface levels …

Transcription Fidelity In The Face Of Oxidative Damage, Eastilan Gyiwah Appiah

Theses and Dissertations

It is very important that the process of transcription is correctly carried out in the cell for the faithful expression of the genetic code. However, should mistakes happen, they can result in transcription errors which interfere with the protein-making machinery of the cell. This will result in accumulation of proteins and dysfunctional proteins that have the potential of causing diseases like Alzheimer’s. Oxidative damage caused by hydrogen peroxide is known to cause transcription errors in organisms like yeast. It is therefore important to investigate the extent to which hydrogen peroxide can damage cells.

Application And Comparison Of Satellite-Derived Sea Surface Temperature Gradients To Identify Seasonal And Interannual Variability Off The California Coast: Preliminary Results And Future Perspectives, Jorge Vazquez-Cuervo, Marisol García-Reyes, David S. Wethey, Daniele Ciani, Jose Gomez-Valdes

Faculty Publications

The application of satellite-derived sea surface temperature in coastal regions is critical for resolving the dynamics of frontal features and coastal upwelling. Here, we examine and compare sea surface temperature (SST) gradients derived from two satellite products, the Multi-Scale Ultra-High Resolution SST Product (MUR, 0.01° grid scale) and the Operational SST and Ice Analysis (OSTIA, 0.05° grid scale), available through the Group for High Resolution SST (GHRSST). Both products show similar seasonal variability, with maxima occurring in the summer time frame. Additionally, both products show an increasing trend of SST gradients near the coast. However, differences exist between the two …

Radioactive Contamination And Climate Warming Affect Physiological Performance Of Chornobyl Barn Swallows, Zbyszek Boratyríski, Timothy Mousseau, Anders Pape Møller

Faculty Publications

Global warming and degradation of natural habitats are the two main factors causing ecophysiological stress on individuals and risk for biodiversity. Hyperthermia is a common response to stress in homeothermic animals, in particular to heat, pathogens and environmental contamination. Resilience of biological systems to global warming may be deteriorated in polluted habitats. Here we investigated how body temperature of a wild bird, the barn swallow (Hirundo rustica), responded to global warming while simultaneously exposed to radioactive contamination from the Chernobyl accident. Our results showed that both high air temperatures (t = 15.55, df = 335, p <  0.0001) and elevated environmental radioactive contamination (t = 5.18, df = 8.09, p = 0.0008) increased internal body temperature of individuals. The additive effect suggests that birds might suffer hyperthermia in locally contaminated habitat (1.47% body temperature increase) while simultaneously exposed to globally rising temperatures (1.95% body temperature increase), potentially reducing the fitness of individual and the maintenance of breeding colonies. The cumulative and interactive negative effects of multiple stressors, such as those emerging from increasing habitat degradation and climate change, will likely contribute to biodiversity losses globally.

Antifungal Peptides From Casein Milk Of Etawa Crossbreed (Capra Hircus) As Biopreservation Agent For Bread And Molecular Docking Studies, Dian Riana Ningsih, Winarto Haryadi, Rachma Wikandari, Tri Joko Raharjo

Karbala International Journal of Modern Science

Bread without peptide fraction treatment started to grow mold on the fourth day with a total of 24x10⁷ fungi colonies/ml. Meanwhile, the addition of peptide fractions GMC5, GMC6, GMC7, and GMC8 effectively preserved bread for up to 4 days, indicated by no mold growth. The best treatment was the GMC6 peptide fraction on day 8 which grew the least amount of fungus at 7x10⁷ spores/ml. Peptide interaction with the CaATPase receptor Aspergillus sp. was carried out using HADDOCK 2.4. The 3D CaATPase structure prediction resulted in a model with good structural quality. This was supported by residues in …

Dopaminergic Neurons In The Zebrafish Subpallium Belong To The Extended Medial Amygdala, Daniel Armbruster, Thomas Mueller, Wolfgang Driever

Department of Biology Faculty Scholarship and Creative Works

The amygdala is a heterogeneous, multinuclear telencephalic structure critical for motivated and emotion-related behaviors in vertebrates. In ray-finned fish (Actinopterygii) like the teleost zebrafish, a telencephalic outward-growing process called eversion makes defining amygdaloid territories particularly challenging. Teleosts are also peculiar in that they develop numerous dopaminergic (DA) neurons in the subpallium, while in tetrapods, such populations are less prominent or appear only transiently. To shed light on the organization of the amygdala in teleosts, we pursued an evolutionary developmental approach focusing on the topological origin of subpallial DA neurons. Specifically, we analyzed the distribution of tyrosine hydroxylase (Th) in conjunction …

Indirect Dna Transfer To Duct Tape Rolls Stored In Cars, Yuching Chung

Student Theses

This project investigated the accumulation of DNA on duct tape rolls stored in cars. Specifically, we analyzed samples recovered from three areas (the inside, outside, and flat sides) of unused duct tape stored under the driver's seat and trunk of cars for seven days. Twelve volunteers were recruited, resulting in 64 DNA samples from 12 cars. We evaluated DNA quantities and STR genotyping outcomes after amplification with the GlobalFiler™ kit. On average, the DNA yields from under the driver's seat were higher than from the trunk, but the difference was not significant. The inside of the tape roll yielded significantly …

The Ring-Finger Ubiquitin E3 Ligase Rfel1 Targets Wheat Npr3 For Degradation To Confer Broad-Spectrum Resistance Against Biotrophic Fungal Pathogens, Liuhui Qiao, Kunpu Zhang, Jinyan Li, Ziming Zhang, Xiao Sun, Huiyun Liu, Ziyue Li, Nannan Ni, Ximei Ma, Jianhui Zhao, Guangwei Li, Xiaohuan Jin, Wenming Zheng, Daowen Wang, Zheng Qing Fu, Huan Wang

Faculty Publications

No abstract provided.

Silicon Is The Next Frontier In Plant Synthetic Biology, Aniruddha Acharya, Kaitlin Hopkins, Tatum Simms

Faculty Publications - Biological Sciences

Silicon has a striking similarity to carbon and is found in plant cells. However, there is no specific role that has been assigned to silicon in the life cycle of plants. The amount of silicon in plant cells is species specific and can reach levels comparable to macronutrients. Silicon is used extensively in artificial intelligence, nanotechnology, and the digital revolution, and thus can serve as an informational molecule such as nucleic acids. The diverse potential of silicon to bond with different chemical species is analogous to carbon; thus, it can serve as a structural candidate similar to proteins. The discovery …

Restoration At The Intersection Of Science And Outreach-The Working Woods Learning Forest, Katharine L. Stuble, David J. Burke, Samuel C. Harbol, Chad Knisely, Jessica Miller Mecaskey, Alexa S. Wagner, Michael Watson, Kevin E. Mueller

Biological, Geological, and Environmental Faculty Publications

Botanical gardens and arboreta have enormous (if often under-realized) potential to increase understanding of restoration as a predictive science while simultaneously serving as platforms promoting large-scale restoration by public and private stakeholders. Public gardens often have deep histories of both research and outreach and, increasingly, engagement in restoration efforts. As a team of researchers and practitioners, we share our experiences using a forest management manipulation at the Holden Arboretum for both research and outreach. Forest management is a key tool for enhancing biodiversity and ecosystem services in young forests. Known as the Working Woods Learning Forest, this restoration simultaneously serves …

Sex, Stress And Hormones : The Role Of Modifiable Risk Factors In The Kinetics Of Alzheimer’S Disease, Hannah Marie Edwards

Arts & Sciences Graduate Student Theses and Dissertations

Alzheimer’s Disease (AD) is a neurodegenerative disease hallmarked by the presence of amyloid- plaques and tau tangles in the brain. The process of the disease begins decades prior to the onset of symptoms and is thought to be driven first by a buildup of amyloid- peptide in the extracellular space, triggering a cascade of pathology and symptomology culminating in loss of cerebral volume and cognitive impairment. Women are diagnosed with AD at a rate 2/3 higher than their male counterparts, even when controlling for age. While most driving factors of the disease are thought to be genetic, roughly 40% of …

Applying Transcriptomics For Technology Development And Conservation In North American Marine Organisms, Cory Von Eiff

Dissertations

RNA biology is a rapidly expanding field, with many avenues of discovery among marine organisms. In this study, we analyze both mollusks and sawfish. First, we perform an evaluation of sRNA biogenesis pathways throughout Mollusca, with emphasis on the easter oyster, Crassostrea virginica. Understanding these molecules prescribes RNAi-based gene silencing approaches, benefiting genetic investigation and biotechnology. Similar to other animal groups, mollusks have conserved microRNAs (miRNAs), with some shared with ecdysozoans and deuterostomes; however, there is no evidence of an endogenous small interfering RNA (siRNA) pathway. These results suggest that long double-stranded RNA (dsRNA)-based RNAi is not appropriate for gene …

Using Published Undergraduate Biomechanics Research On Hydra Mouth Opening To Train Undergraduates, Stephen Hackler, T. Goel, Jonah Pacis , '25, Eva-Maria S. Collins

Biology Faculty Works

Biophysics research is exciting because physical approaches to biology can provide novel insights, and it is challenging because it requires knowledge and skills from multiple disciplines. We have developed an undergraduate biophysics laboratory module that teaches fundamental skills such as time-lapse microscopy, image analysis, programming, critical reading of scientific literature, and basics of scientific writing and peer review. The module is accessible to students who are familiar with introductory statistics, cell biology, and differential calculus. We used published research on the biomechanics of Hydra mouth opening as a framework because it describes a stunning biological phenomenon: Hydra, a freshwater …

Mosquitoes: The 5 C’S Of Developing Disease- Commensals Changing To Consequential Pathogens, Alan L. Gillen, Caleb Mast, Robert Braden Somerville

Faculty Publications and Presentations

Hotter, longer summers and changing weather patterns in the United States are bringing more than just sweat and discomfort. In May 2025, a summer heat wave of 107⁰F hit Austin, Texas, and in humid Houston and San Antonio, Texas, temperatures felt over 100⁰ for several days. Normally, these temperatures don’t come until July and August. With temperatures reaching these marks early and heavy rains coming, mosquito activity and ranges expand. Many state and federal health officials report a rise in mosquito-borne illnesses across the US and globe in the last five years.

Cultivation Of Botryococcus Braunii For The Production Of Hydrocarbons Suitable For Fuel Use, Bryan C. Carroll

All Theses

Energy security, rural poverty, and climate change are pressing issues of our time. Biofuels provide a solution to these issues, with a focus on sustainable aviation fuel, SAF, due to compatibility with aircraft infrastructure and energy density. This research aims to review and produce knowledge about a specific microalga, Botryococcus braunii, for its potential for SAF. First a literature review on the process was conducted followed by an experimental study on the impact of aqueous media and inorganic carbon its growth and hydrocarbon content. The literature review found the process consists of cultivation followed by lipid extraction or hydrothermal …

The Molecular And Behavioral Characterization Of The Murine Cre – Loxp Skeletal Muscle Synthesized Bdnf Knockout Model, Asha E. Rustad

All NMU Master's Theses

Brain derived neurotrophic factor (BDNF) is a neurotrophin essential for supporting the growth, differentiation, and health of neurons within the central and peripheral nervous systems. BDNF is also a member of the myokine family, where muscle synthesized-BDNF (msBDNF) is thought to facilitate the crucial bi-directional communication between the motor neuron and the muscle fibers it innervates. Since 2008, the Ottem Laboratory has investigated the role of msBDNF by employing Cre/LoxP recombinase technology to selectively delete the BDNF coding region within skeletal muscle of mice. This approach generates animals with either heterozygous or homozygous deletions of msBDNF, as well as BDNF …

Raptors As Secondary Dispersers Of Mycorrhizal Fungal Spores, Joseph Anderson

Electronic Theses and Dissertations

Animals aid fungal dispersal by consuming fruiting bodies (e.g., truffles) and depositing spores elsewhere. Predators can act as secondary dispersers by preying on small mammals that eat truffles, although it is unclear how this dispersal may vary among species of raptors (hawks and owls) and fungal taxa. We experimentally fed four truffle taxa (with spores varying in size and wall thickness) to six raptor species (with differing gut morphology and acidity) to assess how spore viability and retention time may change between raptor casts and feces. Viability in smaller spores was more negatively affected by acidity compared to larger spores …

Breaking Confirmatory Spells By Implementing Research- Integrated Cures, J. A.C. Vriezen

Biological Sciences: Faculty Publications

Differences in economic and social growth and academic equity, experi ences, and opportunities have left an achievement gap in STEM for underprivileged students. Course-based Undergraduate Research Experiences (CUREs) have attempted to answer these inequalities by leveling the playing field or by offering course-based research opportunities with minimal requirements for background knowledge. When we ask novel questions, more students get the experience of performing research, which lowers thresholds to pursue research and increases participation. Although the learning outcomes have been largely positive, there is a concern that many CUREs are still too scaffolded. In contrast, I propose to develop exploratory, hypothesis-driven …