Life Sciences Commons^™

Building A Coordinated Framework For Research And Monitoring In Large-Scale International Marine Protected Areas: The Ross Sea Region As A Model System, Cassandra Brooks, Sharon Stammerjohn, Grant Ballard, Alice K. Duvivier, Eileen Hofmann, Michelle Larue, Cara Nissen, Alexander J. Orona, B. Jack Pan, Annie E. Schmidt, Nathan Walker, George M. Watters, John Weller

CCPO Publications

To fulfill their conservation potential and provide safeguards for biodiversity, marine protected areas (MPAs) need coordinated research and monitoring for informed management through effective evaluation of ecosystem dynamics. However, coordination is challenging, often due to knowledge gaps caused by inadequate access to data and resources, compounded by insufficient communication between scientists and managers. We propose to use the world's largest MPA in the Ross Sea, Antarctica as a model system to create a comprehensive framework for an interdisciplinary network supporting research and monitoring that could be implemented in other remote large-scale international MPAs. Our proposed framework has three key components: …

Epigenetic Mechanism Of Ebp1 In Nlrp-Dependent Development, Summer Reign Moore

Graduate Theses/Dissertations

ErbB3-binding protein 1 (EBP1) helps regulate gene expression through various epigenetic modifications and is crucial for embryotic development. NLRP2 and NLRP7 are more commonly known for their roles in the immune system, however, recent research has implicated NLRP2 and 7 as critical factors in embryonic development. EPB1, NLRP2, and NLRP7 dysfunction is a known cause of recurrent miscarriages and other developmental diseases, including infertility. NLRP2 and NLRP7 are also known to affect the levels of DNA methylation, despite that they are located exclusively in the cytoplasm. However, EBP1 can be located in the nucleus and cytoplasm, and is known to …

Heterogeneity Of Nitrogen Fixation In The Mesopelagic Zone Of The South China Sea, Siqi Wu, Xianhui Sean Wan, Moge Du, Xirong Chen, Corday R. Selden, Mar Benavides, Sophie Bonnet, Carolin R. Löscher, M. Robert Hamersley, Margaret R. Mulholland, Xiuli Yan, Shuh-Ji Kao

OES Faculty Publications

Biological dinitrogen (N₂) fixation, the energetically expensive conversion of N₂ gas to ammonia, plays an essential role in balancing the nitrogen budget in the ocean. Accumulating studies show detectable N₂ fixation rates below the euphotic zone in various marine systems, revealing new insights of marine N₂ fixation. However, the reported rates are highly variable and frequently fall close to detection limits, raising the question of the ubiquity and significance of N₂ fixation in the global dark ocean. Using highly sensitive isotopic labeling incubation including a set of control incubations, we confirm the occurrence of mesopelagic N₂ fixation in the South …

Cd46 Isoforms And Viral Receptor For Adenovirus Type 64d, Corina Stasiak

Honors Theses

Adenovirus Type 64 (Ad.64) belongs to the adenovirus subgroup D, which causes epidemic keratoconjunctivitis (EKC), otherwise known as viral pink eye. There is currently no known effective treatment for EKC. Membrane Cofactor Protein (CD46) is an integral membrane glycoprotein that, in previous studies, has been identified as a protein receptor for the closely related Ad.37. It has been determined that Ad.64 uses CD46 as a receptor on the cell surface in HeLa cells. CD46 is alternatively spliced when expressed to have different isoforms of interest, including the BC and C isoforms. Certain cell types, like A549 lung carcinoma cells, express …

Cd46 Is A Protein Receptor For Human Adenovirus Type 64, Alexander Michael Robertson

Honors Theses

Adenoviruses are important gene delivery vectors and causative agents for a variety of human diseases such as the common cold and gastrointestinal infections. Human adenovirus type 64 (Ad64; formerly 19c) and type 37 are associated with epidemic keratoconjunctivitis. Based upon its high homology and similar disease tropism to Ad37, we hypothesized that Ad64 would have the same protein receptor, CD46 (membrane cofactor protein), as Ad37. We show that a recombinant Ad64 containing an enhanced Green Fluorescent Protein transgene (Ad64.eGFP) enters Chinese hamster ovary cells expressing human CD46 (CHO-CD46) on the surface. Entry into human cervical carcinoma (HeLa) cells is increased …

Development Of A Diaryl Oxazole-Based Cleavable Linker For Peptides, Evan Wolff

Honors Theses

The development of new cleavable linkers increases the diversity of compatible conditions for peptide discovery platforms. Potential applications for these linkers include high-throughput pharmaceutical candidate screening when utilized in Peptide Encoded Libraries (PELs). This thesis describes the development of a bifunctional diaryl oxazole-based cleavable linker that may be incorporated into compounds through Solid-Phase Peptide Synthesis (SPPS). This oxazole-based linker may be rapidly cleaved by cerium ammonium nitrate in aqueous conditions and is compatible with most natural amino acids and a variety of unnatural amino acids. This linker represents the first single-electron oxidant labile linker described to our knowledge and it …

Structural Phylogenetics Of A Family Dna Polymerases, Yagmur Bingul

Honors Theses

The transition from the RNA to the DNA world stands as an important event, demanding the emergence of enzymatic activities for DNA precursor synthesis, retro-transcription of RNA templates, and replication of single and double-stranded DNA molecules. The distribution of protein families associated with these activities across the three domains of life—Archaea, Eukarya, and Bacteria—adds layers of complexity to the narrative. While Archaea and Eukarya often share similar protein structures, structural biology shows homologous, but distinct, structures in Bacteria. On the other hand, viral polymerases emerge as a crucial part of genome replication and transcription. Their versatility, including RNA-dependent RNA polymerase, …

Assessing Evolution Of Reproduction Traits Along Seasonal Transitions And Latitudinal Gradients In An Invasive Species Of Fruit Fly, Zaprionus Indianus, Ansleigh Gunter

Honors Theses

This thesis examines the reproductive traits of Zaprionus indianus, an invasive species to the United States, to assess the possibility of rapid evolution. Significant differences in fecundity and diapause incidence have been seen in other Drosophilid fly species across the seasonal transition, from early to late season, and across the latitudinal gradient, from north to south. For this reason, fecundity, the reproductive ability of a female fly, and diapause incidence, a stress-induced reproductive arrest, were selected as variables of choice. Field collections and experiments revealed unexpected patterns in fecundity and diapause incidence, challenging initial hypotheses. While no significant differences in …

Heterocycles As Peptide-Based Cleavable Linkers, John Blobe

Honors Theses

As cancer cases continue to rise, the need for advancing the treatment options for cancer is ever increasing. Current cancer therapeutics, while effective at treating localized cancers and a fraction of advanced cancers, generally lack the specificity needed to target more advanced cancers. Recent advancements in cancer treatments have leveraged antibodies to target certain cancers. A class of drugs that utilize antibodies to deliver anti-cancer therapy preferentially to cancer cells, termed antibody-drug conjugates (ADCs), have been quite effective in treating certain advanced forms of certain cancers. These ADCs could be more effective if they could allow for the facile release …

Functionalized Gold Nanoparticles And Halogen Bond Interactions With Neonicotinoid Pesticides, Molly Mccuen “Mackey” Sherard

Honors Theses

Neonicotinoid (NN) pesticides have emerged globally as one of the most widely used agricultural tools for protecting crops from pest damage and boosting food production. Unfortunately, some NN compounds, such as extensively employed imidacloprid-based pesticides, have also been identified as likely endangering critical pollinating insects like honey bees. To this end, NN pesticides pose a potential threat to world food supplies. As more countries restrict or prohibit the use of NN pesticides, tools are needed to effectively and quickly identify the presence of NN compounds like imidacloprid on site (e.g., in storage areas on farms or pesticide distribution warehouses). This …

The Effects Of Parasitoid Wasps On The Intra- And Interspecific Competition Of Zaprionus Indianus, Camille R. Walsh-Antzak

Honors Theses

Understanding the mechanisms underlying the success of biological invasions is essential to employ effective prediction and management strategies. The release of natural enemies in invaded regions (enemy release hypothesis) and increased competitive ability are major hallmarks of invasive species, however, these two processes are rarely studied within the same context. Here, we examined the role of ERH in influencing the competitive outcomes of an invasive insect pest, the African fig fly (Zaprionus indianus). In Virginia orchards, Z. indianus repeatedly outcompetes co-occurring drosophilid species. However, the mechanisms underlying the success of Z. indianus are poorly understood. Parasitoid wasps specializing in Camill …

Cd46 Interaction With Adenovirus Type 64, A Causative Agent For Viral Pink Eye, Hanglin (Henry) Zhu

Honors Theses

Human adenovirus type 64 (Ad64) is a causative agent of contagious viral pink eye. We do not understand why Ad64 causes eye infections. One likely reason is the presence of a receptor molecule on the exposed surface of eye cells, but not other cells. Ad64 binds to a protein called CD46 on the cell surface. We aim to visualize how CD46 binds to the surface of Ad64. I mixed the extracellular portion of CD46 with purified Ad64 virus, then visualized it using negative stain transmission electron microscopy. In order to gain insight into how the virus binds CD46, we used …

Low Energy Availability, Disordered Eating, Exercise Dependence, Injury Prevalence, And Fueling Habits In Female Crossfit® Participants, Alyssum Reno-Smith

Dissertations

Disordered eating (DE) is primarily observed in endurance athletes and sports with aesthetics emphases. The prevalence of DE in resistance trained individuals, particularly CrossFit^®, is not well understood. CrossFit® promotes a culture encouraging strong, athletic, or muscular bodies, and both CrossFit® and endurance athletes aim to achieve a low body fat percentage to improve performance. This may lead to body dissatisfaction, exercise dependence (EXD), and/or DE behaviors, which may contribute to Relative Energy Deficiency in Sport (REDs). This cross-sectional study investigated DE prevalence and relationship with EXD risk, body dissatisfaction, and fueling habits in female CrossFit® only (CO) …

Chitin-Enriched Insect Frass Fertilizer As A Biorational Alternative For Root-Knot Nematode (Meloidogyne Incognita) Management, James Kisaakye, Dennis Beesigamukama, Solveig Haukeland, Sevgan Subramanian, Paul K. Thiongo, Segenet Kelemu, Chrysantus M. Tanga

All Peer-Reviewed Publications

Root-knot nematodes (Meloidogyne spp.) are serious pests of most food crops, causing up to 100% yield loss. Nevertheless, commercial nematicides are costly and harmful to the environment. While the nematicidal potential of crustacean and synthetic chitin has been demonstrated globally, research on the potential of insect-derived chitin for nematode control has received limited attention. Here, seven chitin-fortified black soldier fly frass fertilizer extracts (chFE) were assessed for their suppressiveness of Meloidogyne incognita and impacts on spinach growth in comparison with a commercial nematicide using in vitro and in vivo bioassays. The performance of chFE and control treatments was assessed by …

Tigra Scientifica, Full Issue

Tigra scientifica

Tigra scientifica, showcasing the outstanding work by Clemson University students in the Creative Inquiry course Popular Science Journalism. Science and technology shape our world in profound ways — from the rise of space tourism to the rapid development of new medical treatments. In a democracy, communicating science is essential for informed debate and decision-making, a responsibility these students have embraced with energy and skill. The magazine began in Spring 2011 under Holly Tuten, Ph.D., who founded the CI course to pass along her passion for science writing. Since then, more than 200 students from 14 majors across five colleges have …

Development Of Halalan Tayyiban Plant-Based Cheese Formulations, Hasna B. Mazalana, Mas M. Rambli, Syazana A. Lim, Beston F. Nore

ASEAN Journal on Science and Technology for Development

The worldwide cheese production is dominated by animal milk sources with various industrial procedures, including animal rennet. There is a need to diversify the animal-based dairy products into plant-based one, not only to nurture the halalan tayyiban concept for Muslims, but also to accommodate the dietary restriction of some consumers. The objective of this work is to formulate a cheese type derived from plant-based milk with permissible ingredients to create a product for Muslim and non-Muslim consumers. In this study, we explored the use of conventional and non-conventional cheese-making procedures. A total of four experimental formulations (EF1-4) combinations were conducted …

Investigating Genome Evolution Through Reduction In Heritable Endosymbiotic Bacteria, Mariam Topchyan, Mikail Bala, Riley Fanus, Kevin P. Johnson, Bret M. Boyd

Graduate Research Posters

Background: Genome reduction is a common mode of evolution that has played a fundamental role in diversification across all kingdoms of life, and is key to the evolution of heritable bacteria found in insects. However, the reduction process may leave behind gene fragments and non-functional elements that may still be interpreted as intact genes, limiting accurate genome annotation. Motivated by five highly reduced genomes of endosymbiotic bacteria in the genus Enterobacter, this study will investigate the role fragmented genes may play in false gene discovery.

Methods: Predicted protein sequences of five bacterial endosymbiont genomes were clustered into orthologous groups along …

Large T Antigen Mediated Target Gene Replication Improves Site-Specific Recombination Efficiency, Zening Wang, Chuan Chen, Xin Ge

Faculty, Staff and Student Publications

With advantages of high-fidelity, monoclonality and large cargo capacity, site-specific recombination (SSR) holds great promises for precise genomic modifications. However, broad applications of SSR have been hurdled by low integration efficiency, and the amount of donor DNA available in nucleus for SSR presents as a limiting factor. Inspired by the DNA replication mechanisms observed in double-stranded DNA virus SV40, we hypothesized that expression of SV40 large T antigen (TAg) can increase the copy number of the donor plasmid bearing an SV40 origin, and in consequence promote recombination events. This hypothesis was tested with dual recombinase-mediated cassette exchange (RMCE) in suspension …

One-Step Production Of Fully Biotinylated And Glycosylated Human Fc Gamma Receptors, Minhyo Kang, Zening Wang, Xin Ge

Faculty, Staff and Student Publications

Initiating and regulating humoral immunity, Fc gamma receptors (FcγRs) have been identified both as therapeutics and as drug targets, and thus production of biologically active FcγRs is highly demanded for biopharmaceutical development. Focusing on low-affinity FcγRs IIA (131H/R allotypes), IIB, and IIIA (176F/V), this study used human 293-F cells to achieve correct post-translational modifications (PTMs) including biotinylation, N-glycosylation, and disulfides. Approaches involving co-expression of FcγR-AviTag and Escherichia coli biotin ligase BirA, endoplasmic reticulum retention, stable and transient transfections, and optimization of transgene ratio were investigated. Protein electrophoresis under reducing and non-reducing conditions, enzymatic deglycosylation, streptavidin pull-down assays, and binding kinetic …

From The Ground Up: A Complex Systems Approach To Climate Change Adaptation In Agriculture, Karen Buchsbaum

Antioch University Dissertations & Theses

Climate change presents an unprecedented challenge to global agriculture and food security. Small farms are especially vulnerable to the local impacts of large-scale drivers of change. Effective adaptation in agriculture requires working across scales, and geographic, political, and disciplinary boundaries to address barriers. I use elements of case study, agent-based modeling and serious games, to design a model of farmer decision-making using the sociocognitive framework of climate change adaptation. I examine how adaptation functions as a process, how complex dynamics influence farmer behavior, and how individual decisions influence collective behavior in response to climate change. This novel approach to adaptation …

Navigating The Noise: Implications Of Increasing Ship Noise For An Arctic Ocean Soundscape, Andrea Lynn

Antioch University Dissertations & Theses

There is no quiet way to churn water. Noise pollution caused by ships is increasing in the Arctic Ocean as sea ice melts, creating more open channels for vessels. This study provides a glimpse into the sources and balance of sounds in a portion of the Arctic Ocean soundscape surrounding the Norwegian archipelago of Svalbard. Characterization of the soundscape provides essential data as the region quickly transforms. This study also considers human perceptions of underwater ocean noise and its impacts in the region, and it reviews current ocean policy, suggesting mitigation strategies and ways forward. Before the rapid development of …

Influence Of Landscape Characteristics On Eastern Gray Treefrog (Hyla Versicolor) Occupancy Within Managed Forests Of Pennsylvania And Virginia, Susanna G. Sousa

Antioch University Dissertations & Theses

Understanding the characteristics that influence amphibian occupancy within forest ecosystems is necessary for effective conservation and management. My study focused on how eastern gray treefrog (Hyla versicolor) occupancy is influenced by environmental attributes quantified at various spatial extents. From May through July 2020 and 2021, we deployed autonomous recording units at 986 unique locations within managed forests in Pennsylvania and Virginia. Landcover class and road density were evaluated around each sampling location at ten spatial extents between 60 and 4000 m. Additionally, I measured aspect, elevation, soil drainage class, distance to nearest wetland, and basal area at each …

Inservice Needs Of Selected Arkansas Agriculture Teachers Related To Precision Agriculture, Henry O. Akwah, Donald M, Johnson, George W. Wardlow, Cengiz Koparan, Aurelie Poncet

Agricultural Education, Communications and Technology Faculty Publications and Presentations

The purpose of this study was to determine selected Arkansas school-based agricultural education (SBAE) teachers’ perceptions of the importance, ability to teach, inservice needs, and barriers relative to incorporating precision agriculture (PA) into their programs. A non-probability sample (n = 44) of teachers participating in an introductory PA workshop completed the survey. Teachers rated each of the  PA competencies as being above average or high importance but rated their ability to teach each competency as being none or below average. When competencies were grouped into seven PA topics, teachers had inservice needs for each topic with mean weighted discrepancy …

In Vitro Assessment Of The Anti-Biofilm Effectiveness Of Copper And Zinc Enhanced Borate Bioactive Glass Using Processed Microscopic Images, Sarah Fakher, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

The escalating burden of nosocomial infections presents a formidable challenge to healthcare systems worldwide, leading to increased morbidity, prolonged hospital stays, and elevated healthcare costs. These infections are often resistant to conventional antibiotic therapies due to their association with biofilms which contribute to the persistence and resistance of pathogens. In addressing the challenge of biofilm-associated nosocomial infections, borate bioactive glasses (BBGs) have emerged as promising biomaterials. Doping these glasses with antimicrobial metals could potentially harness their antibacterial properties to prevent biofilm formation. This study undertakes a rigorous evaluation of the anti-biofilm efficacy of copper and zinc-doped BBGs by employing processed …

The Impacts Of Anthropogenic Activity And Climate Change On The Formation Of Harmful Algal Blooms (Habs) And Its Ecological Consequence, Zhangxi Hu, Aifeng Li, Zhun Li, Margaret R. Mulholland

OES Faculty Publications

No abstract provided.

Nitrogen Uptake Rates And Phytoplankton Composition Across Contrasting North Atlantic Ocean Coastal Regimes North And South Of Cape Hatteras, Yifan Zhu, Margaret R. Mulholland, Peter W. Bernhardt, Aimee Renee Neeley, Brittany Widner, Alfonso Macías Tapia, Michael E. Echevarria

OES Faculty Publications

Understanding nitrogen (N) uptake rates respect to nutrient availability and the biogeography of phytoplankton communities is crucial for untangling the complexities of marine ecosystems and the physical, biological, and chemical forces shaping them. In the summer of 2016, we conducted measurements of bulk microbial uptake rates for six ¹⁵N-labeled substrates: nitrate, nitrite, ammonium, urea, cyanate, and dissolve free amino acids across distinct marine provinces, including the continental shelf of the Mid-and South Atlantic Bights (MAB and SAB), the Slope Sea, and the Gulf Stream, marking the first instance of simultaneously measuring six different N uptake rates in this dynamic region. …

Diel Vertical Migration Rates Of The Dinoflagellate Species Margalefidinium Polykrikoides In A Lower Chesapeake Bay Tributary, S. Clayton, Jacqueline B. Chrabot, Michael Echevarria, Leah Gibala-Smith, Kathryn Mogatas, Peter Bernhardt, Margaret R. Mulholland

OES Faculty Publications

Margalefidinium polykrikoides is a mixotrophic dinoflagellate harmful algal bloom (HAB) species that blooms annually in the lower Chesapeake Bay. M. polykrikoides undertakes a diel vertical migration (DVM) which may give it a competitive advantage over purely phototrophic organisms who cannot access deeper nutrient pools and allow it to form large toxic blooms. Laboratory-based estimates of M. polykrikoides’ DVM rates suggest that it is one of the fastest known dinoflagellate swimmers and understanding this behavior is likely important for modeling and predicting M. polykrikoides blooms. However, to date, no field-derived estimates of M. polykrikoides’ DVM rates have been made in the …

Submarine Groundwater Discharge As A Major Nutrient Source In River-Fed Vs. Tidally Dominated Estuaries, Stephanie J. Wilson, Joseph J. Tamborski, Bongkeun Song, Peter Bernhardt, Margaret R. Mulholland

OES Faculty Publications

The tidal tributaries of the lower Chesapeake Bay experience seasonally recurring harmful algal blooms and the significance of submarine groundwater discharge (SGD) as a nutrient vector is largely unknown. Here, we determined seasonal SGD nutrient loads in two tributaries with contrasting hydrodynamic conditions, river-fed (York River) vs. tidally dominated (Lafayette River). Radon surveys were performed in each river to quantify SGD at the embayment-scale during spring and fall 2021. Total SGD was determined from a ²²²Rn mass balance and Monte Carlo simulations. Submarine groundwater discharge rates differed by a factor of two during spring (Lafayette = 11 ± 17 cm …

Testing Differential Predation As A Mechanism Of Color Polymorphism In A Cryptic Lizard., Justin A. Sanclemente

College of Graduate Studies: Theses & Dissertations

Selection via predation is a strong evolutionary force on small organisms, producing unique phenotypic adaptations. In cryptic species, different populations may exhibit color polymorphisms to better match multiple substrates or backgrounds. Here, I conducted a clay model study in the Ocala National Forest of Florida (USA) to test predation as a selective mechanism for color polymorphism in the Florida scrub lizard (Sceloporus woodi). Clay models were constructed to resemble light and dark morphs of S. woodi and placed on contrasting substrates in longleaf pine and Florida scrub stands. It is hypothesized Florida Scrub Jays (Aphelocoma coerulescens) …

Plasmid-Borne Biosynthetic Gene Clusters Within A Permanently Stratified Marine Water Column, Paraskevi Mara, David Geller-Mcgrath, Elizabeth A. Suter, Gordon T. Taylor, Maria G. Pachiadaki, Virginia P. Edgcomb

BCES: Faculty Publications

Plasmids are mobile genetic elements known to carry secondary metabolic genes that affect the fitness and survival of microbes in the environment. Well-studied cases of plasmidencoded secondary metabolic genes in marine habitats include toxin/antitoxin and antibiotic biosynthesis/resistance genes. Here, we examine metagenome-assembled genomes (MAGs) from the permanently-stratified water column of the Cariaco Basin for integrated plasmids that encode biosynthetic gene clusters of secondary metabolites (smBGCs). We identify 16 plasmid-borne smBGCs in MAGs associated primarily with Planctomycetota and Pseudomonadota that encode terpenesynthesizing genes, and genes for production of ribosomal and non-ribosomal peptides. These identified genes encode for secondary metabolites that are …