Digital Commons Network^™

A Deeper Understanding Of Noise Effects On Cetaceans, Jason N. Bruck

Faculty Publications

Recent research with cetaceans under human care is illuminating just how dolphins are affected by human-made noise both in terms of their ability to cooperate as well as their ability to habituate to such noise. This research is providing granular detail to regulators assessing the problems associated with anthropogenic effects and is highlighting a role for behavior/cognition research in conservation.

Exrna-Eclip Intersection Analysis Reveals A Map Of Extracellular Rna Binding Proteins And Associated Rnas Across Major Human Biofluids And Carriers, Emily L Laplante, Alessandra Stürchler, Robert Fullem, David Chen, Anne C Starner, Emmanuel Esquivel, Eric Alsop, Andrew R Jackson, Ionita Ghiran, Getulio Pereira, Joel Rozowsky, Justin Chang, Mark B Gerstein, Roger P Alexander, Matthew E Roth, Jeffrey L Franklin, Robert J Coffey, Robert L Raffai, Isabelle M Mansuy, Stavros Stavrakis, Andrew J Demello, Louise C Laurent, Yi-Ting Wang, Chia-Feng Tsai, Tao Liu, Jennifer Jones, Kendall Van Keuren-Jensen, Eric Van Nostrand, Bogdan Mateescu, Aleksandar Milosavljevic

Faculty, Staff and Students Publications

Although the role of RNA binding proteins (RBPs) in extracellular RNA (exRNA) biology is well established, their exRNA cargo and distribution across biofluids are largely unknown. To address this gap, we extend the exRNA Atlas resource by mapping exRNAs carried by extracellular RBPs (exRBPs). This map was developed through an integrative analysis of ENCODE enhanced crosslinking and immunoprecipitation (eCLIP) data (150 RBPs) and human exRNA profiles (6,930 samples). Computational analysis and experimental validation identified exRBPs in plasma, serum, saliva, urine, cerebrospinal fluid, and cell-culture-conditioned medium. exRBPs carry exRNA transcripts from small non-coding RNA biotypes, including microRNA (miRNA), piRNA, tRNA, small …

An Argument For The Utilization Of Amphibian Stress As An Indicator Of Wetland Condition, Andrew W. Sisson

Honors College Theses

Traditional forms of rapid wetland condition assessments focus on foliage health, nutrient enrichment, chemical contamination, and surrounding land usage, often overlooking an evaluation of the animals living in the wetland. More intense assessments include the National Wetland Condition Assessment (NWCA) and indices of biotic integrity, which focus on community composition (e.g., diversity and species richness) and abundances. These indices require expertise in species identification and do not provide information about the animal’s fitness. Animal stress physiology, which generally correlates with measures used to quantify animal fitness (e.g., survival, reproduction, and body condition), may provide a complementary rapid assessment method aimed …

Smile For The Camera: Patterns Of Mammal Abundance In Great Hill Forest Through Four Years Of Camera Trapping, Alexander Gonatas

Honors Program Theses and Projects

Snapshot USA is a nationwide camera trapping project aiming to determine biodiversity and abundance of animal populations across all 50 states. Since 2019, participants have used camera traps to document wildlife every September and October, coinciding with animal activity patterns and North American academic year starts. Understanding biodiversity through long-term monitoring is an important topic to study, because the knowledge obtained can help track populations and better understand wildlife responses to disturbances. Since Snapshot USA participants use the same methods and trapping season, the information we collect can be directly compared to other Snapshot USA locations. At Great Hill Forest …

Consolidated Chamber Design And Protocol For Olfactory Conditioning Assay With Drosophila Melanogaster, Sasha Bronovitskiy, Andres Castillo, Michael Yan, Fang Ju Lin

Journal of the South Carolina Academy of Science

The olfactory conditioning assay is widely used in Alzheimer’s disease research to quantify learning and memory in Drosophila melanogaster. The assay tests ability to recall an aversive conditioned stimulus of scent paired with electrical shock when presented a choice between shock-associated and unrelated scents. The T-maze, a commonly used apparatus for olfactory conditioning assays, employs an elevator mechanism to transfer live flies from the shock-delivering training chamber to the scent selection point. This elevator mechanism is known to cause fly casualty. T-mazes are not commercially available and often difficult to reproduce. Other existing variations of olfactory conditioning apparatuses use …

Measuring Selenoprotein Content In False Map Turtles (Graptemys Pseudogeographica) Along The Missouri River, Ruby A. Hawks

Honors Thesis

Metals and metalloids are becoming more prevalent in lakes and reservoirs of South Dakota which are toxic and hazardous in high concentrations or when biomagnified through trophic levels. Selenium is of particular concern as it can bind into the structures of proteins in place of other elements, changing protein structure and function within affected organisms. Zebra mussels (Dreissena polymorpha) are an invasive filter-feeding metal-bioaccumulating species that are rapidly spreading upstream through the Missouri River. They can take up selenium and directly transfer it to higher trophic level taxa. False map turtles (Graptemys pseudogeographica) are a common …

Sex And Environmental Effects On Chemical Signals Of Gryllus Rubens, Marion Davis Creech Iii, Marion Davis Creech Iii

Honors College Theses

Many animals communicate with one another in the context of reproduction, utilizing different modalities. In some cases, more than one modality is used by the sender and receiver. Each modality can provide different sets of information, or function in a different context. Importantly, no matter the modality, the signals should be clearly distinguishable between males and females and need to be reliable even in the face of environmental changes.

In field crickets, there are two major modes of communication. For long-range communication, the males produce acoustic signals to attract females. At short-range, chemical communication involving cuticular hydrocarbons (CHCs) in males …

Involvement Of Trpm7 In Alcohol-Induced Damage Of The Blood-Brain Barrier In The Presence Of Hiv Viral Proteins, Michelle L. Mack

Seton Hall University Dissertations and Theses (ETDs)

Ethanol (EtOH) exerts its effects through various protein targets, including transient receptor potential melastatin 7 (TRPM7) channels, which play an essential role in cellular homeostasis. We demonstrated that TRPM7 was expressed in rat brain microvascular endothelial cells (rBMVECs), the major cellular component of the blood–brain barrier (BBB). Heavy alcohol drinking is often associated with HIV infection, however mechanisms underlying alcohol-induced BBB damage and HIV proteins, are not fully understood. We utilized the HIV-1 transgenic (HIV-1Tg) rat to mimic HIV-1 patients on combination anti-retroviral therapy (cART) and demonstrated TRPM7 expression in rBMVECs was lower in adolescent HIV-1Tg rats compared to control …

Lessons From Chloroviruses: The Complex And Diverse Roles Of Viruses In Food Webs, John Delong, James L. Van Etten, David Dunigan

School of Biological Sciences: Faculty Publications

Viruses can have large effects on the ecological communities in which they occur. Much of this impact comes from the mortality of host cells, which simultaneously alters microbial community composition and causes the release of matter that can be used by other organisms. However, recent studies indicate that viruses may be even more deeply integrated into the functioning of ecological communities than their effect on nutrient cycling suggests. In particular, chloroviruses, which infect chlorella-like green algae that typically occur as endosymbionts, participate in three types of interactions with other species. Chlororviruses (i) can lure ciliates from a distance, using them …

The Relationship Between Cerebrovascular Impairment And Behavioral Abnormalities In Rats Exposed To Alcohol In Utero, Tiffany M. Knecht

Honors Thesis

Maternal consumption of alcohol during pregnancy can result in fetal alcohol spectrum disorders (FASD), which describes a range of developmental disorders. The goal of this study was to examine the association between impaired cerebrovascular function and behavioral abnormalities associated with FASD. We fed Sprague-Dawley dams a liquid diet with or without alcohol (3% ethanol) for the duration of their pregnancy. We then performed short-term memory and motor coordination assessments on the offspring during adolescence or adulthood. Next, we examined cerebral arteriole reactivity to the vasodilators nitroglycerin, adenosine diphosphate, N-methyl-D-aspartate, and iloprost. We found impairment in eNOS-, nNOS-, and K-channel-dependent dilation …

Ecological And Evolutionary Drivers Of Chameleon Forelimb Variation, Ellie M. Schley

Honors Thesis

Skeletal anatomy can vary greatly among individuals of the same family that share a common ancestor. Differences in skeletal anatomy and morphology allow species to be better suited to their environments. The study of skeletal anatomy variation as it pertains to species relatedness and habitat variation can provide useful insight into what may be driving evolutionary patterns among species. Specifically, studying skeletal anatomy of the forelimb could allow for better understanding of how the forelimb anatomy differs based on the arboreality of the species, which allows for better understanding of how habitat can affect morphology. To study the skeletal structure …

Characterization Of Molecular Content, Cytotoxicity, And Anti-Inflammatory Activity Of Extractions From Eupatorium Serotinum, Jordy Sloan

Electronic Theses and Dissertations

Inflammation is a complex and varied immune response which can be expressed chronically or as a temporary reaction to foreign invaders. Symptoms of inflammation include swelling, pain, soreness, and difficulty of motion. Recently, the effect of sesquiterpene lactones such as Helenalin from Arnica montana have been studied for their anti-inflammatory properties. In this study, we identified and harvested samples of Eupatorium serotinum, a plant historically used by Native Americans to treat a variety of medical illnesses. Crude extracts of the leaves, flowers, roots, and stems were prepared by ethanol extraction. The cytotoxicity of the different extracts on HEK293 cells …

Disease Prevalence And Selenium Bioaccumulation In Northern Leopard Frogs (Lithobates Pipiens), Emily B. Eisenbraun

Honors Thesis

Most amphibians are becoming imperiled in today’s world via environmental contamination and emerging infectious diseases. This project's main objective was to determine the relationship between the prevalence of Ranavirus and selenium bioaccumulation in amphibians in South Dakota. I selected northern leopard frogs (Lithobates pipiens) to focus on specifically because they are susceptible to Ranavirus and are found ubiquitously throughout eastern South Dakota wetlands. The secondary objective of this project was to determine if disease prevalence was correlated with areas of agricultural runoff in South Dakota’s prairie pothole wetlands. Intensive field sampling was conducted across five wetlands in Eastern South Dakota …

Community And Population Dynamics Of Diatoms In Recovering Agricultural Stream And Ubiquitous Taxon In Low-Impact Sites Across Southeastern United States, Sydney Brown

Biology Theses

Streams play vital roles to surrounding communities and provide essential ecosystem services. The protection of streams is important, legally protected under the Clean Water Act (CWA) and can be monitored through the continuous analyses of biological data, like algal or other aquatic communities. Diatoms are a group of algae characterized by rigid glass cell walls and ubiquitous distribution. They are typically identified using the morphological species concept and an ever-varying range of sizes may pose challenges in the identification process. However, when identified and applied correctly, diatoms are robust bioindicators. This research identifies and analyzes low-impact sites across the Southeastern …

Dolphin Behavioral Responses To Uncrewed Aerial Systems As A Function Of Exposure, Height, And Type, Savannah Damiano

Electronic Theses and Dissertations

Uncrewed aerial systems (UAS) are becoming a standard tool in the study of cetaceans, however, a comparative assessment of animal responses to UAS has not been established to gauge the most effective systems for cetacean study. We utilized Dolphin Quest Bermuda’s eleven bottlenose dolphins as subjects for such an investigation taking place over five weeks in 2022 and five weeks in 2023. The dolphins were evaluated for investigative behavioral responses to six off-the-shelf UAS types and a custom fixed wing system. Each UAS was flown in decreasing height vertically above the main dolphin lagoon to evaluate dolphin behavioral responses in …

Cannabidiol As A Synergist In Chemotherapy, Liam Pontes

Honors Program Theses and Projects

Cannabidiol (CBD) is a non-psychoactive compound commonly found in hemp and non-hemp plants. It has a molecular effect on cells, but its effect in modifying cellular signaling pathways has not been thoroughly tested until recently. Experimentation was done to determine whether CBD could induce cell death in MCF7 breast cancer cells. Both normal MCF7 cells and Cisplatin resistant MCF7 cells were used for these experiments. The cells were dosed with 0, 0.5, and 1.0 g/ml CBD dissolved in methanol. Later micrographs of the treated cells were collected and Annexin staining to determine the effect of CBD on cell death was …

Proximate Causes Of Alternative Reproductive Tactics In Blue Ridge Two-Lined Salamanders (Eurycea Cf. Wilderae), Yatin Kalki

Master of Science in Integrative Biology Theses

Alternative reproductive tactics (ARTs) refer to discrete variation in reproductive behavior between members of a sex and within a species. ARTs are present in Blue Ridge two-lined salamanders (Eurcyea cf. wilderae) in the form of male polymorphism. Two male morphs exist: “searching” males and “guarding” males. Each phenotype has a unique reproductive ecology and associated discrete morphological differences. Another trait that shows discrete variation in E. cf. wilderae is the larval period, which may be one or two years in length. This thesis explores the proximate causes of ARTs in a population of E. cf. wilderae from the …

An Overview Of Viruses And The Infamous Sars-Cov-2, Jake Sun

The Confluence

Background information on viruses is first presented which include topics like evolution, ecology, history, identification, structure, and application. The novel SARS-CoV-2, which causes COVID-19, pandemic originated in Wuhan, China in December 2019. Millions of people were infected with the virus in a short time period causing urgent concern worldwide. The purpose of this review is to provide a brief and general understanding of the SARS-CoV-2 to increase awareness and actions toward preventive measures. COVID-19 is a (+) ssRNA spherical enveloped virion that causes primarily respiratory illnesses. The S protein interacts with ACE-2 receptors on the host cell to gain entry …

A Sister-Group Comparison Of Branching And Pedicellariae In Brittlestar S (Echinodermata: Ophiuroidea), Richard L. Turner, Brenna O. O'Neill

Ocean Engineering and Marine Sciences Faculty Publications

Branching of arms and presence of pedicellariae are characters among ophiuroids found only in the order Euryalida (snakestars and basketstars). Family Asteronychidae has neither character; family Euryalidae has 2 small clades with branched arms; and family Gorgonocephalidae has all species with pedicellariae and 3 or 4 clades with branched arms. Despite the rare occurrence of these characters in the Ophiuroidea, they might be key adaptations within the Euryalida that have led to relatively high diversification. Sister-group comparison of the distribution of these 2 characters among taxa indicates that neither character alone explains diversity patterns within the order. In particular, branching …

Relationships Between Vector Mosquitoes And Climate Change Derived From Long Term Ecological Data In The United States, Nicholas Scott

Honors Program Theses and Projects

Climate change has significant ecological and societal consequences as evident from the past few decades. It has had a large impact on many species, including vector mosquitoes. Although how climate change impacts mosquitoes of the tropical world has been explored, temperate areas remain inadequately studied. Therefore, the medical and healthcare sectors are underprepared for treating mosquito-borne diseases (EEE and Western Nile virus). Based on a long-term ecological dataset covering the past ~10 years across 45 sites, we streamlined, processed, and subsequently analyzed data by building statistical models to understand changes among mosquito populations in the US in response to climate …

Temporal Changes In Biological Community Structure In Response To Wetland Restoration: A Study Based On Amphibians And Reptiles, Kayla Keith

Honors Program Theses and Projects

Wetland degradation is a serious environmental concern worldwide. In the United States, over half of the wetland ecosystems have degraded since 1780, which can have numerous, lasting consequences with negative outcomes on ecosystems and human society alike. Ecological restoration can regain both the lost wetland acreage and functions. Both global and national scale interests in ecological restoration have trickled down, which has kindled the local and regional natural resource managers and conservation authorities to invest in restoration. Consequently, large-scale wetland restoration projects are now underway in southeastern Massachusetts, which has coincided with a decline in commercial cranberry farming in the …

Microbial Biofortification: A Sustainable Solution To Feed 10 Billion People, Perrin Thompson, Kathryn Tschida

Celebrating Scholarship and Creativity Day (2018-)

No abstract provided.

Hawk Mountain Raptor Migration Phenology’S Relation To Weather, Eric Burgos

Computer Science and Information Technology Faculty

We have been studying year-round raptor migration phenology across the United States and North America for multiple decades now. Hawk Mountain Sanctuary’s Autumn migration hawk count began in 1934 and is the longest running raptor migration count in the world. A decline in total raptor counts passing through Hawk Mountain’s North Lookout is well documented and much research has already been done in what could be the main causes for this decrease in counts year-over-year. We know that cold front passages have long been associated with autumnal migration in northeastern North America. Using updated analysis techniques, we examined 60 years’ …

Gpr-160 Receptor Signaling In The Dorsal Vagal Complex Of Male Rats Modulates Meal Microstructure And Cart-Mediated Hypophagia, Marcos J. Sanchez-Navarro, Tito Borner, Benjamin C. Reiner, Richard C. Crist, Willis K. Samson, Gina L.C. Yosten, Lauren Stein, Matthew R. Hayes

Biological Sciences Faculty Research & Creative Works

The g-protein coupled receptor GPR-160, recently identified as a putative receptor for the cocaine and amphetamine-regulated transcript (CART) peptide, shows abundant expression in the energy-balance control nuclei, including the dorsal vagal complex (DVC). However, its physiological role in the control of food intake has yet to be fully explored. Here, we performed a virally mediated, targeted knockdown (KD) of Gpr160 in the DVC of male rats to evaluate its physiological role in control of feeding. Our results indicate that DVC Gpr160 KD affects meal microstructure. Specifically, DVC Gpr160 KD animals consumed more frequent, but shorter meals during the dark phase …

Dopamine Injections To The Midbrain Periaqueductal Gray Inhibit Vocal-Motor Production In A Teleost Fish, Alexander Allen, Elizabeth Heisler, James Matthew Kittelberger

Biology Faculty Publications

Across vertebrates, the midbrain periaqueductal gray (PAG) plays a critical role in social and vocal behavior. Dopaminergic neurotransmission also modulates these behaviors, and dopaminergic innervation of the PAG has been well documented. Nonetheless, the potential role of dopamine in shaping vocal production at the level of the PAG is not well understood. Here, we tested the hypothesis that dopamine modulates vocal production in the PAG, using a well-characterized vertebrate model system for the study of vocal communication, the plainfin midshipman fish, Porichthys notatus. We found that focal dopamine injections to the midshipman PAG rapidly and reversibly inhibited vocal production …

Investigation Of The Evolution And Structural Basis Of Caspases: Insights Into Conformational Dynamics, Stability And Allostery, Isha Joglekar

Biology Dissertations - Archive

Caspases, a class of cysteinyl proteases, are well known for their roles in apoptosis or programmed cell death. However, at lower levels of activation in the body, they also play other non-apoptotic roles in cell proliferation, cell differentiation, neuronal development, cell migration and motility, and embryonic development, all of which are poorly understood. Caspases provide an excellent model to study protein evolution since, they evolved from a common ancestral state into two subfamilies having different oligomeric properties: initiators, which exist as monomers, and effectors, which exist as dimers, under physiological conditions in a cell. However, the evolutionary basis for the …

Evolution Of Allostery And Conformational Dynamics Of Caspases Involved In The Extrinsic Pathway Of Apoptosis, Mithun Nag Karadi Giridhar

Biology Dissertations - Archive

Caspases are a class of cysteine proteases that play a crucial role in programmed cell death (apoptosis). We complete an evolutionary picture of folding of caspases in the extrinsic pathway of apoptosis. The folding models show that the conformational free energy of the monomeric fold is conserved in the extrinsic pathway of apoptosis. In addition, with molecular dynamics and mass spectrometry we also show that the small subunit is less stable than the large subunit and charges destabilize allosteric regions in caspases allowing for dynamics. In order to gain insight into the evolution of allostery in caspases across different species, …

Endophytic Bacteria Isolated From Aeschynomene Indica Plants And Their Role In Nod-Factor Independent Nodule Formation And Nitrogen Fixation, Meaghan Alyssa Rose

Biology Dissertations - Archive

The formation of specialized root organs known as nodules is the most defining characteristic of leguminous plants due to the fixation of atmospheric nitrogen to bioavailable forms enabled by rhizobial endosymbionts. This relationship has played an integral role in the agricultural practice of using such crop plants as biofertilizers to reduce the use of and dependency on synthetic chemical fertilizers. Tropical legumes, such as members of the genus Aeschynomene, are particularly recognized for their ability to form stem nodules through an unknown mechanism independently of the canonical Nod Factor signaling pathway used in standard root nodulation. The works in this …

Stress Response Pathways And The Origins Of Novelty: How Snakes Regenerate Organs And Regulate Venom, Aundrea Kristene Westfall

Biology Dissertations - Archive

Snakes have captured evolutionary biologists’ attention for decades as extreme examples of adaptive evolution models for studying how novel and extreme traits evolve in nature, but research has long overlooked or been unable to determine the molecular and genomic bases of these traits, and their underlying mechanisms. Here, I dissect the molecular mechanisms and associated signaling pathways underlying two such extreme traits – extreme intestinal regenerative capacity and the evolution of venom regulation – using functional genomics approaches to understand the conserved and non-canonical gene regulatory cascades that drives them. I first combined physiological data with RNA sequencing, proteomics, and …

The Evolution Of Empathy: Through The Lens Of A Rodent Model., Caroline Driscoll-Braden

Electronic Theses and Dissertations

Empathy is the capacity to be affected by and share the emotions of others, to discern the circumstances prompting another’s emotional state, and to identify with another by adopting their perspective. Research investigating the empathically motivated behavior of rats can help inform the evolutionary history of empathy and provide additional support of the continuity of empathy in animals and humans. In this dissertation, I examine the helping behavior of rats to explore the complexities of rodent empathy. In Chapter I, I review the multiple layers of empathy and describe both historical and contemporary research examining empathy in non-humans. I explain …