Biology Commons^™

Root Traits Of Perennial C4 Grasses Contribute To Cultivar Variations In Soil Chemistry And Species Patterns In Particulate And Mineral-Associated Carbon Pool Formation, Megan J. Kelly-Slatten, Catherine E. Stewart, Malak M. Tfaily, Julie D. Jastrow, Abigail Sasso, Marie-Anne De Graaff

Biology Faculty Publications and Presentations

Recent studies have indicated that the C₄ perennial bioenergy crops switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii) accumulate significant amounts of soil carbon (C) owing to their extensive root systems. Soil C accumulation is likely driven by inter- and intraspecific variability in plant traits, but the mechanisms that underpin this variability remain unresolved. In this study we evaluated how inter- and intraspecific variation in root traits of cultivars from switchgrass (Cave-in-Rock, Kanlow, Southlow) and big bluestem (Bonanza, Southlow, Suther) affected the associations of soil C accumulation across soil fractions using stable isotope techniques. Our …

Nutritional Ecology Of The Western Cottonmouth (Agkistrodon Piscivorus Leucostoma), Jason Ortega

Graduate Theses and Dissertations

Nutritional ecology aims to understand the factors that shape the diets of animals, how these ingested meals are processed, and how the assimilated nutrients are used to shape an organism’s interactions with its environment. As environmental parameters are altered due to anthropogenic changes, the availability and quality of prey may be altered. The alteration of the nutritional landscape can be devastating to nutritional specialists, yet generalist predators may be able to cope with these changes. The western cottonmouth (Agkistrodon piscivorus leucostoma) is a unique semiaquatic pitviper that can both forage along the land-water interface and in upland habitat when faced …

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 …

Cell Division In Mycobacteria: The Role Of Sepiva, Angela H. Freeman

Biology Dissertations - Archive

Today, about a quarter of the world’s population are infected with Mycobacterium tuberculosis (Mtb) and therefore, are at risk of developing tuberculosis (TB) disease. Tuberculosis, on average, takes about six months to treat, and even longer for those with drug resistant Mtb infections (World Health Organization, 2022). Extended treatment times for these infections are caused by the inherent tolerance to antibiotics conveyed by mycobacteria’s distinct cell wall. Mycobacteria have a wide variety of cell wall regulators that help the cell adapt to stress, such as antibiotics. By understanding how these regulators work, we can learn how mycobacteria evade killing by …

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 …

Characterization Of Neutrophil Extracellular Traps In Naked Mole-Rats: A Step Towards Cancer Resistance, Thomas Abraham Smith

Undergraduate Honors Capstone Projects

Cancer is the second leading cause of death in the United States, exceeded only by heart disease. One of every five deaths in the United States is due to cancer. A growing area of research involves the analysis of cancer resistant traits in other species to understand their biological mechanisms and eventually make translations to human cancer research and clinical treatment. Because of their remarkable cancer resistance, the naked mole-rat (NMR) is a prime subject for this research, and various studies have already suggested that the immune mechanisms of the NMR might be harnessed for human cancer therapies^1-4,7. …

Protein Nutrition And Immunity In Male Bumblebees (Bombus Impatiens), Carson Stoker

Undergraduate Honors Capstone Projects

Male bumble bees play a vital but understudied role in their colonies. They are essential to colony reproduction and success, despite not emerging until the end of the colony's life cycle. Even so, the biology of male bumble bees is not well understood, which leaves our understanding of colony health incomplete. This knowledge gap is important because bumblebee populations are declining, which threatens the ecosystems and industries which rely on them for pollination. This study aimed to understand how two understudied factors of bumble bee health—diet and immunity—are related in males. Pollen, a bee’s main source of protein, has been …

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 …

Thermal Tolerance, Physiology, And Microhabitat Use Of Eleutherodactylus Coqui Across An Elevational Gradient In Hawai‘I, Jack Marchetti

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The coqui frog (Eleutherodactylus coqui) is an invasive species in Hawai‘i, and has spread across much of the island. While elevational temperature differences are thought to restrict the coqui’s spread, it is unclear if they have resulted in changes to the coqui’s physiology and microhabitat use as it has expanded into higher elevations.

We first sought to determine if the coqui’s substrate use and baseline physiology differs between elevations. We found that frogs at high elevation were found closer to the forest floor and used different substrates than frogs from low and mid-elevations. This change in microhabitat use …

The Effects Of Recent Climate Change On Spring Phenology, With A Special Focus On Patterns Of Bee Foraging, Michael Stemkovski

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The date on which plants flower and on which bees begin to pollinate varies year-to-year depending on differences in weather. This seasonal timing is known as phenology, and it is already clear that climate change has pushed the spring phenology of many species earlier by increasing temperatures. This is particularly clear in flowering plants, but studying how and why the phenology of pollinators is shifting is more difficult. Most flowering plants rely on pollinators such as bees for their reproduction, and most bees rely on flowers for their sustenance, so bee and flower phenology has to overlap for the crucial …

Investigation Of The Role Of Dax-1 In The Hpa Axis In Human Adrenal Cells, Katerina N. Fargas

Undergraduate Honors Theses

DAX-1 is a nuclear hormone orphan receptor that plays a key role in the development of reproductive tissues and steroid hormone production. The hypothalamic-pituitary-adrenal axis is the pathway for steroid hormone production, primarily glucocorticoids, mineralocorticoids, and adrenal androgens, in the human body. The mechanisms of DAX-1 in hormone production in the adrenal cortex of the HPA axis are not completely understood and, therefore, were the focus of this honors thesis research project. Due to the high level of DAX-1 expression, SW13 adrenal carcinoma cells were conducted for these experiments. We investigated whether glucocorticoids, specifically the synthetic glucocorticoid dexamethasone, had any …

Implications Of Toll-Like Receptor 10 Mutants In Cell Signaling, Sonali Joshi

Undergraduate Honors Theses

Our innate immune system serves the important purpose of quickly recognizing microbial pathogens and providing the first line of defense against infection. Toll-Like Receptors (TLRs) are one class of receptors responsible for enacting our bodies’ innate immune responses. Specifically, TLR10 is an extremely under-researched receptor. Some naturally occurring mutations in TLR10 have been linked with a worsening prognosis of rheumatoid arthritis, with previous research uncovering a mutant form of TLR10 that impairs innate immune system-controlled inflammatory responses. However, other research has found that wild-type forms of TLR10 also contribute to pro-inflammatory pathways in healthy cells. To better understand the wild-type …

Leveraging Population Genomics Across Two Taxonomically Diverse Non-Model Systems To Understand Patterns Of Disease Transmission And Consequences Of Hybridization, Zachary Lamar Nikolakis

Biology Dissertations - Archive

The field of population genomics has been mainly applied to questions centered around understanding molecular variation, impacts of evolutionary processes, and the history of populations. Here I leverage population genomic techniques across two different systems to understand patterns of disease transmission across heavily monitored and controlled parasite populations and consequences of hybridization between divergent rattlesnake lineages. I employed multiple genome sequencing techniques with new methods to infer close-order relatedness from highly inbred human blood fluke populations in order to understand transmission pathways across a region experiencing a resurgence in disease. I then use a comparative population genomic approach by sampling …

Neonate Atlantic Sharpnose Shark (Rhizoprionodon Terraenovae) Relative Abundance And Body Condition In Two South Carolina Estuaries Varying In Urbanization, Rileigh E. Hawk

Electronic Theses and Dissertations

Urbanization near estuaries has been shown to affect the growth and survival of juvenile sharks using the system as a nursery. North Inlet and Murrells Inlet, South Carolina, are similarly-sized, tidally-dominated, bar-built estuaries with extensive Sporobolus-lined tidal creeks but differ in degree of human impact. Previously, Murrells Inlet was shown to have a lower abundance and diversity of large sharks than North Inlet and Atlantic Sharpnose Sharks (Rhizoprionodon terraenovae) were shown to use North Inlet as a primary nursery. To examine potential differences in neonate shark abundance and growth between a developed estuary, Murrells Inlet, and a protected estuary, North …

Development Of Three Novel Edna Assays For Detecting Coastal Sharks, Kristina Dawn Flanigan

Electronic Theses and Dissertations

Environmental DNA (eDNA) analysis is an emerging, non-invasive community monitoring tool. This study aimed to determine if eDNA methods can be reliably used in a large brackish, partially mixed estuary by developing and testing three novel eDNA primers, for Sandbar Sharks (Carcharhinus plumbeus), Blacknose Sharks (Carcharhinus acronotus), and Bonnetheads (Sphyrna tiburo). These primers were designed to target 109, 156, and 120 base pair (bp) fragments, respectively, of the highly conserved NAD2 gene in the mitochondrial genome of each species. Primer function was validated through testing against 102 known genomic source samples and 25 filtered water samples from aquaria in which …

Past And Present Patterns Of Neutral And Adaptive Genetic Diversity In Wild Mandrills (Mandrillus Sphinx), Anna Weber

LSU New Orleans Theses and Dissertations

Although primates have fascinated researchers and the public alike for generations, one species that has remained enigmatic is the mandrill (Mandrillus sphinx), a large Cercopithecine monkey endemic to Central Africa. Mandrills are currently in decline due to bushmeat hunting, urbanization, and habitat loss. Neutral and adaptive genetic diversity are important tools for understanding evolutionary history and future viability, since diversity influences a species’ ability to adapt to a changing environment. However, thus far, minimal genetic information has been available for wild mandrills. Because of the dense vegetation in their tropical forest habitat, studying wild mandrills has proven to …

Wild Sea Cucumber Trade In Rural Madagascar : Consequences For Conservation And Human Welfare, Emily L. Rothamel

Theses, Dissertations and Culminating Projects

Overexploitation of fisheries is a challenge to both marine conservation and human welfare. The trade of sea cucumbers is a multi-billion-dollar market, spanning over 70 countries. Global concern over unsustainable sea cucumber trade led to the inclusion of three species in CITES Appendix II, two of which are found in Madagascar (Holothuria fuscogilva and H. nobilis). I used 792 structured interviews (2015–2020) to study the intensity of sea cucumber collection and exportation in rural northeastern Madagascar, where 30% of all (terrestrial and aquatic) native species are threatened with extinction. Wild sea cucumber collection was common and increased tenfold during the …

The G Protein-Coupled Receptor (Gpcr) Fshr-1 And The Sphk-1 Lipid Kinase Regulate C. Elegans Life- And Healthspans Via A Common Pathway, Ryan Dennis Adkins

Undergraduate Honors Thesis Collection

Later years of life are often characterized by reduced cognitive function and mobility. One contributor is the cellular accumulation of reactive oxygen species (ROS), but our understanding of how cells respond to ROS to promote health and survival is incomplete. Follicle stimulating hormone receptor-1 (FSHR-1) and sphingosine kinase-1 (SPHK-1) mediate responses to oxidative stress and regulate life history traits in the roundworm Caenorhabditis elegans. The genes encoding both proteins are conserved in humans where they are implicated in stress responses, cell survival and neuronal function. fshr-1 and sphk-1 work together to mediate responses to intestinal oxidative stress in C. elegans. …

Environmental Drivers Of Stress In Red Pandas (Ailurus Fulgens) : Behavior And Space Use Changes In Response To Redesigned Naturalistic Enclosures, Alexis Michelle Lawson

Theses, Dissertations and Culminating Projects

Animal welfare encompasses the physical and mental state of an animal, as well as how that animal is cared for. Recently, zoological settings have shifted from strictly housing animals to improving the welfare of the animal such that the goal of captivity is for residents to thrive. This is especially crucial as global wildlife numbers and biodiversity continues to decrease due to anthropogenic impacts such as poaching, mining, habitat destruction, fragmentation. Further confounding this issue is climate change, air pollution, invasive species, ocean acidification, and more. In particular, the red panda (Ailurus fulgens) is an endangered species whose declined 50% …

Effects Of Guest Interactions On Cownose Ray (Rhinoptera Bonasus) Behavior In A Zoo Touch Tank, Lauren Hope

Theses, Dissertations and Culminating Projects

Touch tanks are increasingly popular exhibits at zoos and aquariums, and are at the center of scientific engagement with the public. Touch tanks can provide benefits to marine species through conservation outreach and research, and to guests through education, recreation, and stress reduction. Cownose rays are a popular species found in touch tanks due to their putative stress tolerance and docile nature. Yet, questions remain about ray tolerance to captivity, and studies are rare on their behavioral responses to touch tank environments and guest interactions. Here, I used an observational study to examine: (1) baseline ray behavior in a touch …

The Characterization Of Minicoopr Cell Line Clones For The Expression Of Wild Type Form Of Icer, Samantha Moscoso

Theses, Dissertations and Culminating Projects

The transcriptional repressor Inducible cyclic-AMP Early Repressor (ICER) is an isoform of the cAMP-responsive element modulator (CREM) gene. ICER protein has tumor suppressor activity by regulating cAMP-induced transcription. ICER has been found to be effective in providing an anti-tumor effect when in many tumors including melanomas. Melanoma is an aggressive type of skin cancer that begins when there is an overproduction of melanocytes. Using a zebrafish model for melanoma, our laboratory has recently demonstrated that zebrafish that are expressing ICER in their melanocytes succumbed to malignancies at a much faster rate than the control Green Fluorescent protein (GFP)- expressing fish. …

Neural Correlates Of Sub-Clinical Grandiose Cluster B Personality Disorders, Adriana Lavarco

Theses, Dissertations and Culminating Projects

The Cluster B personality disorders (PDs) include antisocial personality disorder (ASPD), borderline personality disorder (BPD), narcissistic personality disorder (NPD), and histrionic personality disorder (HPD). With impulsivity being a commonly shared symptom across the cluster B personality disorders, specifically in BPD, the right and left dorsolateral prefrontal cortex (DLPFC) was targeted for TMS. Since these personality disorders are grouped together due to their shared ‘dramatic’ characteristics, the current study aimed to investigate the effects of transcranial magnetic stimulation (TMS) on the presence of cluster B personality disorder traits in 13 healthy participants. We found that there is a significant decrease in …

Social Exclusion : How Inhibition And Excitation Of The Dorsal Lateral Prefrontal Cortex (Dlpfc) Influences Feelings Of Social Exclusion, Anthony Minervini

Theses, Dissertations and Culminating Projects

Social exclusion refers to the experience of rejection by one or more people during a social event. Cyberball, a computer program, is one of the most common tools for analyzing social exclusion. Cyberball simulates a game of catch in which any number of individuals or computer- generated players can pass a virtual ball to one another. Regions of the brain that underlies pain perception include networks lined to the Dorsal Lateral Prefrontal Cortex (DLPFC). Direct manipulation of this area may provide a better understanding of how the DLPFC can influence the perception of social exclusion. Transcranial magnetic stimulation (TMS) was …

Black Garlic Extract As An Antiviral For Herpes Simplex Virus-2 In Lung Cells, Jenna Rose Horowitz

Theses, Dissertations and Culminating Projects

Allicin, a sulfur compound, is known for providing garlic with its unique fragrance and taste, as well as for its antimicrobial properties. This is one of many antioxidant compounds found in garlic, along with polyphenols and flavonoids. When raw garlic is aged using high temperatures and high humidity levels, it develops a black color and a sweeter taste. Garlic in this form, referred to as black garlic, contains higher levels of antioxidants than fresh garlic. Antioxidants play a vital role in alleviating cellular stress during viral infections. Once a virus particle attaches and enters a host cell, a slew of …

The Emerging Oral Pathogen, Filifactor Alocis, Modulates Antimicrobial Responses In Primed Human Neutrophils., Ian J. Snider

College of Arts & Sciences Senior Theses

Periodontitis is an irreversible, chronic inflammatory, infectious disease of the oral cavity that affects approximately half of all adults 30 years or older in the USA. The oral cavity is under high immune surveillance because of its constant exposure to microbes in the environment. The primary immune cell responsible for this surveillance is the neutrophil. Pathogens associated with periodontitis possess virulence factors and have evolved strategies to evade neutrophil antimicrobial responses to survive. One such pathogen is Filifactor alocis, whose presence is associated with the progression of periodontitis. F. alocis manipulates several neutrophil antimicrobial functional responses to avoid killing, an …

Impacts Of Dietary Restriction On A Drosophila Model Of Werner Syndrome, Eileen Sember

College of Arts & Sciences Senior Theses

Werner syndrome (WS) is an autosomal recessive disorder that results in premature aging and occurs in 1 in 1,000,0000 to 1 in 10,000,000 people. In humans, WS is the result of mutations that render the WRN gene, that contains a helicase and an exonuclease domain, non-functional. Currently, there is no cure for WS in humans, making dietary and lifestyle interventions attractive for increasing the quality and longevity of lives. Diet restriction (DR) has been shown to extend the lifespan of several model organisms, including Drosophila melanogaster, making it a strong candidate for WS treatment. In this thesis, mutant flies …

Impact Of Lyophilization On Porcine Hemoglobin Properties., Mustafa Almosawi

College of Arts & Sciences Senior Theses

Blood transfusion is the single most often performed lifesaving procedure in hospitals worldwide. Unfortunately, packed red blood cells (RBCs) used for transfusion can only be stored for 42 days at 4 °C before being discarded due to irreversible damage that occurs during storage. Any reduction in available RBCs for an extended period can lead to blood shortages. To increase the shelf-life of RBCs, we investigated freeze-drying (lyophilizing) in the presence of the non-toxic sugar trehalose as a method for long-term preservation. However, the oxidative stress of the lyophilization and storage processes can compromise the functionality of these cells, and the …

A Field‐Capable Rapid Plant Dna Extraction Protocol Using Microneedle Patches For Botanical Surveying And Monitoring, Jonathan Selz, Nicolas R. Adam, Céline E. M. Magrini, Fulvia Malvido Montandon, Sven Buerki, Sebastian J. Maerkl

Biology Faculty Publications and Presentations

Premise: A novel protocol for rapid plant DNA extraction using microneedles is proposed, which supports botanic surveys, taxonomy, and systematics. This protocol can be conducted in the field with limited laboratory skills and equipment. The protocol is validated by sequencing and comparing the results with QIAGEN spin-column DNA extractions using BLAST analyses.

Methods and Results: Two sets of DNA extractions were conducted on 13 species spanning various leaf anatomies and phylogenetic lineages: (i) fresh leaves were punched with custom polymeric microneedle patches to recover genomic DNA, or (ii) QIAGEN DNA extractions. Three plastid (matK, rbcL, and trnH-psbA …

Nuclear And Cytoplasmic Spatial Protein Quality Control Is Coordinated By Nuclear–Vacuolar Junctions And Perinuclear Escrt, Emily M. Sontag, Fabián Morales-Polanco, Jian-Hua Chen, Gerry Mcdermott, Patrick T. Dolan, Dan Gestaut, Mark A. Le Gros, Carolyn Larabell, Judith Frydman

Biological Sciences Faculty Research and Publications

Effective protein quality control (PQC), essential for cellular health, relies on spatial sequestration of misfolded proteins into defined inclusions. Here we reveal the coordination of nuclear and cytoplasmic spatial PQC. Cytoplasmic misfolded proteins concentrate in a cytoplasmic juxtanuclear quality control compartment, while nuclear misfolded proteins sequester into an intranuclear quality control compartment (INQ). Particle tracking reveals that INQ and the juxtanuclear quality control compartment converge to face each other across the nuclear envelope at a site proximal to the nuclear–vacuolar junction marked by perinuclear ESCRT-II/III protein Chm7. Strikingly, convergence at nuclear–vacuolar junction contacts facilitates VPS4-dependent vacuolar clearance of misfolded cytoplasmic …