Research Methods in Life Sciences Commons^™

The Potential Of Stem Cell Therapy In Multiple Sclerosis Treatment: A Review, Sorina Amarculesei, Ava O'Meara Cushen, Cathy Brougham

SURE Journal: Science Undergraduate Research Experience Journal

Multiple Sclerosis is an autoimmune and neurodegenerative disease of the central nervous system. There are currently 2.8 million people living with Multiple Sclerosis worldwide, including 9000 people in Ireland, with a prevalence of 193 per 100,000 people. Symptoms of Multiple Sclerosis include sensory loss, fatigue, cognitive dysfunction, spasticity, depression, optic neuritis, gait ataxia, diplopia, and loss of bladder control. Currently, there is no standardised treatment or cure for Multiple Sclerosis with many strategies focusing on symptoms. Stem cells have emerged as promising approaches for Multiple Sclerosis therapeutics. Clinical trials primarily focus on mesenchymal stem cell-based therapies for Multiple Sclerosis. Furthermore, …

Deep Ocean Vehicle Applications And Modifications, Nichole "Nikki" T. Arm

Master's Theses

This project had two primary goals: (1) to explore opportunities to further a deep-ocean vehicle’s reach using alternative pressure spheres, and (2) to implement an existing deep-ocean vehicle (lander) in active scientific research.

I gained a greater understanding of the limitations and design choices made for existing pressure spheres using Finite Element Analysis (FEA). My simplified FEA model predicted sphere failure for the existing 30% Fiber Glass 70% Nylon injection molded spheres at an external pressure of 3,954psi or 2,690m ocean-depth (only a 7.38% error compared to the tested minimum failure depth), so I determined it a valid model. I …

Impacts Of Disturbance And Nutrient Addition On Coastal Dune Arthropod Communities, Kayla Beitzel

Honors Theses

Coastal dune ecosystems are globally distributed ecosystems that occur from the tropics to the poles and serve as the first line of defense during storms. They are critical habitats for a variety of organisms and also play a critical role in stabilizing coastal habitats. These systems face increased pressure via urban development, recreational expansion, and sea-level rise (Newman et al. 2023; Webster et al. 2005). Insects are vital consumers in coastal ecosystems and act as regulators of plant growth. Low-diversity ecosystems, like coastal dune systems, often contain a higher abundance of low-diverse insect consumers (Ripple et al. 2021), which can …

Human-Bat Interactions In A Disease Emergence Hotspot: Implications For Human Health And Bat Conservation, Reilly Tempest Jackson

Graduate Theses and Dissertations

Bats are an ecologically important taxon that can host zoonotic pathogens. Globally, many bat species are synanthropic and live closely with humans, often roosting in man-made structures. The spatial overlap between humans and bats creates opportunities for human-bat contact, which can lead to human exposure to bat-borne pathogens and conflicts that cause bat mortality. Despite this risk, little is known about the drivers and characteristics of these human-bat interactions in buildings and work is needed to understand this aspect of the wildlife-urban interface. In Chapter I, I present a literature review that identifies the geographic and taxonomic trends in reported …

Unlocking The Mysteries Of Opportunism: Neuroendocrine Insights From An Aseasonal Breeder (Taeniopygia Guttata), Jessica A. Moodie

Graduate Theses and Dissertations (2019 - present)

The regulation of reproductive physiology in animals is mediated by the Hypothalamus-Pituitary-Gonad (HPG) axis. In seasonal breeders, a conserved reciprocal switching of deiodinase enzymes alters thyroid hormone signaling, which controls HPG activity. This study tested the hypothesis that neural regulation of the HPG axis as described in seasonal systems is conserved and repurposed to respond to other cues in aseasonal species. Using water deprivation and nest restriction in the opportunistic Zebra Finch, we were able to create a breeding group and non-breeding group, confirmed by egg laying and changes in ovarian anatomy. Breeding females had clear follicular hierarchy, increased ovary …

Engaging Students In A Genetics Course-Based Undergraduate Research Experience Utilizing Caenorhabditis Elegans In Hybrid Learning To Explore Human Disease Gene Variants, Natalie Forte, Virginia Veasey, Bethany Christie, Amira Carter, Marli Hanks, Alan Holderfield, Taylor Houston, Anil Challa, Ashley Turner

Research, Publications & Creative Work

Genetic analysis in model systems using bioinformatic approaches provides a rich context for a concrete and conceptual understanding of gene structure and function. With the intent to engage students in research and explore disease biology utilizing the nematode Caenorhabditis elegans model, we developed a semester-long course-based undergraduate research experience (CURE) in a hybrid (online/in-person) learning environment—the gene-editing and evolutionary nematode exploration CURE (GENE-CURE). Using a combination of bioinformatic and molecular genetic tools, students performed structure-function analysis of disease-associated variants of uncertain significance (VUS) in human orthologs. With the aid of a series of workshop-style research sessions, students worked in teams …

An Evolutionary Comparative Study Of Congenital Stationary Night Blindness-Associated Trpm1 Genetic Variants Of Uncertain Significance In Horses And Humans Utilizing Caenorhabditis Elegans, Gabrielle Davis

Theses

Congenital stationary night blindness (CSNB) is a heterogeneous collection of genetic diseases affecting the eyes and vision in horses and humans. Current research has implicated several genetic mutations impacting different genes involved in phototransduction and signal transmission, including TRPM1. In horses, genetic mutations in TRPM1 also result in a leopard spotting pattern or leopard complex. The goal of this study is to examine the potential impact of CSNB associated TRPM1 missense variants of uncertain significance (VUS). Previous research in Caenorhabditis elegans have revealed an orthologous TRPM1 gene known as gon-2 that allows for comparative studies. The evolutionary relationship of …

Cadmium And Salinity Stressor Antagonism On Vallisneria Neotropicalis, Christopher P. Mikolaitis

Graduate Theses and Dissertations (2019 - present)

Submerged macrophytes form the foundation of freshwater ecosystems. These organisms are sessile and are very susceptible to shifts in their environment. Heavy metals are of particular concern as they can be sequestered indefinitely in sediments and are readily taken up by rooted vegetation. In the presence of saltwater intrusions, these metals can interact with salt ions potentially changing their availability to submerged vegetation. In this study a freshwater macrophyte, Vallisneria neotropicalis, was used as a test species for interactive effects between Cd, a non-essential heavy metal, and salt stress. The metrics used to establish the individual as well as …

Evaluating The Impact Of Temperature And Artificial Light At Night On The Growth, Swimming Performance, And Corticosterone Levels Of Southern Leopard Frog (Lithobates Sphenocephalus) Tadpoles, Skylar Alexander

Honors Theses

Anthropogenic activities caused by urbanization have considerably altered our world’s ecosystems which has led to a global amphibian population decline. Encroaching and unyielding urbanization by humans has contributed to a rise in artificial light at night due to light pollution as well as increased temperature due to climate change. Both rising temperatures and artificial light at night (ALAN) have been shown to individually have negative effects on amphibian physiology such as increased stress and decreased behavior. However, due to the drastic nature of human imposition, amphibians typically encounter these anthropogenic stressors in combination. Therefore, it is important to understand how …

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 …

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 …

Analysis Of Wild Rodent Gut Microbiota As A Function Of Exposure To Ticks And Tick-Borne Pathogens, Joshua Pandian

Honors Theses

Due to advances in high-throughput parallel sequencing, researchers have conducted novel studies exploring relationships between microbiome compositions and different aspects of organism health. Some of these studies have shown that the gut microbiome of rodent models has effects on organism health and behavior and that infection with pathogens and the composition of the skin microbiome are linked to changes in gut microbiome composition. While previous studies have shown how vector microbiota impact vector behavior and pathogen transmission, the effect vectors have on reservoir species microbiomes has been a less prominent focus. We were interested in the relationships between tick parasitism, …

An Automatic System To Evaluate Bait Station Visitation By Brown Treesnakes And Mongooses, Robert T. Sugihara, William C. Pitt, Are R. Berentsen, Francis L. Benevides Jr.

Human–Wildlife Interactions

Understanding the temporal, spatial, and behavioral patterns of the free-ranging target species in response to candidate baits and baiting strategies is important to ensure control success. This information can also assist in the development and deployment of feeding stations and can exclude non-target species while constituting effective bait delivery and control strategies for certain invasive animals, especially at environmentally sensitive sites. We used passive integrated transponder (PIT) tags in conjunction with very-high frequency radio-telemetry to remotely record bait station visitations and evaluate bait attractiveness in separate field research studies of brown treesnakes (Boiga irregularis) on Andersen Air Force …

Determining Species-Specific False-Positive Rates Using Visual And Auditory Cues: A Case Study With Sagebrush Steppe Songbirds, Amelia K. Evavold

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Errors in wildlife field data threaten to bias resulting abundance and occupancy estimates if not properly accounted for or minimized. Methods to account for false-positive errors in wildlife data have not been as thoroughly developed as those for false-negative errors despite false-positives being present across diverse wildlife taxa and study systems. The calibration method to account for false-positives involves assessing the field detection method to determine how often false-positive errors occur in the field data. Rates can then be incorporated into estimations based on the field data to improve estimation accuracy. This study presents an application of the calibration approach …

Genetic Evaluation Of The Current Distribution And Possible Diffrentations Between Lasiurus Borealis And Lasiurus Frantzii In Southwestern North America, Zeinab M. Haidar

Cal Poly Humboldt theses and projects

Several recent accounts of overlap and historic misidentifications regarding two species of the genus Lasiurus, Western red bat (Lasiurus frantzii) and Eastern red bat (Lasiurus borealis), have cast doubt on our understanding of their distribution, assumed spatial allopatry, and interactions in the United States Southwest. With the use of morphometrics and genetic sequencing, utilizing tissue collected from specimens throughout California and adjoining states, we have reassessed the current distribution, best practices for field identification, and genetic differentiation between both species. Appropriate species classification by region was achieved utilizing mitochondrial DNA, targeting the cytochrome c oxidase …

The Effects Of Sex On Zebrafish Bone Metabolism, Simon Bagatto

Williams Honors College, Honors Research Projects

I investigated the effects of diet and sex on zebrafish bone metabolism. Zebrafish were subjected to either a high-calorie or low-calorie diet over a five-week period. After this diet, zebrafish scales were used to measure alkaline phosphatase (ALP) and tartrate-resistant acid phosphatase (TRAP) enzyme activity with a fluorescent substrate. The enzyme activities were markers of the osteoblasts (ALP) and the osteoclasts (TRAP). These data were compared among sex and diet of the zebrafish using a repeated measures ANOVA statistical test. I also measured the number of resorption lacunae per scale (another indicator of osteoclast activity). The results showed higher TRAP …

Epithelial Membrane Protein 3 (Emp3b) Is A Novel Regulator Of Sympathetic Nervous System Development In Zebrafish., Jessica M. White

Theses and Dissertations

Notable progress has been made in understanding the development of the neural crest (NC). Neural crest cells (NCCs) can be divided into 4-5 subpopulations. A major lineage among trunk NC derivatives are sympathoadrenal (SA) cells, which give rise to the sympathetic nervous system (SNS). Trunk NCCs follow a ventromedial migration pathway where signals derived from the dorsal aorta instruct migrating NCCs to a SA cell fate. Defects in NC development can result in syndromes known as neurocristopathies. Neuroblastoma is one of the most common forms of pediatric cancer affecting nearly 800 infants each year in the United States (Takita et …

Importance Of The Microhabitat And Microclimate Conditions In The Northern Gray-Cheeked Salamander (Plethodon Montanus) Across An Elevation Gradient, Trevor Chapman

Electronic Theses and Dissertations

The southern Appalachian Mountains have among the highest salamander diversity in the world, largely due to local speciation in the family Plethodontidae. Plethodontid salamanders (i.e., lungless salamanders) are particularly sensitive to habitat climate conditions due to their reliance on cutaneous respiration, and their immediate environmental conditions (microhabitat) likely influence their dispersion and activity more than the large-scale atmospheric conditions. The Northern Gray-cheeked salamander (Plethodon montanus) is restricted to high elevations in the Appalachian Mountains. Our goal was to investigate the relationship between P. montanus and its microhabitat by examining behavioral preference for climatic conditions, characterizing the microclimate with …

Internal Vertebral Morphology Of Bony Fishes Matches The Mechanical Demands Of Different Environments, Dana Baxter, Karly E. Cohen, Cassandra M. Donatelli, Eric D. Tytell

Engineering Faculty Articles and Research

Fishes have repeatedly evolved characteristic body shapes depending on how close they live to the substrate. Pelagic fishes live in open water and typically have narrow, streamlined body shapes; benthic and demersal fishes live close to the substrate; and demersal fishes often have deeper bodies. These shape differences are often associated with behavioral differences: pelagic fishes swim nearly constantly, demersal fishes tend to maneuver near the substrate, and benthic fishes often lie in wait on the substrate. We hypothesized that these morphological and behavioral differences would be reflected in the mechanical properties of the body, and specifically in vertebral column …

Covid-19-Impacted Research And Education In Global Healthcare And Stem: Evaluation Of Case Studies, Yumna Indorewala, Santanu De

Trick to the Treat of Internships and Research

The zoonotic novel coronavirus has posed major challenges to the world’s economy, social development, and public health. Effects in the education and research in the field of healthcare and STEM are accentuated in lower-developed countries or communities where the access to technology and a reliable internet connection are luxuries making it difficult to attain education virtually. The Coronavirus Infectious Disease 2019 (COVID-19) has also disrupted research and training in STEM and healthcare. With significant increases in infection rates there is an urge to redirect projects towards virology research and vaccine development. This comprehensive literature review includes case studies highlighting the …

Global Research In Anatomy And Physiology During Covid-19: Lessons Learnt And Future Recommendations, Harsh Chheda, Jeet Patel, Santanu De

Trick to the Treat of Internships and Research

The ongoing Coronavirus Infectious Disease 2019 (COVID-19) pandemic has caused a significant disruption in several areas of research within the fields of Anatomy and Physiology. With the whole world coming to a standstill, research of any kind was difficult to pursue, especially in these disciplines requiring kinesthetic/tactile application of concepts or testing hypotheses through hands-on engagement, as the new social guidelines and risks to certain groups of people hindered up-to-date research-data collection. However, with new technology and protocols created or adopted, there has been an effort to better help students and scientists to conduct research remotely; such alternatives cannot effectively …

Could Annual Killifish Help Us Treat Macular Degeneration With Carmen Rodriguez, Carmen C. Rodriguez

PDXPLORES Podcast

In this episode of PDXPLORES, Carmen Rodriguez, a Ph.D. student in the biology department, discusses the Annual Killifish--a remarkable organism with the ability to survive long periods without oxygen or water--and how the unusual biology of this fish could unlock treatments for macular degeneration.

Click on the "Download" button to access the audio transcript.

The Effect Of Infection Risk On Female Blood Transcriptomics, Brenna M. G. Gormally, Patricia C. Lopes

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Defenses against pathogens can take on many forms. For instance, behavioral avoidance of diseased conspecifics is widely documented. Interactions with these infectious conspecifics can also, however, lead to physiological changes in uninfected animals, an effect that is much less well understood. These changes in behavior and physiology are particularly important to study in a reproductive context, where they can impact reproductive decisions and offspring quality. Here, we studied how an acute (3 h) exposure to an immune-challenged male affected female blood transcriptomics and behavior. We predicted that females paired with immune-challenged males would reduce eating and drinking behaviors (as avoidance …

Early-Exercise Effects On Mice Tendon Remodeling, Miles Valencia

Electronic Theses, Projects, and Dissertations

Tendons connect and transmit energy between muscles and bones and play a key role in movement. Tendon remodels by breaking down and absorbing tendon components including collagen fibers and elastin while replacing them with newly formed tendon. These processes can be influenced by short- and long-term factors such as exercise and aging; the magnitude of influence on tendon remodeling remains unclear. I researched the effects of maturation and exercise on tendon remodeling using a mice colony artificially selected for high voluntary wheel running called high-runner mice. Control and high-runner linetype mice were separated into 2 age cohorts that started training …

Maternal Responses In The Face Of Infection Risk, Patricia C. Lopes, Brenna M. G. Gormally, Aubrey Emmi, Delilah Schuerman, Chathuni Liyanage, Ursula K. Beattie, L. Michael Romero

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

When animals are sick, their physiology and behavior change in ways that can impact their offspring. Research is emerging showing that infection risk alone can also modify the physiology and behavior of healthy animals. If physiological responses to environments with high infection risk take place during reproduction, it is possible that they lead to maternal effects. Understanding whether and how high infection risk triggers maternal effects is important to elucidate how the impacts of infectious agents extend beyond infected individuals and how, in this way, they are even stronger evolutionary forces than already considered. Here, to evaluate the effects of …

Female Presence Does Not Increase Testosterone But Still Ameliorates Sickness Behaviours In Male Japanese Quail, Brenna M. G. Gormally, Kaelyn Bridgette, Aubrey Emmi, Delilah Schuerman, Patricia C. Lopes

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Infections can dramatically modify animal behaviour. The extent of these changes depends on an animal's environment. It has been proposed that testosterone modulates the suppression of behavioural symptoms of sickness under certain reproductive contexts. To further understand the role played by testosterone in modulating sickness behaviours under reproductive contexts, we studied a species, the Japanese quail, in which female exposure rapidly decreases circulating testosterone in males. Males received either an immune challenge (lipopolysaccharide – LPS) or a control injection and their behaviours, mass change and testosterone levels were quantified in the presence or absence of a female. Both the presence …

Developing A Novel Place Preference Assay To Compare Drosophila Species Over Time, Martha M. Brinson

Honors Theses

Across phylogeny, integration of external factors, memory, and internal states of the organism dictate organismal behavior and mechanisms. The underlying genetic components can affect these behaviors such as in genomic changes arising from speciation. In this thesis, a new place preference assay was evaluated in the analysis and investigation of two species of Drosophila flies (D. melanogaster and D. simulans) to measure similarities and differences and their attraction to two different food substrates. Sleep and circadian measurements were also recorded during experimentation. The Drosophila Activity Monitor 5M (DAM5M) System and Sleep Circadian Analysis MATLAB Program (SCAMP) analysis were …

Cold Shock Induces A Terminal Investment Reproductive Response In C. Elegans, Leah Gulyas, Jennifer R. Powell

Biology Faculty Publications

Challenges from environmental stressors have a profound impact on many life-history traits of an organism, including reproductive strategy. Examples across multiple taxa have demonstrated that maternal reproductive investment resulting from stress can improve offspring survival; a form of matricidal provisioning when death appears imminent is known as terminal investment. Here we report a reproductive response in the nematode Caenorhabditis elegans upon exposure to acute cold shock at 2 °C, whereby vitellogenic lipid movement from the soma to the germline appears to be massively upregulated at the expense of parental survival. This response is dependent on functional TAX-2; TAX-4 cGMP-gated channels …

Self-Conscious Emotions And The Right Fronto-Temporal And Right Temporal Parietal Junction, Adriana Lavarco, Nathira Ahmad, Qiana Archer, Matthew Pardillo, Ray Nunez Castaneda, Anthony Minervini, Julian Keenan

Department of Biology Faculty Scholarship and Creative Works

For more than two decades, research focusing on both clinical and non-clinical populations has suggested a key role for specific regions in the regulation of self-conscious emotions. It is speculated that both the expression and the interpretation of self-conscious emotions are critical in humans for action planning and response, communication, learning, parenting, and most social encounters. Empathy, Guilt, Jealousy, Shame, and Pride are all categorized as self-conscious emotions, all of which are crucial components to one’s sense of self. There has been an abundance of evidence pointing to the right Fronto-Temporal involvement in the integration of cognitive processes underlying the …

People-Powered Research And Experiential Learning: Unravelling Hidden Biodiversity, Melanie Pivarski, Matt Von Konrat, Tom Campbell, Numerous Other Co-Authors

Biology Faculty Publications

Globally, thousands of institutions house nearly three billion scientific collections offering unparallelled resources that contribute to both science and society. For herbaria alone - facilities housing dried plant collections - there are over 3,000 herbaria worldwide with an estimated 350 million specimens that have been collected over the past four centuries. Digitisation has greatly enhanced the use of herbarium data in scientific research, impacting diverse research areas, including biodiversity informatics, global climate change, analyses using next-generation sequencing technologies and many others. Despite the entrance of herbaria into a new era with enhanced scientific, educational and societal relevance, museum specimens remain …