Life Sciences Commons^™

Virology: Mutagenizing The Proteolytic Cleavage Site In The Major Capsid Protein In Ssv1, Thejanee Liyanaarachchi

University Honors Theses

SSV1, spindle-shaped virus 1, is an archaeal virus with a unique shape that belongs to the family of fuselloviruses and infects hyperthermophilic archaea that thrive at 80°C and pH 3. SSV1 has two capsid proteins, VP1 and VP3, that presumably produce the lemon-shaped virion structure characteristic of fuselloviruses. The VP1 amino acid sequence is highly conserved among SSVs. Here, we investigate the importance of the proteolytic cleavage site in position E66 in VP1 by changing its glutamic acid to the other 19 amino acids. We have developed a new protocol for creating SSV1 mutants through HiFi Assembly (NEB) to increase …

Plastic-Eating Microbes: A New Potential Solution To Waste Mitigation?, Megan Forbes

University Honors Theses

Plastic waste is problematic for marine and terrestrial ecosystems due to the mass production of polyethylene terephthalate (PET) single use plastics. What is unclear is a well-thought-out solution to solve pollution problems that will not further damage the environment. Throughout this literature review, I will investigate the role microbes play in plastic degradation, and if plastic eating microbes are an effective solution to the plastic pollution problem. Polyethylene terephthalate (PET) is the chemical name for polyester. It is a clear, strong, and lightweight plastic that is typically used for food and beverage packaging, and other single-use purposes. The most well …

Effects Of Hormone Replacement Therapy (Hrt) On Gene Expression In The Amyloid Processing Pathway Of Ovariectomized Rhesus Macaque Females Under An Obesogenic Diet, Megan Ball

University Honors Theses

Estrogens rapidly decline at the onset of menopause, putting women at higher risk of osteoporosis, obesity, and neurodegenerative diseases, including Alzheimer’s disease (AD). Estradiol hormone therapies (HT) have been suggested to limit these negative effects on women, with controversial findings as to their effectiveness. A study at OHSU recently found differentially expressed genes (DEGs) using RNAseq between ovariectomized/hysterectomized (OvH) old (range = 19.4–23.2 years) female rhesus macaques on HT and those on a placebo on chronic western style diet (WSD). The DEGs identified in the amyloid processing pathway of the amygdala were selected for validation using RT-qPCR because β-amyloid peptide …

Understanding The Effect Of Dietary Palmitic Acid On Glycolysis During Innate Immune Memory In Macrophages, Khaleda A. Aqaei

University Honors Theses

Trained immunity is long-term innate immune memory induced by a primary stimulus, which leads to hyper-inflammation upon secondary stimulation with a homologous or heterologous ligand. Trained immunity is mediated by epigenetic and metabolic reprogramming of the target cell and leads to modification of gene expression and cellular function. Classically, trained immunity is initiated by β-glucans, an inflammatory molecule found on the exterior of fungal species. Interestingly, our lab has recently described that dietary fatty acids can initiate trained immunity, working through similar pathways as β-glucans. Specifically, our data show that a pre-treatment with a specific dietary saturated fatty acid (SFA), …

Beaver Reintroduction And Its Potential As An Ecological Conservation Measure For At-Risk Amphibian Species In The Pacific Northwest, Danielle Schwantes

University Honors Theses

Amphibian decline is a major concern in the Pacific Northwest (PNW), with many amphibian species listed as sensitive, threatened or endangered throughout the region. Some of the predicted main causes of amphibian decline are climate change and loss of habitat. The reintroduction of beavers into ecoregions of the PNW could be an important step in the conservation of this region’s amphibians, due to the beaver’s ability to engineer and structurally manipulate forest ecosystems. Beavers are able to restore wetland quality, productivity and biodiversity, creating vital amphibian habitat. This work explored the linkage between beaver presence and wetland hydrology, geomorphology, landscape …

Examination Of Exhaustion In Larval Pacific Lamprey (Entosphenus Tridentatus) Through Variations Of Temperature, Flow, And Cover, Jessica Falcon

University Honors Theses

Pacific lampreys (Entosphenus tridentatus) are culturally and ecologically valuable throughout the western coast of North America. The larval (ammocoete) stage of the Pacific lamprey spends three to eight years burrowed in the sediment as a filter feeder, and is an essential contributor to many of the Northwest’s freshwater ecosystems. Larval lamprey may be vulnerable to warming waters caused by climate change as well as seasonal dredging and salvaging events that dislodge lamprey from sediment, as they prefer cooler water and are relatively poor swimmers in comparison to other fish such as salmon. In this study, we observed how …

Functional Role Of The N-Terminal Domain In Connexin 46/50 By In Silico Mutagenesis And Molecular Dynamics Simulation, Umair Khan

University Honors Theses

Connexins form intercellular channels known as gap junctions that facilitate diverse physiological roles, from long-range electrical and chemical coupling to nutrient exchange. Recent structural studies on Cx46 and Cx50 have defined a novel and stable open state and implicated the amino-terminal (NT) domain as a major contributor to functional differences between connexin isoforms. This thesis presents two studies which use molecular dynamics simulations with these new structures to provide mechanistic insight into the function and behavior of the NTH in Cx46 and Cx50. In the first, residues in the NTH that differ between Cx46 and Cx50 are swapped between the …

Where To Draw The Line: Evaluating Visuospatial And Attentional Processing In Individuals With Autism Spectrum Disorders, Alisha Steigerwald

University Honors Theses

Objective: We investigated visuospatial processing in individuals with autism using bisection and quadrisection tasks to evaluate the presence of a possible downward vertical spatial bias that could provide insights into the preference for attending to the mouth in ASD populations.

Methods: Twenty participants with ASD and 20 age, IQ, and sex-matched control participants were recruited (ages 6-23). Participants were asked to bisect, quadrisect from the top, and quadrisect from the bottom vertical lines placed in their left, center, and right visual spaces. Distance from the true midpoint and quadripoint were calculated and compared between the two groups.

Results: No significant …

The Role Of Native Lens Α-Crystallin In Amyloid Suppression Using Β-Amyloid As A Model Amyloid Client, Leilani Lopes

University Honors Theses

Cataracts are a result of age-related protein aggregate formation in the eye lens, and the leading cause of blindness worldwide. α-crystallin, a small heat shock protein, acts a molecular chaperone that serves as the primary defense mechanism against protein aggregate formation in the lens. Recent evidence suggest amyloid formation in the lens may contribute to cataract formation, and that β-amyloid is present in lens epithelia of age-related cataracts. Previous studies have shown that αB-crystallin in other parts of the body, such as the brain, is protective against neurodegenerative diseases such as Alzheimer’s disease that are associated with plaque deposits containing …

Bryophyte Ecosystem Services: How Bryophytes Impact Ecosystem Processes And Their Use In Urban Systems, Keila Spangler

University Honors Theses

Bryophytes, which include mosses, liverworts, and hornworts, are non-vascular plants that provide crucial ecosystem services in natural and urban systems. In natural systems, these services include carbon, water, and nutrient cycling and maintenance of community level biodiversity. In urban systems, bryophytes can be used as green roof substrate, as bioindicators to monitor pollution and air quality, for horticulture uses, and in medicine. Although bryophytes possess some qualities, such as reproduction by spores, that may give them an advantage compared to vascular plants as the climate warms, their response to climate change remains understudied. This paper will review the literature on …

Our Peer The Pigeon: Impacts Of The Covid-19 "Anthropause" On Psu Campus Urban Foragers, Audrey Douglass

University Honors Theses

The 2020 COVID Pandemic presented a paradigm shift dubbed, by some scholars, the 'Anthropause', an ecological epoch in which humans faded from the public sphere. As was the case for many urban species that depend on the foraging of food waste, this meant a fundamental disruption to their food systems and to the entire urban eco-web. The PSU Campus Park Blocks presents a unique opportunity to observe animal behavior, while also a succinct microcosm to study food waste flow changes, and compare species layout to other urban parks in the METRO area. Decreased food waste output from proximal …

Human Impact On Pacific Harbor Seals In Urban Southern Puget Sound, Washington, Vicky Gomez

University Honors Theses

This research proposal aims to highlight the quantitative and qualitative impact of human disturbances Pacific Harbor Seals (Phocca vitulina) are experiencing in urban southern Puget Sound, Washington and how the data collected can educate the community to protect and conserve a healthy population of Harbor Seals. Urbanization and areas utilized by harbor seals within urban settings prompted data collection from four nearby sites: site A, Carylon Beach, includes pedestrian and boat disturbances, site B, Tacoma Tidal Flats, only experience boat disturbances, site C, West Bay Marina, experiences motorized and non-motorized boat disturbances and site D, Gertrude Island, is …

Potential Therapeutic Effects Of Snake Venom Components On Pain Management In Rheumatoid Arthritis Patients, Maggie Metzger

University Honors Theses

This paper reviews the existing literature on the uses of snake venom in the treatment of rheumatoid arthritis and pain management. Venom from the families Elapidae and Viperidae have been shown to have anti-inflammatory and analgesic effects. The analgesic findings of research on arthritis murine models are discussed, and the existing uses of snake venom in medicine to suggest the therapeutic potential of venom in the pain management of rheumatoid arthritis are taken into account. Snake venom has anti-inflammatory effects by reducing levels of pro-inflammatory cytokines and increasing levels of anti-inflammatory cytokines. Additionally, snake venom can reduce structural damage from …

The Usage Of Resveratrol For Eye Pain After Refractive Surgery, Dennis Nguyen

University Honors Theses

LASEK and PRK are common laser corrective eye procedures that aim to correct the refractive errors of the eye, although these procedures do carry the potential of post-operation complications of dry eye and symptoms of pain and photophobia as a result of corneal innervation damage. Resveratrol was tested on the surface of the cornea to see if the drug would be effective at attenuating post-corrective eye pain. Male and female rats underwent a unilateral corneal abrasion surgery that aimed to mimic the post-op symptoms of PRK. The rats either received the resveratrol drug treatment or a vehicle formulation. The Rat …

The Effect Of Diazepam On Early Neural Stem Cells Proliferative Activity And Hippocampal-Dependent Memory After Traumatic Brain Injury, Van Khanh Doan

University Honors Theses

Traumatic brain injury (TBI) induces an upregulation of neurogenesis in the brain specifically in the hippocampus, an area pertaining to learning and memory formation. Although this upregulated response is intuitively thought to be restorative, previous studies show that the nascent neurons generated after TBI exhibit abnormalities, such as aberrant morphologies and early migrations, which could suggest to be maladaptive. The GABA-A agonist diazepam has been shown to inhibit this upregulation in neurogenesis and normalizes dendrites after TBI. To determine whether this modulation of neurogenesis is ultimately beneficial or detrimental to cognitive recovery, diazepam was administered to C57BI/6J wild-type mice following …

Density Of Free-Roaming Cats Related To Feeding Stations On Hayden Island, Oregon, Olivia Helback, Joe Liebezeit

University Honors Theses

Free-roaming cats have a devastating impact on wildlife populations with stray/feral cats being the most problematic. In some areas, community members provide these cats with food, water, and shelter often in conjunction with a trap, neuter, return (TNR) program. Hayden Island located north of Portland, Oregon is home to a managed colony of feral and stray cats. Some island residents provide feeding stations for the cats and actively participate in population management. To determine how feeding stations might affect cat spatial distribution, camera traps were placed at 19 different stations in urban and natural areas on Hayden island. Additional annual …