Biology Commons^™

In Sickness And In Health: Parasites Of Stranded Pacific Harbor Seals (Phoca Vitulina Richardii) In Northern Oregon And Southern Washington, Cecily Douglas Bronson

Dissertations and Theses

Parasites have the capability to infect virtually every living organism on the planet and have adapted to infiltrate every trophic level. Many species have complex indirect life cycles and rely upon hosts at different levels of the food web for growth and reproduction. In the marine environment, having a high level of parasite diversity is thought to indicate a more stable ecosystem than an environment with low parasite diversity. As one of the top predators in their environment and because of their amphibious behaviors, pinnipeds (seals and sea lions) are exposed to a wide variety of parasites, making them ideal …

Fitness Effects Of Somatic Mutations Accumulating During Vegetative Growth, Mitchell Cruzan, Matthew A. Streisfeld, Jaime A. Schwoch

Biology Faculty Publications and Presentations

The unique life form of plants promotes the accumulation of somatic mutations that can be passed to offspring in the next generation, because the same meristem cells responsible for vegetative growth also generate gametes for sexual reproduction. However, little is known about the consequences of somatic mutation accumulation for offspring fitness. We evaluate the fitness effects of somatic mutations in Mimulus guttatus by comparing progeny from self-pollinations made within the same flower (autogamy) to progeny from self-pollinations made between stems on the same plant (geitonogamy). The effects of somatic mutations are evident from this comparison, as autogamy leads to homozygosity …

Evaluation Of Postmortem Protein Expression In Determining Cause Of Death, Zoe Robinson

University Honors Theses

Cause of death differentiation during a medicolegal autopsy can be complicated by several factors, including sample conditions which can create uncertainty. Postmortem protein analysis has potential to be used as an additional evidentiary tool in determining cause of death. Proteomic biomarkers offer a method to directly measure physiological conditions at time of death that are stable in a postmortem state. Specific protein expression levels have been studied for their postmortem application in significantly differentiating many different causes of death. Work done in regard to asphyxial, toxicological, and traumatic deaths will be specifically discussed here. Proteins will be reviewed for potential …

The Effect Of Media And Filtration In Inducing The Oxidative Stress Response In Escherichia Coli, Suzanne Hollingsworth

University Honors Theses

Escherichia coli grown in complex medium (LB), but not defined medium (DGC), arrest DNA replication when collected on membrane filters and resuspended in fresh media. The arrest is similar to that observed when cells are challenged with hydrogen peroxide. Yet, the reason behind this arrest is unknown.

I hypothesized that the arrest in replication in complex medium after filtering might be due to oxidative shock, and therefore cells grown in complex medium and filtered should induce an oxidative stress response similar to cells treated with hydrogen peroxide. Utilizing the indicator dye H₂DCFDA, which fluoresces in response to reactive …

Ours Lived Lived: Faculty Responses To Stem Students' Lived Experiences, Stan Nguyen

University Honors Theses

Science, technology, engineering and mathematics (STEM) fields have historically had low undergraduate retention rates. To aid in counteracting this, classroom exercises, or 'belonging interventions' can play a vital role in keeping new STEM students motivated through the "cultural shock" period of the college transition. However, much is still unknown about STEM instructors' perceptions on belonging interventions in STEM classrooms. Would understanding students' lives and experiences in the past and present help them make better informed decisions in their teaching practices?

To answer this question, we drew upon results from a belonging intervention conducted by the Biology Education Research (BER) group …

Terrestrial Movements, Activity Patterns And Habitat Use By Kinosternon Scorpioides (Testudines: Kinosternidae) In Palo Verde National Park, Costa Rica, Jose M. Mora, Franklin E. Castaneda

Biology Faculty Publications and Presentations

The Scorpion Mud turtle, Kinosternon scorpioides, is a widely distributed, semiaquatic species known to engage in regular terrestrial movement and terrestrial estivation. We studied terrestrial behavior in this species in Palo Verde National Park, northwestern Costa Rica. We determined terrestrial activity patterns by searching for active individuals during transects along 3.4 km of trails. We determined the distance that turtles traveled between the wetlands and estivation sites by fitting 10 terrestrially active individuals with a thread-bobbin tracking device attached to the rear of the carapace. We identified sex and marked and measured every turtle found active. We accumulated 92 observations …

Characterizing The Functional Role Of Transcription Factor E In Archaeal Transcription, Madolyn Hofstetter, Michael Bartlett

Student Research Symposium

Archaea and eukaryotes share many homologous proteins and essential mechanisms for survival and DNA replication. It is proposed that Archaea are the ancestors of eukaryotes, suggesting that eukaryotic transcription evolved from the basic archaeal mechanisms. By studying the fundamentals of archaeal transcription, we are in turn understanding more about how eukaryotic transcription functions. Many human diseases are linked to mishaps and mutations in the process of transcribing DNA to mRNA, so it is essential to explore structures and how mutations in these structures affect the essential function of transcription, and if these mutations also play a role in human disease.

Visualization Of Eye Development In Annual Killifish Using Whole-Mount Immunohistochemistry, Carmen Z. Rodriguez, Jason Podrabsky

Student Research Symposium

Vertebrate eye development is highly conserved. Current models have identified the gene networks involved in eye development, but lack the context of extreme environmental conditions that challenge these fundamental programs. Typical vertebrates live for many years while annual killifishes can complete their entire adult lifespan in a matter of weeks. Thus, annual killifishes are a strong model for age-related diseases such as age-related macular degeneration (AMD); an irreversible loss of central vision. Annual killifishes enter embryonic diapause; a period of developmental and metabolic dormancy. These embryos are extremely resistant to environmental stresses such as hypoxia/anoxia that would cause irreparable damage …

Survey Of The Bees And Floral Use At The Leach Botanical Garden, Joshua Page

Student Research Symposium

There have been few studies of the diversity of bee species found in Oregon’s urban areas, and fewer studies that have systematically examined how bee populations change over the seasons. A survey of native bee populations at the Leach Botanical Gardens was conducted to determine what bees were present, how they changed over the season, and what flowers they used. Biweekly over the 2020 and 2021 bee seasons, sections of the garden were sampled in 30 minute equal time intervals, divided among the patches of flowering plants on which bees were observed. Bee specimens were captured with collection vials on …

Mutant Viruses From Hell: Comparing The Capsid Structure Of Vp1 Mutants To The Wild-Type, Jenni Tran, Thejanee Liyanaarachchi, Ignacio De La Higuera, Jono Abshier, Ken Stedman

Student Research Symposium

Viruses can be defined as genetic material tightly packed in a protein coat called the capsid. The spindle-shaped fuselloviruses are found worldwide in hot springs at over 80°C and below pH 4. Sulfolobus spindle-shaped virus 1 (SSV1) is a fusellovirus known to infect the archaea, Saccharolobus solfataricus. This research will provide further insights into the survival of macromolecules, particularly proteins, that are present in extreme environments. To study the interaction of proteins within these extreme environments, we are studying the capsid structure of SSV1. The capsid of SSV1 is composed of two main proteins, VP1 (major) and VP3 (minor). There …

Using Wgcna To Examine Rnaseq Expression Data In The Annual Killifish Austrofundulus Limnaeus, Patrick Clouser, Jason Podrabsky

Student Research Symposium

Annual killifish (Austrofundulus limnaeus) live in ephemeral ponds of Venezuela. They have evolved a unique life history that includes experience embryonic diapause; a period of developmental dormancy and metabolic arrest that supports survival during the dry season. Developing and diapausing embryos are extremely resistant to environmental stresses; for example, they can survive for months without oxygen (anoxia). A. limnaeus’ tolerance to anoxia is an important survival mechanism as they can spend months buried in anoxic soil during development. I hypothesize that this extreme anoxia tolerance is supported by gene expression networks that are different from typical vertebrates. To evaluate this …

An Investigation Of Microbial Symbiosis In Vertebrate Embryonic Diapause Using Austrofundulus Limnaeus As A Model, Jose Camara-Lavadores

Student Research Symposium

Studies emphasizing the crucial dynamic between multicellular organisms and microbes continue to broaden our understanding on how these relationships lead to pathogenicity or mutual benefit. Many studies show that microbes can aid hosts through a variety of mechanisms including: metabolism, neuro development, physical performance, and behavior. In this study we aim to characterize the microbiota of the annual killifish Austrofundulus limnaeus, and investigate the potential role that microbes may have in supporting embryonic diapause. Diapausing embryos can survive extreme environmental stresses such as anoxia, drought, and fluctuating osmolarity and pH. Understanding the potential role that microbes may play in …

How Are Changes In Temperature And Salinity Impacting Intertidal Mussels?, Casey A. Martin

Student Research Symposium

Marine organisms living within the intertidal zones, such as mussels, experience a wide range of environmental conditions every day. Due to Climate change, these environments are transforming in such a way that may impact a mussels ability to successfully reproduce, grow, and live. Previous studies have shown that successful gamete development in freshwater mussels has been linked to temperature and species behavior has been observed to be influenced by salinity levels. In order to test the impact of temperature and salinity on mussel physiology, mussels were exposed to several treatments with varying conditions. Those conditions included a combination of a …

Exploring The Function Of Heart Regeneration In Survival Of Anoxia In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Connor Taylor Kime

Student Research Symposium

Cardiovascular disease is the leading cause of death in the world, half of which is caused by myocardial infarction (MI) or heart attack. Most of the damage resulting from MI is due to oxygen deprivation that leads to cell death. The resulting cardiac scarring due to MI is chronic in humans and is not yet treatable; the only method of restoration is heart transplantation. Other organisms, such as fishes, show great cardiac regenerative capacity. The annual killifish, Austrofundulus limnaeus, can survive for months without oxygen at certain developmental stages. Examining gene expression responses during anoxic exposure and recovery in …

Impacts Of Doliolids On The Marine Microbial Community Off The Oregon Coast, Melissa Steinman, Anne Thompson, Kelly Sutherland

Student Research Symposium

Marine microbes drive global biogeochemical cycling and are critical to sequestering carbon dioxide from the atmosphere to the ocean. Predation on marine microbes by viruses and single-celled microbes is well documented, yet models of microbial mortality with these sources do not account for observations of microbial death. We examined how an understudied group of animals, pelagic tunicates, could feed on marine microbes using an internal mucous mesh. One group of pelagic tunicates, the doliolids, have the potential to reshape marine microbial communities when they bloom. We sampled doliolids off the Oregon Coast and characterized the diversity, taxonomy, and relative abundance …

Measuring Volatile Emissions From Moss Gametophytes: A Review Of Methodologies And New Applications, Danlyn L. Brennan, Leslie M. Kollar, Scott Kiel, Timea Deakova, Aurélie Laguerre, Stuart F. Mcdaniel, Sarah Eppley, Elliott T. Gall, Todd Rosenstiel

Center for Life in Extreme Environments Publications

Mosses inhabit nearly all terrestrial ecosystems and engage in important interactions with nitrogen-fixing microbes, sperm-dispersing arthropods, and other plants. It is hypothesized that these interactions could be mediated by biogenic volatile organic compounds (BVOCs). Moss BVOCs may play fundamental roles in influencing local ecologies, such as biosphere–atmosphere–hydrosphere communications, physiological and evolutionary dynamics, plant–microbe interactions, and gametophyte stress physiology. Further progress in quantifying the composition, magnitude, and variability of moss BVOC emissions, and their response to environmental drivers and metabolic requirements, is limited by methodological and analytical challenges. We review several sampling techniques with various analytical approaches and describe best practices …

Embryological Development And Mortality Of Danio Rerio In Long Term Exposure To 17Α-Ethynylestradiol, Seong A. Jeon

University Honors Theses

Synthetic estrogens as well as other chemicals have become an increasing issue in the impact they have on marine species particularly those sensitive to the environment. A broadly used synthetic estrogen, 17α-ethynylestradiol, has become more widely known to become a growing problem to the ecology of marine wildlife due to increased usage and lack of removal in municipal sewage treatment facilities. This study observes the impact of low level EE2 in embryos following generational exposure. Zebrafish embryos, following three generations of exposure, were observed in rate of mortality, lethality, and hatch success. Concentrations as low as 1ng/L of EE2 has …

Cetacean Strandings In The Us Pacific Northwest 2000–2019 Reveal Potential Linkages To Oceanographic Variability, Amanda J. Warlick, Jessica L. Huggins, Dyanna M. Lambourn, Deborah A. Duffield, Dalin Nichole D'Alessandro, James M. Rice, John Calambokidis, M. Bradley Hanson, Joseph K. Gaydos, Multiple Additional Authors

Biology Faculty Publications and Presentations

Studying patterns in marine mammal stranding cases can provide insight into changes in population health, abundance, and distribution. Cetaceans along the United States West coast strand for a wide variety of reasons, including disease, injury, and poor nutritional status, all of which may be caused by both natural and anthropogenic factors. Examining the potential drivers of these stranding cases can reveal how populations respond to changes in their habitat, notably oceanographic variability and anthropogenic activities. In this study, we aim to synthesize recent patterns in 1,819 cetacean strandings across 26 species in the Pacific Northwest from 2000 to 2019 to …

Mitonuclear Mismatch Is Associated With Increased Male Frequency, Outcrossing, And Male Sperm Size In Experimentally-Evolved C. Elegans, Brent W. Bever, Zachary P. Dietz, Jennifer Anne Sullins, Ariana M. Montoya, Ulfar Bergthorsson, Vaishali Katju, Suzanne Estes

Biology Faculty Publications and Presentations

We provide a partial test of themitonuclear sex hypothesiswith the first controlled study of how male frequencies and rates of outcrossing evolve in response to mitonuclear mismatch by allowing replicate lineages of C. elegans nematodes containing either mitochondrial or nuclear mutations of electron transport chain (ETC) genes to evolve under three sexual systems: facultatively outcrossing (wildtype), obligately selfing, and obligately outcrossing. Among facultatively outcrossing lines, we found evolution of increased male frequency in at least one replicate line of all four ETC mutant backgrounds tested—nuclear isp-1, mitochondrial cox-1 and ctb-1, and an isp-1 IV; ctb-1M mitonuclear double mutant—and confirmed for …

A Literary Examination Of The Efficacy Of Zoological Conservation In The United States Versus Foreign Efforts, Madeleine M. Lecorre

University Honors Theses

Falling into the top four threats to biodiversity, human activity is impacting species around the globe like never before. Zoological conservation of threatened species aids in the support and reestablishment of these dwindling populations. The examination of conservation work done in the U.S compared to foreign efforts provides insight into strengths, reveals weaknesses, and will help us better serve threatened species around the world. The status of conservation in the U.S. as well as foreign efforts were assessed through literary review of published reports from accredited organizations. As zoologic conservation aims to conserve threatened species, it is also important to …

Genome-Wide Identification Of Novel Srnas In Streptococcus Mutans, Madeline Claire Krieger, Justin Merritt, Rahul Raghavan

Biology Faculty Publications and Presentations

Streptococcus mutans is a major pathobiont involved in the development of dental caries. Its ability to utilize numerous sugars and to effectively respond to environmental stress promotes S. mutans proliferation in oral biofilms. Because of their quick action and low energetic cost, non-coding small RNAs (sRNAs) represent an ideal mode of gene regulation in stress response networks, yet their roles in oral pathogens have remained largely unexplored. We identified 15 novel sRNAs in S. mutans and show that they respond to four stress-inducing conditions commonly encountered by the pathogen in human mouth: sugar-phosphate stress, hydrogen peroxide exposure, high temperature, and …

Recombination Mediator Proteins: Misnomers That Are Key To Understanding The Genomic Instabilities In Cancer, Justin Courcelle, Travis K. Worley, Charmain Courcelle

Biology Faculty Publications and Presentations

Recombination mediator proteins have come into focus as promising targets for cancer therapy, with synthetic lethal approaches now clinically validated by the efficacy of PARP inhibitors in treating BRCA2 cancers and RECQ inhibitors in treating cancers with microsatellite instabilities. Thus, understanding the cellular role of recombination mediators is critically important, both to improve current therapies and develop new ones that target these pathways. Our mechanistic understanding of BRCA2 and RECQ began in . Here, we review the cellular roles of RecF and RecQ, often considered functional homologs of these proteins in bacteria. Although these proteins were originally isolated as genes …

Diversity, Biology, And History Of Psilocybin-Containing Fungi: Suggestions For Research And Technological Development, R. C. Van Court, K. W. Meyer, M. S. Wiseman, Daniel J. Ballhorn, K. R. Amses, J. C. Slot, B.T. M. Dentinger, R. Garibay-Orijel, J. K. Uehling

Biology Faculty Publications and Presentations

Therapeutic use of psilocybin has become a focus of recent international research, with preliminary data showing promise to address a range of treatment-resistant mental health conditions. However, use of psilocybin as a healing entheogen has a long history through traditional consumption of mushrooms from the genus Psilocybe. The forthcoming adoption of new psilocybin-assisted therapeutic practices necessitates identification of preferred sources of psilocybin; consequently, comprehensive understanding of psilocybin-containing fungi is fundamental to consumer safety. Here we examine psilocybin producing fungi, discuss their biology, diversity, and ethnomycological uses. We also review recent work focused on elucidation of psilocybin biosynthetic production pathways, especially …

Helminths Of Thomomys Species (Rodentia: Geomyidae) Of Oregon, Malorri Rene Hughes

Dissertations and Theses

Although often viewed as inconsequential, parasites have significant ecological and evolutionary importance, and studying them can generate knowledge regarding their environments and their hosts. Helminths (intestinal parasites) infecting Western pocket gophers (Thomomys species) in Oregon had been documented based only on morphology prior to this study. Basing parasite identification solely on morphology is problematic because the characteristics used to identify species can be vague or similar, leading to misidentification or obscuring the true biodiversity present. Using molecular markers to verify species present not only is more reliable but also can be informative in terms of the host-parasite association. To …

New Opportunities And Untapped Scientific Potential In The Abyssal Ocean, Jeffrey J. Marlowe, Rika E. Anderson, Anna-Louise Reysenbach, Jeffrey S. Seewald, Timothy M. Shank, Andreas P. Teske, V. Dorsey Wanless, S. Adam Soule

Biology Faculty Publications and Presentations

The abyssal ocean covers more than half of the Earth’s surface, yet remains understudied and underappreciated. In this Perspectives article, we mark the occasion of the Deep Submergence Vehicle Alvin’s increased depth range (from 4500 to 6500 m) to highlight the scientific potential of the abyssal seafloor. From a geologic perspective, ultra-slow spreading mid-ocean ridges, Petit Spot volcanism, transform faults, and subduction zones put the full life cycle of oceanic crust on display in the abyss, revealing constructive and destructive forces over wide ranges in time and space. Geochemically, the abyssal pressure regime influences the solubility of constituents such as …

Culturable Fungal Endophyte Communities Of Primary Successional Plants On Mount St. Helens, Wa, Usa, Emily R. Wolfe, Robyn Dove, Cassandra Webster, Daniel J. Ballhorn

Biology Faculty Publications and Presentations

Background: While a considerable amount of research has explored plant community composition in primary successional systems, little is known about the microbial communities inhabiting these pioneer plant species. Fungal endophytes are ubiquitous within plants, and may play major roles in early successional ecosystems. Specifically, endophytes have been shown to affect successional processes, as well as alter host stress tolerance and litter decomposition dynamics—both of which are important components in harsh environments where soil organic matter is still scarce.

Results: To determine possible contributions of fungal endophytes to plant colonization patterns, we surveyed six of the most common woody …

A Survey Of The Solitary Native Bees Of The Leach Botanical Garden, And Their Floral Associations, Joshua Page

Biology Undergraduate Honors Theses

Solitary native bees are known to be diverse, but are not well studied in Oregon. In order to identify the bee genera present in the Leach Botanical Garden, and their floral usage, a survey was conducted over 2020 and 2021. Biweekly sampling was used to collect bees on flowers, in order to obtain floral usage data. Bees were identified to genus with published taxonomic keys. In total, 19 genera of bees were found. Bee abundance fit a normal distribution, and peaked in July. Ceratina and Lasioglossum were a significant proportion of the population, and were present in the garden from …

Species-Specific Interactions In Avian–Bryophyte Dispersal Networks, Matthew Chmielewski, Sarah Eppley

Biology Faculty Publications and Presentations

Studies from seed plants have shown that animal dispersal fundamentally alters the success of plant dispersal, shaping community composition through time. Our understanding of this phenomenon in spore plants is comparatively limited. Though little is known about species-specific dispersal relationships between passerine birds and bryophytes, birds are particularly attractive as a potential bryophyte dispersal vector given their highly vagile nature as well as their association with bryophytes when foraging and building nests. We captured birds in Gifford Pinchot National Forest to sample their legs and tails for bryophyte propagules. We found 24 bryophyte species across 34 bird species. We examined …

Phylogenetics And Genetic Variation Of Heligmosomoides Thomomyos In Western Pocket Gophers (Thomomys Spp.), Malorri R. Hughes, Alexandra A. Gibson, Emily R. Wolfe, Cecily D. Bronson, Deborah A. Duffield

Biology Faculty Publications and Presentations

The host specificities and systematics of North American Heligmosomoides species remain particularly uncertain. The primary aim of this study was to verify that a species described previously based only on morphology, H. thomomyos, from pocket gopher (Rodentia: Geomyidae) hosts in Oregon represented a monophyletic lineage. In order to address this aspect, as well as to further understand relationships and geographic patterns, we carried out phylogenetic, genetic diversity, and population dynamic analyses using partial 18S rRNA and COI mtDNA sequences of Heligmosomoides specimens. Phylogenetic analyses suggested that there are likely multiple Heligmosomoides species present in these hosts. This was supported by …

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 …