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Removal As A Control Method For Trachemys Scripta Elegans And The Response Of Chrysemys Picta Bellii, Jacob Daniel Swanson

University Honors Theses

The red-eared slider is considered one of the most ubiquitous freshwater turtles globally. Several key ecological advantages and life history traits of this species jointly impact growth rates and survivorship of native freshwater turtles where sympatry occurs. Evaluation of current management actions for red-eared slider turtles is limited, resulting in a paucity of information to guide management for the species and conservation of declining native freshwater turtles. We used previously collected mark-recapture and removal sampling data from sites with sympatric populations of red-eared slider and western painted turtles. We examined the effects of control (trapping and removal) of red-eared sliders …

Prochlorococcus Death By A Ubiquitous Zooplankton Filter Feeder, Avery E. Harman

University Honors Theses

Prochlorococcus is a globally abundant cyanobacterium that can help reveal the ecology of microorganisms in the ocean. Specifically, mortality by zooplankton such as appendicularians is globally important and Prochlorococcus can help reveal some of the choices made around feeding for this ubiquitous filter feeder. Two ecotypes of Prochlorococcus were introduced to appendicularians to determine if appendicularian feed selectively between these ecotypes. Further, a single ecotype of Prochlorococcus was fed to appendicularians over a variety of life stages to determine if retention rate changed with appendicularian life stage. My results reveal that there is no significant selection between the two Prochlorococcus …

Oil Identification Of Harp Seal And Other Select Marine Mammals, Meghan Pinedo, Deborah A. Duffield, Dalin N. D’Alessandro, Erin R. Price, Edgard O. Espinoza

Biology Faculty Publications and Presentations

Because of the rich omega-3 fatty acids content, harp seal (Pagophilus groenlandicus) oil is a popular supplement that is packaged as pills in Canada and sold for medicinal purposes, although this practice is banned in the United States. Due to US regulations, it is important to be able to distinguish between fish oil and seal oil, but the taxonomic determination of oils provenance has been a difficult problem to solve. In this study, Direct Analysis in Real Time time-of-flight mass spectrometry (DART TOFMS) was used to analyze the chemotypes of blubber samples collected from seven species of …

The Value Of Support: Stem Intervention Programs Impact Student Persistence And Belonging., Erin E. Shortlidge, Mackenzie J. Gray, Suzanne Estes, Emma C. Goodwin

Biology Faculty Publications and Presentations

In response to unwaveringly high attrition from STEM pathways, STEM Intervention Programs (SIPs) support STEM students in effort to increase retention. Using mixed methods (survey and focus groups), we studied students at one university who were either supported or unsupported by SIPs to understand how students may differ in experiences believed to contribute to STEM persistence. We evaluated: sense of belonging, scientific self-efficacy, scientific community values, scientific identity, and STEM involvement. The enrollment status of students two and a half years postsurvey was also tracked. SIP students reported significantly higher science identity and sense of belonging and were more involved …

Exploring Factors That Contribute To Stem Transfer Student Sense Of Belonging, Brittney R. Gallant, Cate Pocitari

Student Research Symposium

There is an ongoing disconnect between the number of students who enter college intending to earn a STEM degree and the number of students who persist to degree, this is particularly true for transfer students. Sense of belonging has been named as a STEM persistence factor, yet how that belonging develops for transfer students is largely unknown. Here we used a mixed-methods design to explore the experiences of STEM transfer students at PSU (n=38). Participants completed a survey prior to participating in an interview. The survey and interviews explored their science identity, sense of belonging, and involvement in STEM-related activities. …

Mutagenetic Analysis Of The Minor Capsid Protein Vp3 Of The Archaeal Fusellovirus Ssv1, Laura Costal Lagarde

Student Research Symposium

Viruses, while often associated with disease, are integral to life and play an important role in the microbiome. Despite their importance in medical research, archaeal viruses, particularly those found in extreme environments, are not widely understood. The Sulfolobus Spindle-Shaped Viruses (SSVs) of the Fuselloviridae family are unique among viruses in that they do not kill their host, the archaeon Sulfolobus Solfataricus in volcanic hot springs, but rather slow its growth, allowing for halo assay assessments.The study focuses on the type virus SSV1, which is predominantly composed of the Major and Minor capsid proteins vp1 and vp3, respectively. Previous study has …

Examining The Role Of Rgs2 In The Maintenance Of Diapause After Anoxic Stress In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Patrick Clouser

Student Research Symposium

Austrofundulus limnaeus live in ephemeral ponds of Venezuela. They have evolved a unique life history that includes embryonic diapause, a period of developmental dormancy, metabolic arrest, and reduced protein synthesis. Diapausing embryos are resistant to environmental stress and survive months without oxygen (anoxia). A. limnaeus’ anoxia tolerance is an important survival mechanism as they can be buried in anoxic soil during development. Analysis of RNAseq data from diapausing A. limnaeus embryos show significant down-regulation of RGS2 transcripts in anoxic embryos. RGS2 regulates G-protein receptor signaling by inhibiting associated G_a-proteins and can inhibit protein synthesis. I hypothesis that …

Locating Vitamin D Receptors (Vdrs) In Annual Killifish, Austrofundulus Limnaeus, Rosalia N. Tanori, Amie L. Romney, Jason E. Podrabsky

Student Research Symposium

Austrofundulus limnaeus, a species of annual killifish found in unpredictable temporary habitats in South America, has a profound ability to survive long periods without water and oxygen. This tolerance is associated with the ability to enter metabolic dormancy associated with diapause. Entrance into diapause and tolerance of environmental stress is governed by an interplay of genetic and environmental factors. The vitamin D receptor (VDR) is among these factors and plays a crucial role in determining if an embryo will enter diapause or actively develop. My work aims to identify the genomic locations of VDR proteins in the A. limnaeus genome …

Describing Shen & Shen Ming Via A Hybrid Quantum Computational Model, Alex M. Cullen, Johnny Lemau

Student Research Symposium

Definitions for Traditional Chinese Medicine (TCM) terminology within the context of quantum biology (QB) have recently been proposed. These definitions aim to elucidate concepts such as qi meridians in TCM. Our study presents a hypothesis that seeks to provide an operational definition for Spirit (Shen) and Bright Spirit (Shen Ming) in TCM via a scoping review. We propose that Shen represents physical, phenomenological proto-consciousness/consciousness in the forms of computation, such as singular particles/bits/qubits, computers, organisms, or computational strategies, whereas Shen Ming may refer to emergent, quasi-physical meta-proto-consciousness/consciousness formed by coherent relationships of multiple orchestrated/integrated units of computation; manifesting itself as …

Qibc Analysis On Killifish Cells Under Anoxic Conditions, Jaina Canlas

Student Research Symposium

Faithful DNA replication is vital for all living organisms. Environmental stressors can cause a multitude of mutations and DNA lesions during replication leading to cell death if not accurately repaired. The annual killifish, Austrofundulus limnaeus, has a heightened tolerance to many known genotoxic stressors, including anoxia. Embryos of the annual killifish can survive months of anoxia during the dry season when the ephemeral ponds they inhabit, completely dry. During these exposures, they have shown they are capable of repairing substantial amounts of damaged DNA. This resilience has led us to hypothesize that A. limnaeus have enhanced DNA repair capabilities. …

Histone Changes As A Response To Lactic Acid Selection In Cells Of Austrofundulus Limnaeus, Lori Tran, Jason Podrabsky, Chelsea Hughes

Student Research Symposium

The killifish Austrofundulus limnaeus is an extremophile native to small temporary ponds of Venezuela. Normal embryonic development of A. limnaeus is segmented into up to three stages of metabolic depression (diapause), and both developing and diapausing embryos can survive long bouts of the complete absence of oxygen (anoxia) by using anaerobic metabolic pathways. While there has been much focus on how mutations in DNA drive evolution, environmental stress can cause heritable changes to histone post-translational modifications (hPTMs) in multiple species. However, this evolutionary role of hPTMs has never been studied in A. limnaeus. Additionally, the possible evolutionary role of extracellular …

Annual Killifish: Eye Development And Retinal Cell Regeneration, Carmen Z. Rodriguez

Student Research Symposium

Vertebrate eye development is highly conserved. Current models have allowed the understanding of gene expression patterns that support eye development, but lack the context of extreme environmental conditions that challenge these fundamental programs. Typical vertebrate life spans can be years, but annual killifish, Austrofundulus limnaeus, are able to complete their entire adult lifespan in only weeks. Thus, A. limnaeus is a strong model for age-related macular degeneration. A. limnaeus also experiences embryonic diapause; a period of developmental dormancy. Developing/diapausing embryos of A. limnaeus are resistant to environmental stresses such as hypoxia/anoxia that would cause irreparable damage to vital organs, such …

Dragon Pseudoscorpions Shed Light On Ancient Climate History In The Pacific Northwest, Joshua W. Hootman

Student Research Symposium

Pseudoscorpions are an ancient and diverse group of understudied arachnids, and there is much to be learned about their relationships to each other. Pseudoscorpions are one of many leaf-litter dwelling and low dispersing invertebrates that inhabit the forests of the Pacific Northwest. Previous phylogeographic studies of Pacific Northwest taxa have shed light on some of the climatic and geologic events that have shaped the area's flora and fauna. One purpose of this study is to determine if there is similar genetic structuring within the pseudoscorpion populations present in the study area, or if there is even more structure likely influenced …

Construction And Mutagenesis Of Ssv1 Mutants In Extreme Viruses, Lou Ann F. O'Connor, Jono Abshier, Kenneth M. Stedman

Student Research Symposium

Archaeal viruses with unique structures such as spindle-shaped virions are found abundantly in extreme environments like geothermal hot springs around the world. Among all spindle-shaped viruses, the model Sulfolobus Spindle-shaped Virus 1 (SSV1) is best studied. Creating the lemon-shaped or spindle-shaped virion structure are two proteins, VP1 as the major capsid protein, and VP3 as the minor capsid protein. The primary structure of VP1 consists of a proteolytic cleavage site at position 66 that is believed to be necessary for virus evolution. Recent studies showed that genetic mutation of the amino acid, glutamate (E) at position 66 in VP1 which …

Autism Risk Gene Cul3 Alters Neuronal Morphology Via Caspase-3 Activity In Mouse Hippocampal Neurons, Qiang-Qiang Xia, Anju Singh, Jing Wang, Zhong Xin Xuan, Jeffrey D. Singer, Craig M. Powell

Biology Faculty Publications and Presentations

Autism Spectrum Disorders (ASDs) are neurodevelopmental disorders (NDDs) in which children display differences in social interaction/communication and repetitive stereotyped behaviors along with variable associated features. Cul3, a gene linked to ASD, encodes CUL3 (CULLIN-3), a protein that serves as a key component of a ubiquitin ligase complex with unclear function in neurons. Cul3 homozygous deletion in mice is embryonic lethal; thus, we examine the role of Cul3 deletion in early synapse development and neuronal morphology in hippocampal primary neuronal cultures. Homozygous deletion of Cul3 significantly decreased dendritic complexity and dendritic length, as well as axon formation. Synaptic spine density significantly …

Effective Dispersal Patterns In Prairie Plant Species Across Human-Modified Landscapes., Elizabeth C. Hendrickson, Mitchell B. Cruzan

Biology Faculty Publications and Presentations

Effective dispersal among plant populations is dependent on vector behaviour, landscape features and availability of adequate habitats. To capture landscape feature effects on dispersal, studies must be conducted at scales reflecting single-generation dispersal events (mesoscale). Many studies are conducted at large scales where genetic differentiation is due to dispersal occurring over multiple generations, making it difficult to interpret the effects of specific landscape features on vector behaviour. Genetic structure at the mesoscale may be determined by ecological and evolutionary processes, such as the consequences of vector behaviour on patterns of gene flow. We used chloroplast haplotypes and nuclear genome SNP …

Varecia Rubra (Red Ruffed Lemur) Diel Activity And Calling At Andranobe, Masoala National Park, Madagascar, Hannah Elena Hilden-Reid

Dissertations and Theses

With respect to the natural variation in abiotic and biotic conditions present between daytime and nighttime periods, many animal species show evolutionary adaptations specialized for diurnality, nocturnality, or crepuscularity. Biologists have traditionally viewed categorizations of this kind as fixed within taxonomic groups, emphasizing how intricately species’ survival is contingent on the ability to adapt to low light, high light, or twilight conditions. However, movement away from such distinct temporal niche categories began within chronobiological studies following the discovery of more flexible patterns of activity in numerous taxa during the late 1970s. This shift generated increased interest in elucidating the complex …

Rhizobia-Legume Symbiosis Mediates Direct And Indirect Interactions Between Plants, Herbivores And Their Parasitoids, Carlos Bustos-Segura, Adrienne L. Godschalx, Lucas Malacari, Sergio Rasmann, Fanny Deiss, Daniel Ballhorn, Betty Benrey

Biology Faculty Publications and Presentations

Microorganisms associated with plant roots significantly impact the quality and quantity of plant defences. However, the bottom-up effects of soil microbes on the aboveground multitrophic interactions remain largely under studied. To address this gap, we investigated the chemically- mediated effects of nitrogen-fixing rhizobia on legume-herbivore-parasitoid multitrophic interactions. To address this, we initially examined the cascading effects of the rhizobia bean association on herbivore caterpillars, their parasitoids, and subsequently investigated how rhizobia influence on plant volatiles and extrafloral nectar. Our goal was to understand how these plant- mediated effects can affect parasitoids. Lima bean plants (Phaseoulus lunatus) inoculated with rhizobia exhibited …

Genome Editing Using Crispr-Cas9 In Annual Killifish Species, Keria Moritsugu-Vandehey

University Honors Theses

CRISPR-Cas9 genome editing has been used successfully to knock out genes in model organisms such as zebrafish, turquoise killifish, and cichlid fish. CRISPR-Cas9 genome editing has not been verified in the annual killifish, Austrofundulus limnaeus. We hypothesize that targeted editing of the tyrosinase gene in embryos of A. limnaeus will lead to fish without the ability to produce black pigment. Embryos at the 1-cell stage were injected with a Cas9 cocktail containing a mix of guide RNA molecules that target the genomic sequence of the tyrosinase gene and either an mRNA coding for the Cas9 protein or Cas9 protein. …

Ubiquitous Filter Feeders Shape Open Ocean Microbial Community Structure And Function, Anne W. Thompson, Györgyi Nyerges, Kylee M. Brevick, Kelly Sutherland

Biology Faculty Publications and Presentations

The mechanism of mortality plays a large role in how microorganisms in the open ocean contribute to global energy and nutrient cycling. Salps are ubiquitous pelagic tunicates that are a well-known mortality source for large phototrophic microorganisms in coastal and high-latitude systems, but their impact on the immense populations of smaller prokaryotes in the tropical and subtropical open ocean gyres is not well quantified. We used robustly quantitative techniques to measure salp clearance and enrichment of specific microbial functional groups in the North Pacific Subtropical Gyre, one of the largest ecosystems on Earth. We discovered that salps are a previously …

A Genus In The Bacterial Phylum Aquificota Appears To Be Endemic To Aotearoa-New Zealand, Jean F. Power, Carlo R. Carere, Holly E. Welford, Daniel T. Hudson, Kevin C. Lee, John W. Moreau, Anna-Louise Reysenbach, Thijs J.G. Ettema, Multiple Additional Authors

Biology Faculty Publications and Presentations

Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and …

Preparing Teaching Assistants To Facilitate Course-Based Undergraduate Research Experiences (Cures) In The Biological Sciences: A Call To Action, Erin Shortlidge, Amie M. Kern, Emma Goodwin, Jeffrey T. Olimpo

Biology Faculty Publications and Presentations

Course-based undergraduate research experiences (CUREs) offer an expanding avenue to engage students in real-world scientific practices. Increasingly, CUREs are instructed by graduate teaching assistants (TAs), yet TAs may be underprepared to facilitate and face unique barriers when teaching CUREs. Consequently, unless TAs are provided professional development (PD) and resources to teach CUREs effectively, they and their students may not reap the assumed benefits of CURE instruction. Here, we describe three perspectives – that of the CURE TA, the CURE designer/facilitator, and the CURE student – that are collectively intended to inform the development of tentative components of CURE TA PD. …

How Beavers (Castor Canadensis) Affect Habitat Availability For Two Native Oregon Turtles: Actinemys Marmorata And Chrysemys Picta Bellii, Rodé Krige

University Honors Theses

Oregon is home to two native freshwater turtle species: the northwestern pond turtle and the western painted turtle. Both turtles are Oregon conservation strategy species with a status rating of sensitive, indicating declining populations. Oregon’s decline in these turtle’s populations is thought to be predominantly due to loss and degradation of habitat that results from development and urbanization. Beavers’ ability to dam streams and create ponds may be creating habitat usable by turtles, but the relationship is under-studied. This study assessed water temperature, basking habitat, and overall turtle habitat suitability at beaver-dammed and control ponds in Portland, Oregon. Average basking …

Using Biometrics, Behavioral Observations, And Multiple Molecular Techniques To Assess The Impacts Of Changes In Temperature And Salinity On The Common Bay Mussel (Mytilus Trossulus), Casey Martin

Dissertations and Theses

The intertidal zone is a place of rapid and frequent change that is home to a variety of creatures who are essential to the integrity of the habitat. Mussels are robust sessile bivalves that anchor to the rocks of the intertidal. The prominent species on the Oregon Coast, the Common Bay Mussel (Mytilus trossulus), plays an essential role as a coastal food source, water column filter, and barrier to prevent erosion due to wave action. Mytilus trossulus withstands daily shifts in temperature, salinity, and tide, as well as seasonal changes. Global climate change due to excess carbon emissions …

Big Boned: How Fat Storage And Other Adaptations Influenced Large Theropod Foraging Ecology, Cameron Pahl, Luis A. Ruedas

Biology Faculty Publications and Presentations

Dinosaur foraging ecology has been the subject of scientific interest for decades, yet much of what we understand about it remains hypothetical. We wrote an agent-based model (ABM) to simulate meat energy sources present in dinosaur environments, including carcasses of giant sauropods, along with living, huntable prey. Theropod dinosaurs modeled in this environment (specifically allosauroids, and more particularly, Allosaurus Marsh, 1877) were instantiated with heritable traits favorable to either hunting success or scavenging success. If hunter phenotypes were more reproductively successful, their traits were propagated into the population through their offspring, resulting in predator specialists. If selective pressure favored scavenger …

Germ Cell Recovery, Cryopreservation And Transplantation In The California White Sturgeon, Acipenser Transmontanus, Amie L. Romney, Danielle M. Myers, Fatima R. Martin, Tawney N. Scanlan, Stuart A. Meyers

Biology Faculty Publications and Presentations

The white sturgeon (Acipenser transmontanus) is the largest freshwater fish in North America. Because of the unique life history characteristics of sturgeon, including longevity, late maturation and long spawning intervals, their aquaculture can be a significant investment of resources. As a result of habitat loss and overharvesting, natural populations of white sturgeon are threatened and there is a growing effort to improve conservation aquaculture programs. Germ cell transplantation is an innovative technology previously demonstrated in a variety of fish species to be able to produce a surrogate broodstock. The technique relies upon optimal donor germ cell recovery and transplantation into …

Drivers Of Plankton Community Structure In Intermittent And Continuous Coastal Upwelling Systems–From Microbes And Microscale In-Situ Imaging To Large Scale Patterns, Moritz Schmid, Su Sponaugle, Anne W. Thompson, Kelly T. Sutherland, Robert Cowen

Biology Faculty Publications and Presentations

Eastern Boundary Systems support major fisheries whose early life stages depend on upwelling production. Upwelling can be highly variable at the regional scale, with substantial repercussions for new productivity and microbial loop activity. Studies that integrate the classic trophic web based on new production with the microbial loop are rare due to the range in body forms and sizes of the taxa. Underwater imaging can overcome this limitation, and with machine learning, enables fine resolution studies spanning large spatial scales. We used the In-situ Ichthyoplankton Imaging System (ISIIS) to investigate the drivers of plankton community structure in the northern California …

The Influence Of Polystyrene Microplastics On Juvenile Steelhead Trout (Oncorhynchus Mykiss), Kaitlyn Marie Baker

Dissertations and Theses

Mass production of plastic within the past decade has led to over 100 billion tons of plastics being added to the world’s oceans through rivers and effluent disposal and decomposition. For marine environments, the sudden and constant growth of microplastics (plastics 1 µm to 5 mm in diameter), is of particular concern to top-predatory fish such as steelhead trout (Oncorhynchus mykiss), who passively or actively uptake microplastics while consuming prey. Previous research has demonstrated clear detrimental impacts of microplastic accumulation in bivalves, seabirds, and zebrafish, including decreased diet, reproduction rates, and metabolism, as well as increased rates of …

Instructors At A Crossroad: Perceptions Of Collaboration And Support Intersect With Intentions To Implement A Cure, Justin Berl

Dissertations and Theses

An ongoing crisis of student drop-off from undergraduate science, technology, engineering and mathematics (STEM) education has led to a sustained call over the last 15+ years for the increased implementation of updated practices in undergraduate STEM education. Though over the past few decades many researchers have developed and analyzed the efficacy of various evidence-based teaching practices (EBTPs) designed to improve the state of undergraduate STEM education throughout the country, the rate at which these EBTPs are implemented in undergraduate STEM classrooms remains low.

In order to better understand the specific factors that affect individual instructors' efforts to implement EBTPs, we …

Resistance To Dna Interstrand Crosslinks In Escherichia Coli Arises Through Prevention Rather Than Repair, Travis Kim Worley

Dissertations and Theses

DNA interstrand crosslinks are particularly lethal lesions that form in DNA when certain molecules intercalate between complementary strands of DNA and form covalent bonds with both strands. Once formed, these lesions present an absolute block to replication and transcription, ultimately resulting in cell death. Because of this lethality, chemicals that form DNA interstrand crosslinks are found in nature as defensive chemicals produced by plants and microbes. Moreover, crosslinking agents have proven effective the treatment of dysplastic conditions and are often first line chemotherapeutics.

However, cancer cells can become resistant to DNA interstrand crosslinks. Unlike other DNA lesions, the double-stranded nature …