Biology Commons^™

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 …

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 …

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 …

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 …

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 …

Computational Analysis Of Plasma Lipidomics From Mice Fed Standard Chow And Ketogenic Diet, Amy L. Seufert, James W. Hickman, Jaewoo Choi, Brooke A. Napier

Biology Faculty Publications and Presentations

Dietary saturated fatty acids (SFAs) are upregulated in the blood circulation following digestion. A variety of circulating lipid species have been implicated in metabolic and inflammatory diseases; however, due to the extreme variability in serum or plasma lipid concentrations found in human studies, established reference ranges are still lacking, in addition to lipid specificity and diagnostic biomarkers. Mass spectrometry is widely used for identification of lipid species in the plasma, and there are many differences in sample extraction methods within the literature. We used ultra-high performance liquid chromatography (UPLC) coupled to a high-resolution hybrid triple quadrupole-time-of-flight (QToF) mass spectrometry (MS) …

Diverse And Variable Community Structure Of Picophytoplankton Across The Laurentian Great Lakes, John Gale, Carey P. Sweeney, Sarah Paver, Maureen L. Coleman, Anne W. Thompson

Biology Faculty Publications and Presentations

The Laurentian Great Lakes provide economic support to millions of people, drive biogeochemical cycling, and are an important natural laboratory for characterizing the fundamental components of aquatic ecosystems. Small phytoplankton are important contributors to the food web in much of the Laurentian Great Lakes. Here, for the first time, we reveal and quantify eight phenotypically distinct picophytoplankton populations across the Lakes using a multilaser flow cytometry approach, which distinguishes cells based on their pigment phenotype. The distributions and diversity of picophytoplankton flow populations varied across lakes and depths, with Lake Erie standing out with the highest diversity. By sequencing sorted …

Drivers And Dynamics Of Phytoplankton Communities And Harmful Algal Blooms In Mountain Lakes, Lara Stephanie Jansen

Dissertations and Theses

Harmful cyanobacterial blooms (cyanoHABs) are a complex and widespread disturbance in freshwater water bodies, impacting water quality for wildlife and human populations. While cyanobacteria often bloom in warm lakes impacted by human development like agriculture, blooms are increasingly reported in cooler waters with limited development in the surrounding watershed. As much of cyanoHAB research has focused on lakes in highly developed watersheds, the understanding of factors leading to cyanobacteria dominance and blooms in the absence of major development remains limited. Mountain lakes can serve as ideal systems to study bloom-forming cyanobacteria in watersheds with minimal development. In addition, mountain lakes …

Cullin 3–Mediated Regulation Of Intracellular Iron Homeostasis Promotes Thymic Invariant Nkt Cell Maturation, Emily L. Yarosz, Ajay Kumar, Jeffrey Singer, Cheong-Hee Chang

Biology Faculty Publications and Presentations

The E3 ubiquitin ligase cullin 3 (Cul3) is critical for invariant NKT (iNKT) cell development, as iNKT cells lacking Cul3 accumulate in the immature developmental stages. However, the mechanisms by which Cul3 mediates iNKT cell development remain unknown. In this study, we investigated the role of Cul3 in both immature and mature thymic iNKT cells using a mouse model with a T cell–specific deletion of Cul3. We found that mature iNKT cells lacking Cul3 proliferated and died more than wild-type cells did. These cells also displayed increased glucose metabolism and autophagy. Interestingly, we found that tight regulation of iron homeostasis …

Diving Into Aquatic Microbial Ecology And Evolution With Anne Thompson, Anne Thompson

PDXPLORES Podcast

On this episode of PDXPLORES, Assistant Professor of Biology, Anne Thompson, discusses her award-winning research work studying the diverse ecology of microorganisms found in Earth’s oceans. Thompson’s research examines microbial mortality impacts on the structure of oceanic food webs, carbon flow, and cell interactions that create dynamic patterns of nutrient and energy abundance within diverse aquatic ecosystems.

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

Effects Of Heterozygous Deletion Of Autism-Related Gene Cullin-3 In Mice, Qiang-Qiang Xia, Angela K. Walker, Chenghu Song, Jing Wang, James A. Mobley, Jeffrey Singer, Anju Singh, Craig M. Powell

Biology Faculty Publications and Presentations

Autism Spectrum Disorder (ASD) is a developmental disorder in which children display repetitive behavior, restricted range of interests, and atypical social interaction and communication. CUL3, coding for a Cullin family scaffold protein mediating assembly of ubiquitin ligase complexes through BTB domain substrate-recruiting adaptors, has been identified as a high-risk gene for autism. Although complete knockout of Cul3 results in embryonic lethality, Cul3 heterozygous mice have reduced CUL3 protein, demonstrate comparable body weight, and display minimal behavioral differences including decreased spatial object recognition memory. In measures of reciprocal social interaction, Cul3 heterozygous mice behaved similarly to their wild-type littermates. In …

Embryonic Development Of Natural Annual Killifish Populations Of The Genus Austrolebias: Evolutionary Parallelism And The Role Of Environment, Hellen Schlueb, Daniel Blanco, Daniel García, Jason Podrabsky

Biology Faculty Publications and Presentations

1. Repeated, independent emergence of the same trait within different phylogenetic lineages is termed parallel evolution. It typically occurs as a result of similar selective pressures. Annual killifish have adapted to survive in the extreme habitat of temporary pools on three continents and present an especially amenable system for studying fundamental principles of evolutionary parallelism. When the pools dry, annual killifish embryos survive through the dry phase in the bottom substrate in a stage of dormancy—a diapause. The diapause is a complex set of three different developmental stages, none of which is obligate, thus leading to a multitude of potential developmental …

Evolutionary Codependency: Insights Into The Mitonuclear Interaction Landscape From Experimental And Wild Caenorhabditis Nematodes, Suzanne Estes, Zachary P. Dietz, Vaishali Katju, Ulfar Bergthorsson

Biology Faculty Publications and Presentations

Aided by new technologies, the upsurgence of research into mitochondrial genome biology during the past 15 years suggests that we have misunderstood, and perhaps dramatically underestimated, the ongoing biological and evolutionary significance of our long-time symbiotic partner. While we have begun to scratch the surface of several topics, many questions regarding the nature of mutation and selection in the mitochondrial genome, and the nature of its relationship to the nuclear genome, remain unanswered. Although best known for their contributions to studies of developmental and aging biology, Caenorhabditis nematodes are increasingly recognized as excellent model systems to advance understanding in these …

Pleurotus Spp. As Agents Of Mycoremediation: A Review, Colin Innes

University Honors Theses

Elemental and molecular contaminants of anthropogenic origin represent an increasing threat to virtually all terrestrial and aquatic environments as well as their surrounding atmosphere. The decontamination and restoration of these environments pose a significant and expensive challenge. Although chemical treatment or physical removal of contaminated substrates often is the most direct response to eliminate contaminants, due to the complexity and sensitivity of many natural systems, technologies involving biological remediation can provide viable alternatives. While plant, bacterial, and fungal organisms have the abilities to accumulate or to metabolize toxic compounds, fungal organisms are uniquely suited to do so. Their fast growth …

Novel Viruses Of The Family Partitiviridae Discovered In Saccharomyces Cerevisiae, Angela M. Crabtree, Ignacio De La Higuera, Kenneth Stedman, Multiple Additional Authors

Biology Faculty Publications and Presentations

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S. cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S. cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite …

Predation Of Lepidophyma Flavimaculatum (Squamata: Xantusiidae) By Basiliscus Plumifrons (Squamata: Corytophanidae), Mauricio Quirós Rosales, José Manuel Mora, Randy Alvarado

Biology Faculty Publications and Presentations

Lizards are the most diversified group of living reptiles with 7176 species worldwide (Uetz 2022). They play key roles in ecosystems where they are prey to a wide variety of predators, including snakes, other lizards, mammals, birds, and invertebrates (Pianka and Vitt 2006). The tropical forests of the new world contain a high variety of species of different sizes, shapes, and colors. In Costa Rica in particular, at least 80 species of lizards have been reported (Leenders 2019). They occupy highly diverse habitat types where they participate in food webs that involve many other species of vertebrates and invertebrates.

Investigating The Role Of Holoenzyme C In Restoring Replication Following Uv-Induced Dna Damage In Escherichia Coli, Rahul Shimpi

University Honors Theses

The recovery of replication following UV-induced DNA damage in Escherichia coli correlates with the time at which the lesions are repaired, suggesting that the two processes may be coupled. holC encodes the Chi-subunit of replicative DNA polymerase III, and is nonessential for viability, but renders cells hypersensitive to UV-induced damage when mutated, suggesting it may play a specific role in restoring replication when it encounters DNA damage. Here, I characterized the role of HolC in restoring DNA replication following disruption by UV-induced damage. I found that survival following UV in strains deleted for holC was similar to that of strains …

A New Frontier For Fat: Dietary Palmitic Acid Induces Innate Immune Memory, Amy L. Seufert, Brooke A. Napier

Biology Faculty Publications and Presentations

Dietary saturated fats have recently been appreciated for their ability to modify innate immune cell function, including monocytes, macrophages, and neutrophils. Many dietary saturated fatty acids (SFAs) embark on a unique pathway through the lymphatics following digestion, and this makes them intriguing candidates for inflammatory regulation during homeostasis and disease. Specifically, palmitic acid (PA) and diets enriched in PA have recently been implicated in driving innate immune memory in mice. PA has been shown to induce long-lasting hyper-inflammatory capacity against secondary microbial stimuli in vitro and in vivo, and PA-enriched diets alter the developmental trajectory of stem cell progenitors in …

Inference And Reconstruction Of The Heimdallarchaeial Ancestry Of Eukaryotes, Laura Eme, Daniel Tamarit, Eva F. Caceres, Courtney W. Stairs, Valerie De Anda, Max E. Schön, Kiley W. Seitz, Nina Dombrowski, Anna-Louise Reysenbach, Multiple Additional Authors

Biology Faculty Publications and Presentations

In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors— members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2–4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage …

Comparison Of General Population Vs. U.S. Military Veterans Eating Disorder Prevalence, Micah Callahan

University Honors Theses

Eating disorders disrupt the psychological wellbeing, work ability and daily functioning of many individuals. There is currently no data to compare the prevalence of eating disorders in the general public compared to the military population. The hypothesis was that the military population would be significantly higher in prevalence compared to the general population within the general eating disorder, subcategories of eating disorders and between sex. To analyze the data collected from two studies, sixteen two-proportion Z tests were conducted to determine if the proportions of DSM-V eating disorders differed within and between sex for total incidence and sub-category incidence for …

Chi Sequences Switch The Recbcd Helicase–Nuclease Complex From Degradative To Replicative Modes During The Completion Of Dna Replication, Avery E. Jehru, Charmain Courcelle, Justin Courcelle, Multiple Additional Authors

Biology Faculty Publications and Presentations

Accurately completing DNA replication when two forks converge is essential to genomic stability. The RecBCD helicase–nuclease complex plays a central role in completion by promoting resection and joining of the excess DNA created when replisomes converge. chi sequences alter RecBCD activity and localize with crossover hotspots during sexual events in bacteria, yet their functional role during chromosome replication remains unknown. Here, we use two-dimensional agarose gel analysis to show that chi induces replication on substrates containing convergent forks. The induced replication is processive but uncoupled with respect to leading and lagging strand synthesis and can be suppressed by ter sites …

Paternity Patterns In A Long-Term Resident Bottlenose Dolphin Community, Debbie Duffield, Randall Wells

Biology Faculty Publications and Presentations

Genetic analyses, initiated in 1984, have played a major role in our understanding of the structure and social relationships of the long-term resident community of common bottlenose dolphins (Tursiops truncatus) in Sarasota Bay, Florida (SBDC). One component of our ongoing study of the community’s social system involves using blood samples from periodic catch-and-release sampling for life history and health assessment studies, as well as skin from biopsy dart sampling studies and strandings, to investigate paternity and mating strategies in this community. These analyses, covering a span of four generations of calves, were originally based on chromosomes and protein electrophoresis, but …

Methanocaldococcus Lauensis Sp. Nov., A Novel Deep-Sea Hydrothermal Vent Hyperthermophilic Methanogen, Stéphane L'Haridon, Steven Goulaouic, Emily St John, Stephanie Fouteau, Anna-Louise Reysenbach

Biology Faculty Publications and Presentations

Three hyperthermohphilic methanogens, designated strain SG7T, strain SG1 and strain SLH, were isolated from the ABE and Tu’i Malila deep-sea hydrothermal vent fields along the Eastern Lau Spreading Center. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strains SG7T, SG1 and SLH were affiliated with the genus Methanocaldococcus within the family Methanocaldococcaceae, order Methanococcales. They shared 95.5–99.48 % 16S rRNA gene sequence similarity to other Methanocaldococcus species and were most closely related to Methanocaldococcus bathoardescens. Cells of strains SG7T, SG1 and SLH were cocci, with a diameter of 1.0–2.2 µm. The three strains grew between …

Environmental Enrichment Factors Associated With The Activity Level Of Bottlenose Dolphins Under Professional Care, Lisa K. Lauderdale, K. Alex Shorter, Joaquin Gabaldon, Jill D. Mellen, Multiple Additional Authors

Biology Faculty Publications and Presentations

Environmental enrichment can be used to improve the welfare of dolphins in zoos and aquariums. Bottlenose dolphins under professional care are typically provided with a range of enrichment that has a variety of features and levels of complexity at various frequencies. In the present study, a subset of data from a larger study entitled “Towards understanding the welfare of cetaceans in zoos and aquariums” (colloquially called the Cetacean Welfare Study) was used to examine the relationship between activity level and enrichment buoyancy as well as enrichment provisioning schedules. Survey data were collected from accredited zoos and aquariums related to the …

Selective And Differential Feeding On Marine Prokaryotes By Mucous Mesh Feeders, Carey P. Sweeney, Kelly R. Sutherland, Anne Thompson

Biology Faculty Publications and Presentations

Microbial mortality impacts the structure of food webs, carbon flow, and the interactions that create dynamic patterns of abundance across gradients in space and time in diverse ecosystems. In the oceans, estimates of microbial mortality by viruses, protists, and small zooplankton do not account fully for observations of loss, suggesting the existence of underappreciated mortality sources. We examined how ubiquitous mucous mesh feeders (i.e. gelatinous zooplankton) could contribute to microbial mortality in the open ocean. We coupled capture of live animals by blue-water diving to sequence-based approaches to measure the enrichment and selectivity of feeding by two coexisting mucous grazer …