Biology Commons^™

Impact Of The Urban Heat Mosaic On The Leaf Senescence In Two Acer Species, Jeffrey D. Smith

University Honors Theses

Due to the heterogeneity of the urban heat island, we can think of the variable influence of urbanization on air temperature as more of an urban heat mosaic. Climate change has caused a resurgence of interest in the way temperature affects how organisms, such as street trees, undergo cyclic changes in their life cycle. Such changes include budburst or, less commonly, timing of senescence. Little is known about how the urban heat mosaic could be affecting the phenology of different urban trees. Because street trees are one of the more prominent ecosystem engineers of the urban landscape, variable influences of …

Do Foliar Endophytes Matter In Litter Decomposition?, Emily R. Wolfe, Daniel J. Ballhorn

Biology Faculty Publications and Presentations

Litter decomposition rates are affected by a variety of abiotic and biotic factors, including the presence of fungal endophytes in host plant tissues. This review broadly analyzes the findings of 67 studies on the roles of foliar endophytes in litter decomposition, and their effects on decomposition rates. From 29 studies and 1 review, we compiled a comprehensive table of 710 leaf-associated fungal taxa, including the type of tissue these taxa were associated with and isolated from, whether they were reported as endo- or epiphytic, and whether they had reported saprophytic abilities. Aquatic (i.e., in-stream) decomposition studies of endophyte-affected litter were …

Mitochondrial Dna Variation And Selfish Propagation Following Experimental Bottlenecking In Two Distantly Related Caenorhabditis Briggsae Isolates, Josiah Tad Wagner, Dana K. Howe, Suzanne Estes, Dee R. Denver

Biology Faculty Publications and Presentations

Understanding mitochondrial DNA (mtDNA) evolution and inheritance has broad implications for animal speciation and human disease models. However, few natural models exist that can simultaneously represent mtDNA transmission bias, mutation, and copy number variation. Certain isolates of the nematode Caenorhabditis briggsae harbor large, naturally-occurring mtDNA deletions of several hundred base pairs affecting the NADH dehydrogenase subunit 5 (nduo-5) gene that can be functionally detrimental. These deletion variants can behave as selfish DNA elements under genetic drift conditions, but whether all of these large deletion variants are transmitted in the same preferential manner remains unclear. In addition, the degree to which …

A Basic Ddradseq Two‐Enzyme Protocol Performs Well With Herbarium And Silica‐Dried Tissues Across Four Genera, Ingrid E. Jordon‐Thaden, James B. Beck, Catherine A. Rushworth, Michael D. Windham, Nick Diaz, Jason T. Cantley, Christopher T. Martine, Carl J. Rothfels

Biology Faculty Publications and Presentations

PREMISE: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double-digest restriction site–associated DNA sequencing (ddRADseq) protocol using DNAs from four genera extracted from both silica-dried and herbarium tissue.

METHODS: DNAs from Draba, Boechera, Solidago, and Ilex were processed with a ddRADseq protocol. The effects of DNA degradation, taxon, and specimen age were assessed. RESULTS: Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were …

First Report Of Molecular Characterization And Phylogeny Of Trichuris Fossor Hall, 1916 (Nematoda: Trichuridae), Malorri R. Hughes, Deborah A. Duffield, Dana K. Howe, Dee Denver

Biology Faculty Publications and Presentations

Because species of Trichuris are morphologically similar and ranges of host preference are variable, using molecular data to evaluate species delineations is essential for properly quantifying biodiversity of and relationships within Trichuridae. Trichuris fossor has been reported from Thomomys spp. (Rodentia: Geomyidae, ‘pocket gophers’) hosts based on morphological features alone. Partial 18S rRNA sequences for specimens identified as T. fossor based on morphology, along with sequences from 26 additional taxa, were used for a phylogenetic analysis. Evolutionary histories were constructed using maximum likelihood and Bayesian inference. In both analyses, the specimens fell within the Trichuris clade with 100% support and …

Crossing Boundaries: Steps Toward Measuring Undergraduates' Interdisciplinary Science Understanding, Brie Tripp, Sophia A. Voronoff, Erin Shortlidge

Biology Faculty Publications and Presentations

A desired outcome of education reform efforts is for undergraduates to effectively integrate knowledge across disciplines in order to evaluate and address real-world issues. Yet there are few assessments designed to measure if and how students think interdisciplinarily. Here, a sample of science faculty were surveyed to understand how they currently assess students’ interdisciplinary science understanding. Results indicate that individual writing-intensive activities are the most frequently used assessment type (69%). To understand how writing assignments can accurately assess students’ ability to think interdisciplinarily, we used a preexisting rubric, designed to measure social science students’ interdisciplinary understanding, to assess writing assignments …

Genotypic Diversity And Host-Specificity Of Frankia Bacteria Associated With Sympatric Populations Of Alnus Rubra And Alnus Rhombifolia In Oregon, Mehmet Ali Balkan, Nathan U. Stewart, Emily S. Kauffman, Emily R. Wolfe, Daniel J. Ballhorn

Biology Faculty Publications and Presentations

Biological nitrogen fixation is one of the most critical processes contributing to ecosystem productivity and stability on a global scale. In temperate climates of the northern hemisphere, plant-root associated bacteria of the genus Frankia are the major nitrogen fixers in forest environments. Trees belonging to the genus Alnus are the most widespread hosts of Frankia in the Pacific Northwest, and a myriad of biotic and abiotic factors can influence the robustness of this symbiosis. Host identity and bacterial strain are important features that can impact Alnus-Frankia association, but little is known about the interplay of intrageneric hosts that co-occur in …

Roadmap For Naming Uncultivated Archaea And Bacteria, Alison Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, Peter Kämpfer, Konstantinos T. Konstantinidis, Christopher E. Lane, R. Thane Papke, Anna-Louise Reysenbach, Multiple Additional Authors

Biology Faculty Publications and Presentations

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code …

Integrating Oceanographic Research Into High School Curricula: Achieving Broader Impacts Through Systems Education Experiences Modules, Monica V. Orellana, Claudia Ludwig, Anne W. Thompson, Nitin S. Baliga

Biology Faculty Publications and Presentations

We describe a framework for incorporating cross-disciplinary oceanographic research into high school curriculum modules and discuss how this framework could be adopted broadly by ocean scientists to build cohesive broader impacts programs nested within individual oceanographic research programs.

Reemergence Of Guadalupe Fur Seals In The U.S. Pacific Northwest: The Epidemiology Of Tranding Events During 2005–2016, Erin D'Agnese, Dyanna M. Lambourn, James Rice, Debbie Duffield, Jessica L. Huggins, Terry Spraker, Stephen A. Raverty, Tetiana Kuzmina, Micheal E. Grigg, Kristin Wilkinson, Multiple Additional Authors

Biology Faculty Publications and Presentations

Guadalupe fur seals (GFS), Arctocephalus philippii townsendi, an U.S. Endangered Species Act threatened pinniped, have recently reappeared in their historic range along the western seaboard of the continental United States. Starting 2005 through 2016, 169 GFSs stranded in Washington and Oregon, involving two designated unusual mortality events. The circumstances surrounding GFS strandings, mortality, and their increased presence in Oregon and Washington were analyzed during this study. Detailed necropsies, histopathology (n = 93), and epidemiological analysis found three main causes of death (COD): emaciation (44%), trauma (29%), and infectious disease (19%) and the factors associated with overall strandings and …

Bone Mineral Density Of The Common Bottlenose Dolphin, Tursiops Truncatus: A Proposed Model For Monitoring Osteological And Ecosystem Health, James Wright Burrus Powell

Dissertations and Theses

Bone mineral density (BMD) in the pectoral flipper of the common bottlenose dolphin, Tursiops truncatus, was examined to address the need to define a comprehensive target site for clinical osteodensitometric assessment and to establish ranges of observed bone density values for this species. Radii were analyzed using dual energy X-ray absorptiometry (DXA), the accepted standard in human medical studies. Multiple loci within the radius were identified and assessed for their correlation to BMD of the entire bone. Radii BMD were also examined for differences based on sex, age, total body length, handedness, geographical affinity, and nutritional status at time …

Species-Specific Effects Of Passive Warming In An Antarctic Moss System, Hannah M. Prather, Angélica Casanova-Katny, Andrew F. Clements, Matthew Chmielewski, Mehmet Ali Balkan, Erin Shortlidge, Todd Rosenstiel, Sarah Eppley

Biology Faculty Publications and Presentations

Polar systems are experiencing rapid climate change and the high sensitivity of these Arctic and Antarctic ecosystems make them especially vulnerable to accelerated ecological transformation. In Antarctica, warming results in a mosaic of ice-free terrestrial habitats dominated by a diverse assemblage of cryptogamic plants (i.e. mosses and lichens). Although these plants provide key habitat for a wide array of microorganisms and invertebrates, we have little understanding of the interaction between trophic levels in this terrestrial ecosystem and whether there are functional effects of plant species on higher trophic levels that may alter with warming. Here, we used open top chambers …

Cul3 Regulates Cyclin E1 Protein Abundance Via A Degron Located Within The N-Terminal Region Of Cyclin E, Brittney Marie Davidge, Katia De Oliveira Rebola, Larry N. Agbor, Curt D. Sigmund, Jeffrey D. Singer

Biology Faculty Publications and Presentations

mammalian cells. Increased levels of cyclin E are found in some cancers. Additionally, proteolytic removal of the cyclin E N-terminus occurs in some cancers and is associated with increased cyclin E–Cdk2 activity and poor clinical prognosis. Cyclin E levels are tightly regulated and controlled in part through ubiquitin-mediated degradation initiated by one of two E3 ligases, Cul1 and Cul3. Cul1 ubiquitylates phosphorylated cyclin E, but the mechanism through which Cul3 ubiquitylates cyclin E is poorly understood. In experiments to ascertain how Cul3 mediates cyclin E destruction, we identified a degron on cyclin E that Cul3 targets for ubiquitylation. Recognition of …

Avian Dispersal Networks, Metacommunity Structure, And Bryophyte Community Assemblages, Matthew Wojciech Chmielewski

Dissertations and Theses

Spatial processes have a profound influence on the structure and function of community assemblages. The dispersal of organisms from their place of origin to the location in which they live out their reproductive life is particularly important for plant communities, which generally cannot adjust their location post-germination. Connection between communities at a landscape scale can also influence species persistence, local and regional diversity, and functional turnover at the metacommunity scale. Animals have been shown to disproportionately deposit propagules in particular microsites in many plant species, facilitating the arrival of plants to appropriate niche-space. Birds are particularly notable seed dispersers, given …

Parr Going The Distance: How Migratory Difficulty Influences Red Muscle Lipid Storage In Juvenile Oncorhynchus Mykiss, Emily Jean Morse

Dissertations and Theses

Adult salmonid populations embarking on difficult migrations have evolved to store more somatic energy prior to river entry. While it is known that lipids are the primary fuel for endurance swimming in fish, uncertainty still surrounds how these mechanisms are utilized by juvenile fish during seaward migration. A key phase in salmonid migration is the preparatory season of feeding and growth before swimming downstream. During this period, juvenile fish build somatic fuel stores through dietary uptake. Intestinal microbiota of steelhead trout (Oncorhynchus mykiss) vary drastically across their geographic range, with significant differences in the coastal and inland subspecies' …

A Csra-Binding, Trans-Acting Srna Of Coxiella Burnetii Is Necessary For Optimal Intracellular Growth And Vacuole Formation During Early Infection Of Host Cells, Shaun Wachter, Matteo Bonazzi,, Kyle Shifflett, Abraham Moses, Rahul Raghavan, Michael F. Minnick

Biology Faculty Publications and Presentations

Coxiella burnetii is an obligate intracellular gammaproteobacterium and zoonotic agent of Q fever. We previously identified 15 small non-coding RNAs (sRNAs) of C. burnetii. One of them, CbsR12 (Coxiella b urnetii small RNA 12), is highly transcribed during axenic growth and becomes more prominent during infection of cultured mammalian cells. Secondary structure predictions of CbsR12 revealed four putative CsrA-binding sites in stem loops with consensus AGGA/ANGGA motifs. We subsequently determined that CbsR12 binds to recombinant C. burnetii CsrA-2, but not CsrA-1, proteins in vitro. Moreover, through a combination of in vitro and cell …

Use Of Two-Replisome Plasmids To Characterize How Chromosome Replication Completes, Nicklas Alexander Hamilton

Dissertations and Theses

All living organisms need to accurately replicate their genome to survive. Genomic replication occurs in three phases; initiation, elongation, and completion. While initiation and elongation have been extensively characterized, less is known about how replication completes. In Escherichia coli completion occurs at sites where two replication forks converge and is proposed to involve the transiently bypass of the forks, before the overlapping sequences are resected and joined. The reaction requires RecBCD, and involves several other gene products including RecG, ExoI, and SbcDC but can occur independent of recombination or RecA. While several proteins are known to be involved, how they …

How To Make A Weed: The Saga Of The Slender False Brome Invasion In The North American West And Lessons For The Future, Mitchell B. Cruzan

Biology Faculty Publications and Presentations

Historical herbarium collections and genetic analyses indicate that slender false brome (Brachypodium sylvaticum) was first introduced in test gardens in Oregon in the early 1900 s as part of the USDA’s plant introduction program. A small number of naturalized populations were established, but it was not until several decades later that this alien species became an aggressive invader. The Oregon invasive strains of false brome were generated as a consequence of mating among genetically divergent lineages. The resulting hybrid populations contained high levels of genetic variation that fueled the evolution of specific adaptations to the Pacific Northwest climate and ultimately …

Complex History Of Codiversification And Host Switching Of A Newfound Soricid-Borne Orthohantavirus In North America, Schuyler W. Liphardt, Hae Ji Kang, Laurie J. Dizney, Luis A. Ruedas, Joseph A. Cook, Richard Yanagihara

Biology Faculty Publications and Presentations

Orthohantaviruses are tightly linked to the ecology and evolutionary history of their mammalian hosts. We hypothesized that in regions with dramatic climate shifts throughout the Quaternary, orthohantavirus diversity and evolution are shaped by dynamic host responses to environmental change through processes such as host isolation, host switching, and reassortment. Jemez Springs virus (JMSV), an orthohantavirus harbored by the dusky shrew (Sorex monticola) and five close relatives distributed widely in western North America, was used to test this hypothesis. Total RNAs, extracted from liver or lung tissue from 164 shrews collected from western North America during 1983–2007, were analyzed for orthohantavirus …

Snowy Plover Demography In Oregon, Eleanor Prindiville Gaines

Dissertations and Theses

A thorough understanding of demographic parameters and their contribution to overall population growth is fundamental to effective conservation of small populations, but this information is often lacking. The Pacific Coast population of the Western Snowy Plover (Charadrius nivosus nivosus) is listed as threatened and has been the target of long-term, multi-pronged management in Oregon. The Oregon coastal population has been intensively monitored since 1990, and over 80% of the population is color banded, but a comprehensive analysis of demographic parameters and the effect of management on vital rates and population growth has been unavailable until now. Here, the …

Antioxidant Capacity And Anoxia-Tolerance In Austrofundulus Limnaeus Embryos, Josiah Tad Wagner, Michael J. Knapp, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Embryos of Austrofundulus limnaeus can tolerate extreme environmental stresses by entering into a state of metabolic and developmental arrest known as diapause. Oxidative stress is ubiquitous in aerobic organisms and the unique biology and ecology of A. limnaeus likely results in frequent and repeated exposures to oxidative stress during development. Antioxidant capacity of A. limnaeus was explored during development by measuring antioxidant capacity due to small molecules and several enzymatic antioxidant systems. Diapause II embryos can survive for several days in 1% hydrogen peroxide without indications of negative effects. Surprisingly, both small and large molecule antioxidant systems are highest during …

Isoprene Emission In Polytrichaceae Mosses, Timea Deakova

Dissertations and Theses

Our first aim was to identify and quantify Biological Volatile Organic Compound (BVOC) emissions, specifically emissions of isoprene, from the moss Polytrichum juniperinum during its earliest stage of life. Isoprene emission from mosses could be a significant component of the total global budget of BVOC emissions. Data concerning the spatial and temporal variability of these emissions are lacking due to poor characterization of the physical and biological factors controlling isoprene synthesis in both vascular and non-vascular plants. We found that P. juniperinum in its early life stage (protonema) can emit isoprene at detectable levels at day five after spore germination. …

Amino-Terminal Sequencing Of Ssv1 Major Capsid Protein Vp1 Mutants, Nichole D. Procter, Kenneth M. Stedman, Ignacio De La Higuera, George Kasun, Ajay Sapre

Student Research Symposium

Unique lemon-shaped viruses, the Fuselloviridae, or Sulfolobus Spindle-Shaped Viruses (SSVs) of hyperthermophilic archaea are characterized by both their unusual structure and extreme thermal tolerance. The most well characterized of the SSVs is SSV1. Wild-type SSV1 tolerates multiple mutations to its genome while still remaining infectious, making this virus ideal to study molecular processes in extreme environments. The major capsid protein, VP1 forms the unique structure of the virus and provides protection for the genome. The amino terminus of the VP1 protein purified from wild-type SSV1 is glutamate 66 (E66) indicating proteolytic cleavage. E66 is universally conserved in all SSVs. Interestingly, …

Molecular Systematics Of Odonata, Kristin Anderson, Susan Masta

Student Research Symposium

Dragonflies and damselflies together compose the order Odonata. Odonates are insectivorous, filling a crucial niche in aquatic communities. When Odonates are present in communities, it's a sign of ecosystem health. Because of their comparatively large size and bright colors, they are often popular insects with the public and can serve as a flagship species in conservation initiatives. Odonate systematics has been greatly debated in the literature over last hundred years, and there are still many unanswered questions to ponder. This study tests paraphyletic families and the deepest nodes of evolutionary divergence within the order Odonata. Sequences accessed from GenBank NCBI …

A Framework To Guide Undergraduate Education In Interdisciplinary Science, Brie Tripp, Erin E. Shortlidge

Biology Faculty Publications and Presentations

An expanded investment in interdisciplinary research has prompted greater demands to integrate knowledge across disciplinary boundaries. Vision and Change similarly made interdisciplinary expectations a key competency for undergraduate biology majors; however, we are not yet synchronized on the meaning of interdisciplinarity, making this benchmark difficult to meet and assess. Here, we discuss aspects of interdisciplinarity through a historical lens and address various institutional barriers to interdisciplinary work. In an effort to forge a unified path forward, we provide a working definition of interdisciplinary science derived from both the perspectives of science faculty members and scientific organizations. We leveraged the existing …

Differences Between Male And Female Elite Free-Style Wrestlers In The Effects Of “Set Up” On Leg Attack, Sho Ito, Larry Crawshaw, Kazuyuki Kanosue

Biology Faculty Publications and Presentations

Leg attack is the most basic skill in free-style wrestling. Before executing a leg attack, balance and anticipation of the opponent must be disrupted. We defined this action as the “set up”. The aim of this study is knowledge about the effects of “set up” on the success rate of leg attacks, and answer to question: whether or not a gender difference exists in the use and effectiveness of “set ups” in the elite level of the wrestling matches. Material and Methods: We analyzed video recordings of 57 matches of male free-style wrestling seniors, 58 matches of female seniors, 60 …

The Interactive Effect Of Temperature And Salinity In The Nile Tilapia (Oreochromis Niloticus), Rachel Marie Palmer

Dissertations and Theses

Frequent measures that aim to identify the tolerance of an organism to various environmental conditions rely on the mortality of said organism. However, the effects of sub-lethal stress can be just as important to consider as they may give rise to how an organism may live in such an environment (growth, reproduction, etc.). Coping with changes in environmental conditions can have a high energy cost. Even starting a cellular stress response alone has proven to be costly. It is therefore reasonable that organisms in stressful situations will dedicate energy sources to survival mechanisms, and downregulate non-necessary activities like growth, and …

The Influence Of Hibernation Temperature On Deiodinase 2 In Red-Sided Garter Snakes (Thamnophis Sirtalis Parietalis), Kalera Stratton

Dissertations and Theses

Environmental cues such as day length and temperature contribute to timing of biological rhythms in seasonal breeders. Life-history transitions such as spring emergence from hibernation, migration, or mating must be coordinated with environmental conditions or survival is compromised. Therefore, there must be chemical signaling pathways in the brain that transduce seasonally-changing sensory inputs into signals that initiate a hormonal cascade, culminating in reproductive behavior. The relative importance of environmental cues to reproductive timing varies with species, time of year, and sex, and the mechanisms driving these differences remain unknown. The role of photoperiod in regulating reproductive behavior has been explored …

Symbiosis In Archaea: Functional And Phylogenetic Diversity Of Marine And Terrestrial Nanoarchaeota And Their Hosts, Emily Joyce St. John

Dissertations and Theses

The Nanoarchaeota are an enigmatic lineage of Archaea found in deep-sea hydrothermal vents and geothermal springs across the globe. These small (~100-400 nm) hyperthermophiles live ectosymbiotically with diverse hosts from the Crenarchaeota. Despite their broad distribution in high-temperature environments, very few Nanoarchaeota have been successfully isolated in co-culture with their hosts and nanoarchaeote genomes are poorly represented in public databases. However, the Nanoarchaeota provide unique insights into the structure and function of symbiosis in the archaeal domain. This study describes novel nanoarchaeotes from multiple geothermal habitats, using a combination of direct cultivation techniques and genomic analysis. A new nanoarchaeote …

Despite Similar Perceptions And Attitudes, Postbaccalaureate Students Outperform In Introductory Biology And Chemistry Courses, Erin E. Shortlidge, Liz Rain-Griffith, Chloe Shelby, Gwen Shusterman, Jack Barbera

Biology Faculty Publications and Presentations

Embedding active learning is a common mechanism for meeting science, technology, engineering, and mathematics (STEM) education reform goals. Researchers have identified student benefits from such strategies, yet these benefits may not be universal for all students. We sought to identify how students at a nontraditional university perceive introductory biology and chemistry courses, and whether perceptions relate to course type, performance, or student status. We surveyed students (n = 601) using open-ended prompts regarding their perceptions of factors that impact their learning and interest, and about specific learning strategies. Generally, students did not differ in what influenced their learning or …