Digital Commons Network^™

Understanding The Importance Of Intermittently Fragmented Stream Habitat For Isolated Westslope Cutthroat Trout (Oncorhynchus Clarki Lewisi) In The Colville National Forest, Washington, Forrest Michael Carpenter

Dissertations and Theses

Climate change and anthropogenic effects have vastly reduced Westslope Cutthroat Trout (Oncorhynchus clarki lewisi, WCT) habitat throughout their range, including the Colville National Forest in northeastern Washington where this study was conducted. Many native salmonid populations have declined in abundance since the early 1900s due to a variety of climate- and human-driven forces. Westslope Cutthroat Trout are especially sensitive to habitat loss or degradation and to climate change. Together, climate change, habitat degradation, and non-native salmonid invasions are contributing to increasingly fragmented WCT populations. Ongoing and predicted future warming trends are expected to further fragment these populations and …

Surviving Catastrophe: Resource Allocation And Plant Interactions Among The Mosses Of Mount St. Helens Volcano, Trevor David Williams

Dissertations and Theses

Mosses are some of the first colonizers to disturbed sites, yet their roles in early plant community structuring are not well understood. The primary succession zones of volcanoes provide opportunities to conduct natural experiments into how mosses contribute to early plant community formation, as well as how the unique environments found in such zones affect plant traits, particularly those associated with stress tolerance. Though plant community changes have been well-documented since Mount St. Helens (MSH) volcano erupted in 1980, the volcano's moss assemblages, their influence on other plants, and their potential roles in chemical-mediated competition and biogeochemical cycling have garnered …

Peering Below The Diffraction Limit: Robust And Specific Sorting Of Viruses With Flow Cytometry, Shea T. Lance, David J. Sukovich, Kenneth M. Stedman, Adam R. Abate

Biology Faculty Publications and Presentations

Background: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population. Specific sorting opens new avenues in the study of uncultivable viruses, including recovering the full genomes of viruses based on genetic fragments in metagenomes, or identifying the …

How To Assess Your Cure: A Practical Guide For Instructors Of Course-Based Undergraduate Research Experiences, Erin Shortlidge, Sara Brownell

Biology Faculty Publications and Presentations

Integrating research experiences into undergraduate life sciences curricula in the form of course-based undergraduate research experiences (CUREs) can meet national calls for education reform by giving students the chance to “do science.” In this article, we provide a step-by-step practical guide to help instructors assess their CUREs using best practices in assessment. We recommend that instructors first identify their anticipated CURE learning outcomes, then work to identify an assessment instrument that aligns to those learning outcomes and critically evaluate the results from their course assessment. To aid instructors in becoming aware of what instruments have been developed, we have also …

Reduced Snow Cover Alters Root-Microbe Interactions And Decreases Nitrification Rates In A Northern Hardwood Forest, Patrick O. Sorensen, Pamela H. Templer, Lynn M. Christenson, Jorge Durán, Timothy J. Fahey, Melany C. Fisk, Peter M. Groffman, Jennifer L. Morse, Adrien C. Finzi

Environmental Science and Management Faculty Publications and Presentations

Snow cover is projected to decline during the next century in many ecosystems that currently experience a seasonal snowpack. Because snow insulates soils from frigid winter air temperatures, soils are expected to become colder and experience more winter soil freeze-thaw cycles as snow cover continues to decline. Tree roots are adversely affected by snowpack reduction, but whether loss of snow will affect root-microbe interactions remains largely unknown. The objective of this study was to distinguish and attribute direct (e.g., winter snow-and/ or soil frost-mediated) vs. indirect (e.g., root-mediated) effects of winter climate change on microbial biomass, the potential activity of …

Effects Of Antibiotic Mixtures Across Marine Intertidal Trophic Levels: Examining Environmentally-Relevant Contaminant Concentrations, Jaclyn Rebecca Teixeira

Dissertations and Theses

Approximately 48% of Americans use prescription drugs within each 30-day period, and there are signs this trend is increasing. Although many studies track pharmaceuticals’ fates in contaminating waterways, only fairly recent efforts have examined the potential impacts of these drugs on non-target organisms. The antibiotics sulfamethoxazole and trimethoprim, often prescribed together to treat bacterial infections, have been detected worldwide in marine and estuarine environments at concentrations up to 700-800 ng/L each. Toxic effects of these drugs have been identified in freshwater organisms, with synergistic effects observed in short-term studies of mixtures of the two; however, little research has examined possible …

Cho Endonuclease Functions During Dna Interstrand Crosslink Repair In Escherichia Coli, Anthonige Vidya Perera, James Brian Mendenhall, Charmain T. Courcelle, Justin Courcelle

Biology Faculty Publications and Presentations

DNA interstrand crosslinks are complex lesions that covalently link both strands of the duplex DNA. Lesion removal is proposed to initiate via the UvrABC nucleotide excision repair complex, however less is known about the subsequent steps of this complex repair pathway. In this study, we characterized the contribution of nucleotide excision repair mutants to survival in the presence of psoralen-induced damage. Unexpectedly, we observed that the nucleotide excision repair mutants exhibit differential sensitivity to psoralen-induced damage, with uvrC mutants being less sensitive than either uvrA or uvrB. We show that Cho, an alternative endonuclease, acts with UvrAB and is …

Systems Thinking In The Forest Service: A Framework To Guide Practical Application For Social-Ecological Management In The Enterprise Program, Megan Kathleen Kmon

Dissertations and Theses

The U.S. Forest Service (USFS) Enterprise Program (EP), which provides fee-for-service consulting services to the USFS, is interested in integrating systems thinking into its service offerings. Despite there being several excellent sources on the range and diversity of systems thinking, no single framework exists that thoroughly yet concisely outlines what systems thinking is along with its deep history, theoretical tenets, and soft and hard approaches. This thesis is an attempt to create such a framework, aimed specifically at practical application in a land management agency, through literature synthesis injected with original analysis. The usefulness of the framework is then tested …

The Village Market: New Columbia Goes Shopping For Food Justice, Jane Therese Waddell

Dissertations and Theses

The Village Market is a nonprofit Healthy Corner Store that has been open since May of 2011 in the mixed-use, mixed-income New Columbia housing development in Portland, Oregon's Portsmouth neighborhood. The venture began as a "community-led" effort in partnership with Janus Youth Programs and Home Forward. The project was conceived after a private enterprise in the small grocery space designed into the development failed, leaving the neighborhood without easy access to healthy foods. This dissertation is a case study of the development process, the operation of the market, and the degree to which it addresses food justice and health equity …

Mitochondrial Dna Sequence And Lack Of Response To Anoxia In The Annual Killifish Austrofundulus Limnaeus, Josiah Tad Wagner, Florisela Herrejon Chavez, Jason E. Podrabsky

Center for Life in Extreme Environments Publications

The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in regions of Venezuela, South America. Permanent populations of A. limnaeus are maintained by production of stress-tolerant embryos that are able to persist in the desiccated sediment. Previous work has demonstrated that A. limnaeus have a remarkable ability to tolerate extended periods of anoxia and desiccating conditions. After considering temperature, A. limnaeus embryos have the highest known tolerance to anoxia when compared to any other vertebrate yet studied. Oxygen is completely essential for the process of oxidative phosphorylation by mitochondria, the intracellular organelle responsible for the majority of adenosine triphosphate production. Thus, …

A Francisella-Like Endosymbiont In The Gulf Coast Tick Evolved From A Mammalian Pathogen, Jonathan G. Gerhart, Abraham S. Moses, Rahul Raghavan

Biology Faculty Publications and Presentations

Ticks (order Ixodida) vector pathogenic bacteria that cause diseases in humans and other mammals. They also contain bacteria that are closely related to pathogens but function as endosymbionts that provide nutrients that are missing from mammalian blood—their sole food source. For instance, mammalian pathogens such as Coxiella burnetii and Francisella tularensis, as well as Coxiella-like and Francisella-like endosymbionts (CLEs and FLEs, respectively) occur in ticks worldwide. However, it is not clear whether the pathogens evolved from symbionts or symbionts from pathogens. Recent studies have indicated that C. burnetii likely originated from a tick-associated ancestor, but the origins …

Group I Intron Internal Guide Sequence Binding Strength As A Component Of Ribozyme Network Formation, Elizabeth Satterwhite, Jessica Anne Mellor Yeates, Niles Lehman

Chemistry Faculty Publications and Presentations

Origins-of-life research requires searching for a plausible transition from simple chemicals to larger macromolecules that can both hold information and catalyze their own production. We have previously shown that some group I intron ribozymes possess the ability to help synthesize other ribozyme genotypes by recombination reactions in small networks in an autocatalytic fashion. By simplifying these recombination reactions, using fluorescent anisotropy, we quantified the thermodynamic binding strength between two nucleotides of two group I intron RNA fragments for all 16 possible genotype combinations. We provide evidence that the binding strength (K_D) between the 3-nucleotide internal guide sequence …

Paternal Mitochondrial Transmission In Intra-Species Caenorhabditis Briggsae Hybrids, Joseph A. Ross, Dana K. Howe, Anna Luella Coleman-Hulbert, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

To study mitochondrial-nuclear genetic interactions in the nematode Caenorhabditis briggsae, our three laboratories independently created 38 intra-species cytoplasmic-nuclear hybrid (cybrid) lines. Although the cross design combines maternal mitotypes with paternal nuclear genotypes, eight lines (21%) unexpectedly contained paternal mitotypes. All eight share in common ancestry of one of two genetically related strains. This unexpected parallel observation of paternal mitochondrial transmission, undesirable given our intent of creating cybrids, provides a serendipitous experimental model and framework to study the molecular and evolutionary basis of uniparental mitochondrial inheritance.

Reproductive Output Of Mosses Under Experimental Warming On Fildes Peninsula, King George Island, Maritime Antarctica, Angélica Casanova-Katny, G. A. Torres-Mellado, Sarah M. Eppley

Biology Faculty Publications and Presentations

Background: Mosses dominate much of the vegetation in the Antarctic, but the effect of climatic change on moss growth and sexual reproduction has scarcely been studied. In Antarctica, mosses infrequently produce sporophytes; whether this is due to physiological limitation or an adaptive response is unknown. We studied the effect of experimental warming (with Open Top Chambers, OTCs) on sporophyte production on Fildes Peninsula, King George Island for four moss species (Bartramia patens, Hennediella antarctica, Polytrichastrum alpinum, and Sanionia georgicouncinata). To determine whether reducing cold stress increases sexual reproduction as would be predicted if sex is …

Insulin-Like Growth Factor Pathway Described In Austrofundulus Limnaeus Diapause And Escape Embryos, Steven Cody Woll

Dissertations and Theses

Development in the annual killifish Austrofundulus limnaeus can follow two distinct developmental trajectories. Typical development includes the entrance of embryos into a state of metabolic and developmental arrest termed diapause. Alternately, embryos can escape diapause and develop directly without pause. These two trajectories are characterized by differences in the rate and timing of developmental, morphological, and physiological traits. Insulin and Insulin-like growth factor (IGF) signaling (IIS) is known to regulate entrance into diapause in a variety of invertebrates. In this thesis I explore the possible role of IGFs in the regulation of development and diapause in embryos of A. limnaeus …

Mitochondrial Dna Sequence And Lack Of Response To Anoxia In The Annual Killifish Austrofundulus Limnaeus, Josiah T. Wagner, Florisela H. Chavez, Jason E. Podrabsky

Biology Faculty Publications and Presentations

The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in regions of Venezuela, South America. Permanent populations of A. limnaeus are maintained by production of stress-tolerant embryos that are able to persist in the desiccated sediment. Previous work has demonstrated that A. limnaeus have a remarkable ability to tolerate extended periods of anoxia and desiccating conditions. After considering temperature, A. limnaeus embryos have the highest known tolerance to anoxia when compared to any other vertebrate yet studied. Oxygen is completely essential for the process of oxidative phosphorylation by mitochondria, the intracellular organelle responsible for the majority of adenosine triphosphate production. Thus, …

A Landscape Approach To Determining And Predicting Juvenile Coho Salmon (Oncorhynchus Kisutch) Movement Timing And Growth Patterns Prior To Ocean Entry, Amelia Lee Johnson

Dissertations and Theses

Coho salmon (Oncorhynchus kisutch) rely on unique habitats during the winter season, which may dictate how much individuals may grow and when migration from freshwater rearing habitat to the ocean occurs. Here I analyze movement timing and growth patterns for coho salmon through a field-based study and a literature review. For the field portion, I examined hatchery-stocked juvenile coho salmon across four stream basins in the Russian River watershed, California to determine the relative importance of climate, landscape, and fish size metrics in predicting movement and growth patterns over a winter rearing and spring smolt outmigration time period …

Improving The Roadside Environment Through Integrating Air Quality And Traffic-Related Data, Christine M. Kendrick

Dissertations and Theses

Urban arterial corridors are landscapes that give rise to short and long-term exposures to transportation-related pollution. With high traffic volumes, congestion, and a wide mix of road users and land uses at the road edge, urban arterial environments are important targets for improved exposure assessment to traffic-related pollution. Applying transportation management strategies to reduce emissions along arterial corridors could be enhanced if the ability to quantify and evaluate such actions was improved. However, arterial roadsides are under-sampled in terms of air pollution measurements in the United States and using observational data to assess such effects has many challenges such as …

Rare, Threatened And Endangered Species Of Oregon (2016), James S. Kagan, Sue Vrilakas, John A. Christy, Eleanor P. Gaines, Lindsey Wise, Cameron Pahl, Kathy Howell

Institute for Natural Resources Publications

Extinction is a natural process. Today, however, plant and animal species are disappearing world-wide at an accelerated pace. Based on current trends, half of the species on earth will be extinct within the next 100 years. The major reasons for this are human caused changes to the environment, which continue to increase - in Oregon and throughout the world.

Once lost, a species can never be recovered, and there is no way of knowing how useful it may have been. We do know that human beings and many of their industries depend on plant and animal products. About 50% of …

Coevolution Of Cyanogenic Bamboos And Bamboo Lemurs On Madagascar, Daniel J. Ballhorn, Fanny Patrika Rakotoarivelo, Stefanie Kautz

Biology Faculty Publications and Presentations

Feeding strategies of specialist herbivores often originate from the coevolutionary arms race of plant defenses and counter-adaptations of herbivores. The interaction between bamboo lemurs and cyanogenic bamboos on Madagascar represents a unique system to study diffuse coevolutionary processes between mammalian herbivores and plant defenses. Bamboo lemurs have different degrees of dietary specialization while bamboos show different levels of chemical defense. In this study, we found variation in cyanogenic potential (HCNp) and nutritive characteristics among five sympatric bamboo species in the Ranomafana area, southeastern Madagascar. The HCNp ranged from 209±72 μmol cyanide* g^-1 dwt in Cathariostachys madagascariensis to no cyanide …

The Intervening Sequence Of Coxiella Burnetii: Characterization And Evolution, Indu Warrier, Mathias C. Walter, Dimitrios Frangoulidis, Rahul Raghavan, Linda D. Hicks, Michael F. Minnick

Biology Faculty Publications and Presentations

The intervening sequence (IVS) of Coxiella burnetii, the agent of Q fever, is a 428-nt selfish genetic element located in helix 45 of the precursor 23S rRNA. The IVS element, in turn, contains an ORF that encodes a hypothetical ribosomal S23 protein (S23p). Although S23p can be synthesized in vitro in the presence of an engineered E. coli promoter and ribosome binding site, results suggest that the protein is not synthesized in vivo. In spite of a high degree of IVS conservation among different strains of C. burnetii, the region immediately upstream of the S23p start codon …

Do Forest Commons Contribute To International Environmental Initiatives? A Socio-Ecological Analysis Of Nepalese Forest Commons In View Of Redd+, Harisharan Luintel

Dissertations and Theses

Forests in developing countries have the potential to contribute to global efforts to mitigate climate change, promote biodiversity and support the livelihoods of rural, local people. Approximately one-fourth of such forests are under the control of local communities, which primarily manage forests for subsistence and to meet their livelihood needs. The trend of bottom-up community control is increasing through the adoption of decentralization reforms over the last 40 years. In contrast, the United Nations has introduced the top-down program, Reducing Emissions from Deforestation and Forest Degradation (REDD+) for the conservation and enhancement of forest carbon and the sustainable management of …

Biofouling Management In The Pacific Northwest And Predation On Native Versus Non-Native Ascidians, Erin Suzanne Kincaid

Dissertations and Theses

Marine non-native species threaten economic and environmental health, making it crucial to understand factors that make them successful. Research on these species, therefore, allows for greater preparedness and informed management of biological invasions and increases understanding of elements structuring biological communities. Among the marine non-native species, and particularly the fouling community, non-native ascidians are a taxon of particular concern because they can crowd out native benthic species and smother mariculture products. This thesis addresses management for ascidians and other fouling organisms and includes research on the invasiveness of this taxon in addition to the invasibility of recipient fouling communities. On …

Genomics-Informed Isolation And Characterization Of A Symbiotic Nanoarchaeota System From A Terrestrial Geothermal Environment, Louie Wurch, Richard J. Giannone, Bernard S. Belisle, Carolyn Swift, Sagar Utturkar, Robert L. Hettich, Anna-Louise Reysenbach, Mircea Podar

Biology Faculty Publications and Presentations

Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism’s physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota (‘Nanopusillus acidilobi’) and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment. The cells of ‘Nanopusillus’ are among the smallest known cellular organisms (100–300 nm). They appear to have a complete genetic information processing machinery, but lack almost all primary biosynthetic functions as well as respiration and …

Bayesian Methods For Comparing Species Physiological And Ecological Response Curves, Michael B. Ashcroft, Angélica Casanova-Katny, Kerrie Mengersen, Todd N. Rosenstiel, Johanna D. Turnbull, Jane Wasley, Melinda J. Waterman, Gustavo E. Zúñiga, Sharon A. Robinson

Biology Faculty Publications and Presentations

Many ecological questions require information on species' optimal conditions or critical limits along environmental gradients. These attributes can be compared to answer questions on niche partitioning, species coexistence and niche conservatism. However, these comparisons are unconvincing when existing methods do not quantify the uncertainty in the attributes or rely on assumptions about the shape of species' responses to the environmental gradient. The aim of this study was to develop a model to quantify the uncertainty in the attributes of species response curves and allow them to be tested for substantive differences without making assumptions about the shape of the responses. …

Walking Behavior Of Zoo Elephants: Associations Between Gps-Measured Daily Walking Distances And Environmental Factors, Social Factors, And Welfare Indicators, Matthew Robert Holdgate, Cheryl L. Meehan, Jennifer N. Hogan, Lance J. Miller, Josesph Soltis, Jeff Andrews, David J. Shepherdson

Biology Faculty Publications and Presentations

Research with humans and other animals suggests that walking benefits physical health. Perhaps because these links have been demonstrated in other species, it has been suggested that walking is important to elephant welfare, and that zoo elephant exhibits should be designed to allow for more walking. Our study is the first to address this suggestion empirically by measuring the mean daily walking distance of elephants in North American zoos, determining the factors that are associated with variations in walking distance, and testing for associations between walking and welfare indicators. We used anklets equipped with GPS data loggers to measure outdoor …

Recumbence Behavior In Zoo Elephants: Determination Of Patterns And Frequency Of Recumbent Rest And Associated Environmental And Social Factors, Matthew Robert Holdgate, Cheryl L. Meehan, Jennifer N. Hogan, Lance J. Miller, Jeff Rushen, Anne-Marie De Passillé, Josesph Soltis, Jeff Andrews, David J. Shepherdson

Biology Faculty Publications and Presentations

Resting behaviors are an essential component of animal welfare but have received little attention in zoological research. African savanna elephant (Loxodonta africana) and Asian elephant (Elephas maximus) rest includes recumbent postures, but no large-scale investigation of African and Asian zoo elephant recumbence has been previously conducted. We used anklets equipped with accelerometers to measure recumbence in 72 adult female African (n = 44) and Asian (n = 28)elephants housed in 40 North American zoos. We collected 344 days of data and determined associations between recumbence and social, housing, management, and demographic factors. African elephants were recumbent less (2.1 hours/day, S.D. …

The Other Lives Of Ribosomal Proteins, Metrah M. Nader

PSU McNair Scholars Online Journal

Cellular mRNAs are produced in the nucleus and exported to the cytoplasm through nuclear pore complexes (NPC) that are found in the nuclear membrane. The correctly processed mRNAs are exported in the form of messenger ribonucleoproteins (mRNPs). Since the NPC allows the passage of only one mRNA molecule at a time, export of large ribonucleoproteins (megaRNP) found in the nucleus cannot be transported through the NPC. However, a recent study has discovered an alternative export mechanism known as nuclear envelope budding, which allows megaRNP granules to be exported. This study particularly focuses on identifying ribosomal proteins (RPs) found within large …

Gene Expression Patterns Of Bone Morphogenetic Proteins (Bmps) During Early Embryonic Development In The Annual Killifish Austrofundulus Limnaeus, Eva Y. Chan

PSU McNair Scholars Online Journal

The developmental pattern of the annual killifish Austrofundulus limnaeus is unusual compared to other fish. First, the cell movements associated with gastrulation are separated from formation of the embryonic axis. In addition, embryonic diapause can occur. Diapause II and III are often observed when embryos are incubated at 25^oC. Maternal influences and incubation environment are the factors that determine entrance into embryonic diapause, but the molecular mechanisms that regulate diapause are still unknown. Interestingly, embryonic diapause and the unusual cell movements observed during early development are always found together in species of annual killifish that exhibit diapause. Bone …

Investigating The Origin And Functions Of A Novel Small Rna In Escherichia Coli, Fenil Rashmin Kacharia

Dissertations and Theses

Non-coding small RNAs (sRNAs) regulate various cellular processes in bacteria. They bind to a chaperone protein Hfq for stability and regulate gene expression by base-pairing with target mRNAs. Although the importance of sRNAs in bacteria has been well established, the mode of origination of novel sRNA genes is still elusive, mainly because the rapid rate of evolution of sRNAs obscures their original sources. To overcome this impediment, we identified a recently formed sRNA (EcsR2) in E. coli, and show that it evolved from a degraded bacteriophage gene. Our analyses also revealed that young sRNAs such as EcsR2 are expressed …