Life Sciences Commons^™

Partitioning The Fitness Components Of Rna Populations Evolving In Vitro, Carolina Diaz Arenas, Niles Lehman

Chemistry Faculty Publications and Presentations

All individuals in an evolving population compete for resources, and their performance is measured by a fitness metric. The performance of the individuals is relative to their abilities and to the biotic surroundings – the conditions under which they are competing – and involves many components. Molecules evolving in a test tube can also face complex environments and dynamics, and their fitnessmeasurements should reflect the complexity of various contributing factors as well. Here, the fitnesses of a set of ligase ribozymes evolved by the continuous in vitroevolution system were measured. During these evolution cycles there are three different catalytic …

Novel Thermophilic Bacteria Isolated From Marine Hydrothermal Vents, Christine Demko Sislak

Dissertations and Theses

As part of a large study aimed at searching for patterns of diversity in the genus Persephonella along the north to south geochemical gradient of the ELSC, ten novel strains of Alphaproteobacteria were isolated unexpectedly. Using defined media under microaerophilic conditions to enrich for Persephonella from chimney samples collected at the seven vent fields on the ELSC and the dilution to extinction by serial dilution method to purify cultures, a total of ten strains belonging to the Alphaproteobacteria were isolated. Two of these isolates, designate MN-5 and TC-2 were chosen for further characterization and are proposed as two new species …

Soil Development And Vegetation Response To Removal Of A Small Dam, Lassen Volcanic National Park, California, Stephanie Kay Rohdy

Dissertations and Theses

Dam removal is increasing as dams age, yet little is understood about the pedogenic response to dam removal. This study reports on the edaphic changes of reservoir sediments and vegetation cover one year following removal of a small earthen dam in Northern California. In August 2012, I sampled surface sediments from the former Dream Lake reservoir in Lassen Volcanic National Park, and compared their physical and chemical properties with soil samples from two reference sites. I also estimated percent cover of vegetation in the former reservoir and reference sites. My results show that the reservoir was under reduced conditions, as …

Investigation Of The Structure And Dynamics Of Regioisomeric Eu³⁺ And Gd³⁺ Chelates Of Nb-Dotma: Implications For Mri Contrast Agent Design, Benjamin Charles Webber

Dissertations and Theses

The detection of disease and abnormal pathology by magnetic resonance imaging (MRI) has been aided significantly by the use of gadolinium (Gd³⁺)-based contrast agents (CAs) over the past three decades. MRI and MRI CAs play a critical role in diagnosing tumors and diseases of the central nervous system. The agents used clinically have been shown to safely increase MRI contrast despite the toxicity of Gd³⁺, owing to the high kinetic and thermodynamic stability of these chelates. However, current CAs enhance contrast at a small fraction of what is theoretically possible. This leads to the necessity of …

Food Sovereignty: An Alternative Paradigm For Poverty Reduction And Biodiversity Conservation In Latin America, M. Jahi Chappell, Hannah Wittman, Christopher M. Bacon, Bruce G. Ferguson, Luis Garcia Barrios, Raúl Garcia Barrios, Daniel Jaffee, Jefferson Lima, V. Ernesto Méndez, Helda Morales, Lorena Soto-Pinto, John Vandermeer, Ivette Perfecto

Sociology Faculty Publications and Presentations

Strong feedback between global biodiversity loss and persistent, extreme rural poverty are major challenges in the face of concurrent food, energy, and environmental crises. This paper examines the role of industrial agricultural intensification and market integration as exogenous socio-ecological drivers of biodiversity loss and poverty traps in Latin America. We then analyze the potential of a food sovereignty framework, based on protecting the viability of a diverse agroecological matrix while supporting rural livelihoods and global food production. We review several successful examples of this approach, including ecological land reform in Brazil, agroforestry, milpa, and the uses of wild varieties in …

Taxis Toward Hydrogen Gas By Methanococcus Maripaludis, Kristen A. Brileya, James M. Connolly, Carey Downey, Robin Gerlach, Matthew W. Fields

Biology Faculty Publications and Presentations

Knowledge of taxis (directed swimming) in the Archaea is currently expanding through identification of novel receptors, effectors, and proteins involved in signal transduction to the flagellar motor. Although the ability for biological cells to sense and swim toward hydrogen gas has been hypothesized for many years, this capacity has yet to be observed and demonstrated. Here we show that the average swimming velocity increases in the direction of a source of hydrogen gas for the methanogen, Methanococcus maripaludis using a capillary assay with anoxic gas-phase control and time-lapse microscopy. The results indicate that a methanogen couples motility to hydrogen concentration …

The Effects Of Large Wildfires On Employment And Wage Growth And Volatility In The Western United States, Max Nielsen-Pincus, Cassandra Moseley, Krista Gebert

Environmental Science and Management Faculty Publications and Presentations

We examined the effect of large wildfires on economic growth and volatility in the western United States. We matched wildfire data with quarterly employment and earnings growth data to assess the specific effect of wildfire on employment and wage growth in western US counties. Wildfires generally tended to exhibit positive effects on employment and wage growth in the quarter(s) during which suppression efforts were active. However, this effect transitioned to increased economic volatility following a wildfire. The effect of wildfire also varied by the type of county in which wildfire occurred. The amount of suppression costs invested locally had the …

Intrinsic Disorder Within An Akap-Protein Kinase A Complex Guides Local Substrate Phosphorylation, F. Donelson Smith, Steve L. Reichow, Jessica L. Esseltine, Dan Shi, Lorene K. Langeberg, John D. Scott, Tamir Gonen

Chemistry Faculty Publications and Presentations

Anchoring proteins sequester kinases with their substrates to locally disseminate intracellular signals and avert indiscriminate transmission of these responses throughout the cell. Mechanistic understanding of this process is hampered by limited structural information on these macromolecular complexes. A-kinase anchoring proteins (AKAPs) spatially constrain phosphorylation by cAMP-dependent protein kinases (PKA). Electron microscopy and three-dimensional reconstructions of type-II PKA-AKAP18γ complexes reveal hetero-pentameric assemblies that adopt a range of flexible tripartite configurations. Intrinsically disordered regions within each PKA regulatory subunit impart the molecular plasticity that affords an ∼16 nanometer radius of motion to the associated catalytic subunits. Manipulating flexibility within the PKA holoenzyme …

Effect Of Mycorrhizal Colonization And Light Limitation On Growth And Reproduction Of Lima Bean (Phaseolus Lunatus L.), Daniel J. Ballhorn, Jess A. Millar

Biology Faculty Publications and Presentations

Plants can respond with sink stimulation of photosynthesis when colonized with fungal or bacterial root symbionts, compensating costs of carbohydrate allocation to the microbes. However, constraints may arise under light limitation when plants cannot extensively increase photosynthesis. We hypothesize that under such conditions the costs for maintaining the symbiosis outweigh the benefits, ultimately turning the mutualist microbes into parasites, resulting in reduced plant growth and reproduction.

Using lima bean (Phaseolus lunatus) as experimental plant, we applied two levels of light (full light, 75% shading) and microbial inoculation (sterile soil, mycorrhizal fungi) and quantified both vegetative and generative plant …

Carbon Dynamics In The Future Forest: The Importance Of Long-Term Successional Legacy And Climate–Fire Interactions, E. Louise Loudermilk, Robert M. Scheller, Peter J. Weisberg, Jian Yang, Thomas E. Dilts, Sarah L. Karam, Carl Skinner

Environmental Science and Management Faculty Publications and Presentations

Understanding how climate change may influence forest carbon (C) budgets requires knowledge of forest growth relationships with regional climate, long-term forest succession, and past and future disturbances, such as wildfires and timber harvesting events. We used a landscape-scale model of forest succession, wildfire, and C dynamics (LANDIS-II) to evaluate the effects of a changing climate (A2 and B1 IPCC emissions; Geophysical Fluid Dynamics Laboratory General Circulation Models) on total forest C, tree species composition, and wildfire dynamics in the Lake Tahoe Basin, California, and Nevada. The independent effects of temperature and precipitation were assessed within and among climate models. Results …

Reversible Inactivation And Desiccation Tolerance Of Silicified Viruses, James R. Laidler, Jessica A. Shugart, Sherry L. Cady, Keith S. Bahjat, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Long-distance host-independent virus dispersal is poorly understood, especially for viruses found in isolated ecosystems. To
demonstrate a possible dispersal mechanism, we show that bacteriophage T4, archaeal virus Sulfolobus spindle-shaped virus Kamchatka, and vaccinia virus are reversibly inactivated by mineralization in silica under conditions similar to volcanic hot
springs. In contrast, bacteriophage PRD1 is not silicified. Moreover, silicification provides viruses with remarkable desiccation
resistance, which could allow extensive aerial dispersal.

Spatial Analysis Of Climate And Winegrape Production In Winegrape Growing Regions Of Oregon, United States Of America, Willow Devin Campbell

Dissertations and Theses

American Viticultural Areas (AVAs) are susceptible to small variations in climate and microclimates and are found within a narrow latitudinal range of prime climate conditions. These AVAs are geographically determined based on the best soil, climate, precipitation and temperature combinations for specific winegrape regions. As climate change continues to alter the local weather and the greater climate region of the Western United States, winegrape growing regions in Oregon are being affected. In an effort to determine what the pattern of change is, and compare previous studies of climate change using climate indices, a comparative study based in part on prior …

Climate Change And Fire Management In The Mid-Atlantic Region, Kenneth L. Clark, Nicholas Skowronski, Heidi Renninger, Robert M. Scheller

Environmental Science and Management Faculty Publications and Presentations

In this review, we summarize the potential impacts of climate change on wildfire activity in the mid­-Atlantic region, and then consider how the beneficial uses of prescribed fire could conflict with mitigation needs for climate change, focusing on patters of carbon (C) sequestration by forests in the region. We use a synthesis of field studies, eddy flux tower measurements, and simulation studies to evaluate how the use of prescibed fire affects short-and long-term forest C dynamics. Climate change may create weather conditions more conducive to wildfire activity, but successional changes in forest composition, altered gap dynamics, reduced understory and forest …

Gene Expression Life History Markers In A Hatchery And A Wild Population Of Young-Of-The-Year Oncorhynchus Mykiss, Ian D. F. Garrett

Dissertations and Theses

Life history within a single species can vary significantly. Many of these differences are associated with varying environmental conditions. Understanding what environmental conditions cue alternate life histories within a single species has been researched extensively. In salmonid fishes, more than almost any other group, varying environmental conditions give rise to individuals within species that take markedly different life history trajectories.

Oncorhynchus mykissis a species of salmonid native to the Pacific Northwest region of North America. This species has two life history forms, anadromous and resident. The anadromous form spends a portion of its life in ocean while the resident life …

Avoidance Of Apoptosis In Embryonic Cells Of The Annual Killifish Austrofundulus Limnaeus Exposed To Anoxia, Camie Lynn Meller, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Embryos of the annual killifish Austrofundulus limnaeus have unequalled ability among vertebrates to survive long-term anoxia. Surprisingly, these embryos can survive for months in anoxia despite a large-scale decrease in ATP levels during the initial hours of anoxic exposure. These conditions are known to trigger apoptotic cell death in mammalian cells as a result of ischemia or anoxia. Anoxia-induced induction of apoptosis was investigated in four developmental stages of A. limnaeus that differ in their tolerance of anoxia, and thus may respond to anoxia uniquely. Exposure to staurosporine was used to determine if A. limnaeus cells were competent …

Job Growth And Loss Across Sectors And Time In The Western Us: The Impact Of Large Wildfires, Max Nielsen-Pincus, Cassandra Moseley, Krista Gebert

Environmental Science and Management Faculty Publications and Presentations

The link between economic growth and natural hazards has long been studied to better understand the effects of natural hazards on local, regional, and country level growth patterns. However, relatively little generalizable research has focused on wildfires, one of the most common forest disturbances in the western United States (US). We examined the effect of large wildfires on employment growth across sectors and time in the western US.We matched wildfire occurrences from 2004 to 2008 and their duration with monthly employment data to identify the effect of wildfire on employment growth. Wildfires generally tended to exhibit positive effects on employment …

Allosteric Mechanism Of Water Channel Gating By Ca2+–Calmodulin, Steve Reichow, Daniel M. Clemens, J. Alfredo Freites, Karin L. Németh-Cahalan, Matthias Heyden, Douglas J. Tobias, James E. Hall, Tamir Gonen

Chemistry Faculty Publications and Presentations

Calmodulin (CaM) is a universal regulatory protein that communicates the presence of calcium to its molecular targets and correspondingly modulates their function. This key signaling protein is important for controlling the activity of hundreds of membrane channels and transporters. However, our understanding of the structural mechanisms driving CaM regulation of full-length membrane proteins has remained elusive. In this study, we determined the pseudo-atomic structure of full-length mammalian aquaporin-0 (AQP0, Bos Taurus) in complex with CaM using electron microscopy to understand how this signaling protein modulates water channel function. Molecular dynamics and functional mutation studies reveal how CaM binding inhibits AQP0 …

Thinking Aloud In The Science Classroom: Can A Literacy Strategy Increase Student Learning In Science?, Lindsey Joan Mockel

Dissertations and Theses

This research study investigated the effect of using the think aloud protocol while reading informational text on students' ability to learn from text in a secondary science classroom. The participants in this study were high school students (n=47) in three classes of a mixed-grade Integrated Biology, Chemistry, and Physics course. The study tracked student achievement during a four-week curriculum unit on the theory of evolution and evidence for biological evolution. All students received instruction on using the think aloud protocol, and all students practiced the think aloud protocol when reading short articles related to scientific evidence for evolution. The researcher …

Tracking Fish And Human Response To Abrupt Environmental Change At Tse-Whit-Zen: A Large Native American Village On The Olympic Peninsula, Washington State, Kathryn Anne Mohlenhoff

Dissertations and Theses

Evidence of large earthquakes occurring along the Pacific Northwest coast is reflected in coastal stratigraphy from Oregon to British Columbia, where there also exists an extensive archaeological record of Native American occupation. Tse-whit-zen, a large Native American village dating between 1824 and 54 cal B.P. located on the Olympic Peninsula of Washington State, was excavated with exceptionally fine stratigraphic control allowing for precise comparison of natural and cultural records. Here I report on the >10,000 fish remains from one 2x2 m excavation block; this assemblage spans one earthquake event, allowing study of changes in relative taxonomic abundance through time that …

Modeling The Distribution Of Bobcats And Areas Of Reintroduction For Fisher In The Southern Washington Cascades, Shiloh Michael Halsey

Dissertations and Theses

The fisher (Martes pennanti) is a medium sized member of the mustelid family that once roamed the forests of Washington and whose historic range in the western United States once spread throughout the northern Rocky Mountains, the Cascade and Coast Ranges, and the Sierra Nevada (Carroll, Zielinski, and Noss 1999; Powell 1993, Spencer et al. 2011). Due to pressures from trapping and habitat fragmentation, the abundance of the species in the western United States has decreased dramatically and is thought to be limited to several small, isolated populations. In 2008, fishers were reintroduced to the Olympic Peninsula; however, bobcat (Lynx …

Exploring Tissue Engineering: Vitamin D3 Influences On The Proliferation And Differentiation Of An Engineered Osteoblast Precursor Cell Line During Early Bone Tissue Development, Shelley S. Mason

Dissertations and Theses

Most of the load-bearing demand placed on the human body is transduced by skeletal tissue, and the capacity of the skeleton to articulate in various opposing directions is essential for body movement and locomotion. Consequently, cartilage and bone defects due to trauma, disease, and developmental abnormalities result in disabling pain and immobility for millions of people worldwide. A novel way of promoting cartilage and bone regeneration is through the incorporation of either primary cells or multipotent progenitor cells in a three-dimensional (3D) biomaterial scaffold, and/or the addition of exogenous growth and differentiation factors. The first part of this study reports …

Ccaat/Enhancer-Binding Protein Delta (C/Ebp-Delta) Expression In Antarctic Fishes: Implications For Cell Cycle And Apoptosis, Isaac Martin Sleadd

Dissertations and Theses

Chapter 1: Antarctic fishes are extremely cold adapted. Despite their inability to upregulate heat shock proteins, recent studies have demonstrated a capacity for heat response in these animals. A cDNA microarray study looked at the Notothenioid fish Trematomus bernacchii and revealed heat sensitivities for hundreds of genes, two of which code for members of the CCAAT/Enhancer-binding protein (C/EBP) family of transcription factors. These molecular switches are best known for their roles in apoptosis, inflammation and cell cycle arrest. This dissertation further elucidates the role of C/EBP-delta in the Antarctic fishes T. bernacchii and Pagothenia borchgrevinki.

Chapter 2: C/EBP-delta is constitutively …

Ecomorphology And Mating Behavior Of Two Species Of Night-Stalking Tiger Beetles, Omus Audouini And O. Dejeanii, Robert Kent Richardson

Dissertations and Theses

Night-stalking tiger beetles (Cicindelinae: Omus) are among the least studied members of the highly diverse Carabid sub-family Cicindelinae, the tiger beetles. Despite populations of Omus being common in the forest floor habitats of the west coast of North America and their conspicuous predatory role within terrestrial arthropod communities, little is known about the biology and ecology of Omus.

Field studies showed that two species of Omus existed in the forested areas of Powell Butte Nature Park, Portland, Oregon, USA: Omus audouiniand O. dejeanii. The co-occurrence of sympatric, and likely syntopic, species allowed for a comparative approach in examining and analyzing …

The Role Of Wood Microsites At Timberline-Alpine Meadow Borders For Conifer Regeneration, Adelaide Chapman Johnson

Dissertations and Theses

This research aimed to determine whether wood microsites ("nurse logs"), which are regeneration sites in Pacific Northwest (PNW) subalpine forests, supported regeneration at timberline-alpine meadow borders. Upward advance of forests and conifer invasion into alpine meadows, which may be occurring in conjunction with climate warming, have gained worldwide attention. Successful alpine meadow seedling regeneration depends on suitable substrate availability, or microsites, for seedling establishment. To better understand factors associated with wood microsite occurrence, mechanisms of wood input were determined and four specific hypotheses were posed to assess: (1) seedling density and seedling survival; (2) growing season length, summer mean growing …

Mesoaciditoga Lauensis Gen. Nov., Sp. Nov., A Moderate Thermoacidophilic Thermotogales From A Deep-Sea Hydrothermal Vent, Anna-Louise Reysenbach, Yitai Liu, Annie R. Lindgren, Issac D. Wagner, Christine Demko Sislak, Anchelique Mets, Stefan Schouten

Biology Faculty Publications and Presentations

A novel moderately thermophilic, heterotrophic bacterium was isolated from a deep-sea hydrothermal vent deposit from the Mariner field along the Eastern Lau Spreading Center, Southwestern Pacific. Cells were short motile rods (about 0.4 μm-0.8 μm) that occurred singly or in pairs and were surrounded by a sheath-like membrane or ‘toga’. The cells grew between 45 and 65°C (optimum 57-60°C), pH 4.1-6.0 (optimum pH 5.5-5.7) and optimally at 3% (w/v) NaCl. The isolate grew on a range of carbon and proteinaceous substrates and reduced sulfur. The G + C content of the DNA was about 45 mol%. Phylogenetic analysis of the …

An Evaluation Of The Nontarget Effects Of Transgenic Bacillus Thuringiensis Maize On Arbuscular Mycorrhizal Fungi In The Soil Ecosystem, Tanya Elizabeth Amy Cheeke

Dissertations and Theses

My dissertation research examined the effect of the cultivation of insect-resistant Bacillus thuringiensis (Bt) maize on the soil environment with a goal of understanding how to obtain a balance between technological advancement and maintenance of a healthy soil ecosystem. Although Bt plants may help to reduce pesticide use, conferring benefits to farm workers and the environment, there are still unresolved questions about how the cultivation of Bt plants affects soil organisms. For this dissertation project, I used 14 different genotypes of Bt maize and non-Bt maize (Zea mays) to investigate the effects of transgenic Bt plants on the colonization ability, …

Cross-Species Array Comparative Genomic Hybridization Identifies Novel Oncogenic Events In Zebrafish And Human Embryonal Rhabdomyosarcoma, Eleanor Y. Chen, Kimberly P. Dobrinski, Kim H. Brown, Ryan Clagg, Elena Edelman, Myron S. Ignatius, Jin Yun Helen Chen, Jillian Brockmann, G. Petur Nielsen, Sridhar Ramaswamy, Charles Keller, Charles Lee, David M. Langenau

Biology Faculty Publications and Presentations

Human cancer genomes are highly complex, making it challenging to identify specific drivers of cancer growth, progression, and tumor maintenance. To bypass this obstacle, we have applied array comparative genomic hybridization (array CGH) to zebrafish embryonal rhabdomyosaroma (ERMS) and utilized cross-species comparison to rapidly identify genomic copy number aberrations and novel candidate oncogenes in human disease. Zebrafish ERMS contain small, focal regions of low-copy amplification. These same regions were commonly amplified in human disease. For example, 16 of 19 chromosomal gains identified in zebrafish ERMS also exhibited focal, low-copy gains in human disease. Genes found in amplified genomic regions were …

The View From The Table: An Analysis Of Participant Reactions To Community-Based Dialogues On Food And Justice, Jennifer Turner

Dissertations and Theses

While Portland, Oregon's sustainable food movement wins accolades for explicitly situating itself in opposition to the industrialized global food system, it often fails to address systems of oppression that are reproduced within the alternative agri-food movement itself. This demonstrated aversion towards the messy, complex, contingent nature of the social world reflects larger processes of "de-politicization" of the overall sustainability agenda, which leads to the favoring of technological and/or spatial solutions that may undermine the social equity and justice dimensions of the "triple bottom line." This thesis focuses on an action research project involving a series of community dialogues that provided …

Efferent Copy And Corollary Discharge Motor Control Behavior Associated With A Hopping Activity, Wangdo Kim, António P. Veloso, Filipa João, Sean S. Kohles

Mechanical and Materials Engineering Faculty Publications and Presentations

Hoppers respond not only to stimuli from the ground surfaces but also to cues generated by their own behaviors. This leads to desensitization because although the afferent and reafferent signals have distinct causes, they are carried by the same sensory channels. From a behavioral viewpoint, it may be necessary to distinguish between signals from the two causes especially when monitoring changes in the external environment separate from those due to self-movement. We were able to separate afferent sensory stimuli from self-generated, reafferent signals using an action oriented perception system and dynamic programming approach. This effort addressed the question of how …

On The Edge Of Agriculture: An Interview With Narendra Varma And Gianna Banducci Of Our Table Cooperative, Mike Simpson

Metroscape

One mile outside Portland’s urban growth boundary near Sherwood OR, a new farm business is modeling innovative practices that could become the future of Oregon agriculture. The Our Table Cooperative brings stakeholders from all levels of the food system together as member-owners within the same organizational structure. By sharing costs and infrastructure, the cooperative seeks to show that small and medium scale agricultural production can be economically viable. The farm also emphasizes diversity of crops over industrial efficiency, and its management is based on dynamic governance.. Recently, Metroscape sat down with two members of the cooperative to discuss their vision, …