Biology Commons^™

Fecal-Sac Ingestion By Spotted Towhees, Jenny E. Mckay, Michael T. Murphy, Sarah Bartos Smith, Jennifer K. Richardson

Biology Faculty Publications and Presentations

Altricial nestlings encase excrement in fecal sacs that parents remove by either ingesting them or transporting them away from the nest. Ingestion may allow energetically or nutritionally deprived parents to recapture energy or nutrients that might be lost because of nestlings' inefficient digestion (the "parental-nutrition hypothesis"), but ingestion may also permit parents to avoid flights from the nest that interfere with parental care (e.g., brooding young; the "economic-disposal hypothesis"). We used a hypothetico-deductive approach to test the two hypotheses' ability to account for fecal-sac ingestion by the Spotted Towhee (Pipilo maculatus). We confirmed the parental-nutrition hypothesis' predictions that …

Phylogeographic And Phylogenetic Exploration Of Plethodon (Plethodontidae, Caudata) Salamanders In The Pacific Northwest, Tara Anne Pelletier

Dissertations and Theses

Genetic studies of amphibians often reveal substantial population structure due to either historical demographics from changing climate and geographic features over varying timeframes. Eight species of terrestrial salamanders (Family: Plethodontidae, Genus: Plethodon) reside in forests of the Pacific Northwest (PNW). Plethodon vehiculum is the most widespread and abundant terrestrial salamander in the PNW yet evolutionary studies are lacking. Using mitochondrial DNA (mtDNA) sequence data (D-loop and cytb) questions regarding the phylogeography of P. vehiculum and phylogenetics of western Plethodons are explored. Two major clades were defined in P. vehiculum, a southern clade in the Klamath-Siskiyou region and a …

Analysis And Classification Of Sounds Produced By Asian Elephants (Elephas Maximus), Sharon Stuart Glaeser

Dissertations and Theses

Relatively little is known about the vocal repertoire of Asian elephants (Elephas maximus), and a categorization of basic call types and modifications of these call types by quantitative acoustic parameters is needed to examine acoustic variability within and among call types, to examine individuality, to determine communicative function of calls via playback, to compare species and populations, and to develop rigorous call recognition algorithms for monitoring populations.

This study defines an acoustic repertoire of Asian elephants based on acoustic parameters, compares repertoire usage among groups and individuals, and validates structural distinction among call types through comparison of manual and automated …

Preliminary Characterization Of Mitochondrial Atp-Sensitive Potassium Channel (Mitokatp) Activity In Mouse Heart Mitochondria, Venkat Raghav Aachi

Dissertations and Theses

Myocardial ischemia, infarction, heart failure and arrhythmias are the manifestations of coronary artery disease. Reduction of ischemic damage is a major concern of cardiovascular biology research. As per recent studies, the mitochondrial ATP-sensitive potassium channel (mitoK_ATP) opening is believed to play key role in the physiology of cardioprotection, protection against ischemia-reperfusion injury or apoptosis. However, the structural information of mitoK_ATP is not precisely known. Elucidating the structural integrity and functioning of the mitoK_ATP is therefore a major goal of cardiovascular biology research. The known structure and function of the cell ATP-sensitive potassium channel (cellK_ATP) …

Molecular Coevolution Of Pacific Northwest Hantaviruses And Their Host, The Deer Mouse, Peromyscus Maniculatus, Philip Darren Jones

Dissertations and Theses

Sin Nombre virus (SNV, family Bunyaviridae, genus Hantavirus), hosted by the deer mouse, Peromyscus maniculatus (family Cricetidae, Subfamily Neotominae), is the primary etiological agent of Hantavirus pulmonary syndrome (HPS) in the western United States. HPS, with known pathogenicity only to humans and for which there is no cure or prophylaxis, affects the epithelium of the lungs by making the capillaries leaky, thereby resulting in bilateral infiltrates, and eventually leading to respiratory failure and death by drowning in approximately 38% of hospitalized patients.

In the Americas, Peromyscus has been co-evolving with hantaviruses for approximately 12–20 million years, since the first …

Dna Before Proteins? Recent Discoveries In Nucleic Acid Catalysis Strengthen The Case, Aaron Steven Burton, Niles Lehman

Chemistry Faculty Publications and Presentations

An RNA-DNA World could arise from an all-RNA system with the development of as few as three ribozymes— a DNA-dependent RNA polymerase, an RNA-dependent DNA polymerase, and a catalyst for the production of DNA nucleotides. A significant objection to DNA preceding proteins is that RNA has not been shown to catalyze the production of DNA. However, RNA- and DNAzymes have been recently discovered that catalyze chemical reactions capable of forming deoxyribose, such as mixed aldol condensation of 5’-glyceryl- and 3’- glycoaldehyde-terminated DNA strands. Thus, the only remaining obstacles to RNA-catalyzed in vitro DNA synthesis are alterations of substrate and template …

Towards The Identification Of Lampreys (Lampetra Spp.) In Archaeological Contexts, Ross E. Smith, Virginia L. Butler

Anthropology Faculty Publications and Presentations

Lampreys were and continue to be an important resource for Native Americans in the Pacific Northwest. Lampreys possess several skeletal structures that are regularly identified in marine mammal and bird stomach contents and fecal samples, suggesting that lamprey elements may preserve in archaeological contexts. However, their remains have not been identified in archaeological faunal samples in the Pacific Northwest. This may be due to the lack of an adequate "search image" for lamprey remains among faunal analysts and limited use of line screen sampling. Descriptions and photographs of lamprey remains that are most likely to survive in archaeological contexts are …

Cardioprotective Signal Transduction To Mitochondria, Casey Lee Quinlan

Dissertations and Theses

Intracellular responses to external stimuli require reception of the message at the plasma membrane followed by encoding and transmission of the message to its effectors downstream. In this process, diverse cellular responses are mediated by many redundant molecular players. The apparent generality and redundancy of many kinases, such as the mitogen-activated protein kinases (MAPKs), suggests that signal transduction must gain specificity through tight regulation. Diffusion and random collisions of relevant signaling components seem insufficient to explain the multilayered complexity observed in cell signaling cascades. Emerging hypotheses suggest that signaling machinery may achieve enhanced specificity and control by exploiting the compartmentalization …

Zoonotic Disease Emergence : A Study Of Host-Pathogen-Ecosystem Dynamics, Laurie Jeanne Dizney

Dissertations and Theses

A growing body of work demonstrates that loss of biodiversity negatively impacts ecosystem functions. One function, or service, that biodiverse ecosystems provide is suppression of zoonotic diseases, which are defined as diseases carried by wildlife hosts that can spill over into human populations. Ebola, SARS, West Nile virus, Hantavirus, Avian Influenza and Lyme disease are just a few of the recently emerging zoonotic diseases. Disease suppression has been shown for Lyme disease by the dilution effect, whereby increasing species diversity decreases disease prevalence in the host populations. But does a dilution effect apply to other disease systems? To test this …

The Reproductive And Conservation Biology Of The Spotted Towhee In Urban Forest Fragments, Sarah Bartos Smith

Dissertations and Theses

I studied the demography, reproductive biology, and mating behavior of Spotted Towhees (Pipilo maculatus) in four urban parks in relation to park area, the presence of recreational trails, and the effects of habitat edges. Despite high towhee abundance in the parks, two of the four are population sinks with levels of yearly reproductive productivity that do not offset adult survival. The other two parks have sufficient reproduction to adequately result in stable or growing population sizes. Park area and the proportion of habitat edge had no influence on population growth rate, reproductive productivity, or survival. However, trail density …

The Role Of Mitochondria Atp-Sensitive Potassium Channel In Cardioprotection, Ksenia Andrukhiv Everton

Dissertations and Theses

Mitochondrial ATP-sensitive potassium channel (mitoK_ATP) has been suggested to be the mediator of cardiac preconditioning. All of the diverse pharmacological and physiological agents that open mitoK_ATP provide protection against ischemia-reperfusion injury. Some investigators have pointed out that some of these mitoK_ATP channel openers also inhibit succinate dehydrogenase (SDH), complex II of the electron transport chain. Based on this observation they suggest that it is the inhibition of SDH, and not the opening of mitoK_ATP channel, that mediates the observed cardioprotection. In this study, I examined four chemically distinct and unrelated pharmacological agents, diazoxide, 3-Nitropropionic Acid …

Microbial Colonization Of Deep-Sea Hydrothermal Vent Chimneys, Antoine Pagé

Dissertations and Theses

Deep-sea hydrothermal vent chimneys harbor some of the most extreme environments supporting life on Earth. In the absence of sunlight, the microbial communities that colonize these deposits are based on energy harvested by chemolithoautotrophs exploiting the chemical disequilibria created as hydrothermal fluids mix with seawater. Although controversial, several models consider deep-sea vent chimneys as likely habitats for primitive ecosystems that developed during the Archean.

The goal of this study was to describe spatial and temporal patterns of microbial colonization in deep-sea vent chimneys emitting high temperature (>300°C) fluids. Microbial community composition and structure were evaluated through analyses of 16S …

An Embarrassment Of Riches: The Enzymology Of Rna Modification, Dirk Iwata-Reuyl

Chemistry Faculty Publications and Presentations

The maturation of transfer RNA (tRNA) involves extensive chemical modification of the constituent nucleosides and results in the introduction of significant chemical diversity to tRNA. Many of the pathways to these modified nucleosides are characterized by chemically complex transformations, some of which are unprecedented in other areas of biology. To illustrate the scope of the field, recent progress in understanding the enzymology leading to the formation of two distinct classes of modified nucleosides, the thiouridines and queuosine, a 7-deazaguanosine, is reviewed. In particular, recent data validating the involvement of several proposed intermediates in the formation of thiouridines are discussed, including …

The Family Fuselloviridae : Diversity And Replication Of A Hyperthermic Virus Infecting The Archaeon Genus Sulfolobus, Adam Joseph Clore

Dissertations and Theses

The virus family Fuselloviridae infects the hyperthermophilic and acidophilic Crenarchaeon genus Sulfolobus and has been isolated from terrestrial hotsprings worldwide. Two previously uncharacterized Fuselloviruses, SSV-13 and SSV-L1, were isolated and sequenced and are compared to the five fully sequenced viruses presently in the public databases. Conserved promoters in all viruses and similar putative origins of replication suggest that these viruses use a transcriptional and genomic replication program similar to the relatively well-characterized SSV1. Pairwise comparisons of conserved genes in the seven virus genomes show that, like its host Sulfolobus, these viruses' genetic divergence correlates with geographic separation. Genome rearrangements, horizontal …

Mechanisms Of Covalent Self-Assembly Of The Azoarcus Ribozyme From Four Fragment Oligonucleotides, Will E. Draper, Eric John Hayden, Niles Lehman

Chemistry Faculty Publications and Presentations

RNA oligomers of length 40–60 nt can self-assemble into covalent versions of the Azoarcus group I intron ribozyme. This process requires a series of recombination reactions in which the internal guide sequence of a nascent catalytic complex makes specific interactions with a complement triplet, CAU, in the oligomers. However, if the CAU were mutated, promiscuous self-assembly may be possible, lessening the dependence on a particular set of oligomer sequences. Here, we assayed whether oligomers containing mutations in the CAU triplet could still self-construct Azoarcus ribozymes. The mutations CAC, CAG, CUU and GAU all inhibited self-assembly to some degree, but did …

Sporophytic Inbreeding Depression In Mosses Occurs In A Species With Separate Sexes But Not In A Species With Combined Sexes, Philip J. Taylor, Sarah M. Eppley, Linley K. Jesson

Biology Faculty Publications and Presentations

Inbreeding depression is a critical factor countering the evolution of inbreeding and thus potentially shaping the evolution of plant sexual systems. Current theory predicts that inbreeding depression could have important evolutionary consequences, even in haploid-dominant organisms. To date, no data have been reported on inbreeding depression in moss species. Here, we present data on the magnitude of inbreeding depression in sporophytic traits of moss species with contrasting breeding systems. In eratodon purpureus (Ditrichaceae), a moss species with separate sexes, self-fertilizations between sibling gametophytes (intergametophytic selfing) significantly reduced fitness in two of four traits quantified, with seta length and capsule length …

Lifetime Reproductive Success Of Female Eastern Kingbirds (Tyrannus Tyrannus): Influence Of Lifespan, Nest Predation And Body Size, Michael T. Murphy

Biology Faculty Publications and Presentations

I report on the lifetime reproductive success (LRS) of female Eastern Kingbirds (Tyrannus tyrannus) in central New York. I investigated the major correlates of LRS and specifi cally tested the hypothesis that small body size yields reproductive benefi ts. Lifetime reproductive success varied widely: 15–20% of females failed to fledge young over their life, whereas 50% of young were fledged by 20% of females. Female lifespan varied between one and eight years, and females that died after one breeding season tended to be smaller-bodied than long-lived females (≥2 seasons). I therefore conducted analyses of LRS for the entire sample and …

Spiders Fluoresce Variably Across Many Taxa, Kindra Andrews, Scott M. Reed, Susan E. Masta

Biology Faculty Publications and Presentations

The evolution of fluorescence is largely unexplored, despite the newfound occurrence of this phenomenon in a variety of organisms. We document that spiders fluoresce under ultraviolet illumination, and find that the expression of this trait varies greatly among taxa in this species-rich group. All spiders we examined possess fluorophores in their haemolymph, but bright fluorescence appears to result when a spider sequesters fluorophores in its setae or cuticle. By sampling widely across spider taxa, we determine that fluorescent expression is labile and has evolved multiple times. Moreover, examination of the excitation and emission properties of extracted fluorophores reveals that spiders …

A Cautionary Tale: Cryptic Sexual Size Dimorphism In A Socially Monogamous Passerine, Michael T. Murphy

Biology Faculty Publications and Presentations

Among socially monogamous birds, standard metrics suggest that males are only ∼5% larger than females. An untested assumption is that, with the exception of reproductive systems, males and females are scaled mirror images of one another. I used external morphological and skeletal data, and information on muscle mass and organ size, to test this assumption in a population of breeding Eastern Kingbirds (Tyrannus tyrannus). Male and female Eastern Kingbirds exhibited no differences in body mass or standard measures of size, except in a longer (∼6%) wing chord and tail in males. However, keel length, a character rarely measured …

The Effects Of Western Dwarf Mistletoe (Arceuthobium Campylopodum) On Radial Growth Of Ponderosa Pine (Pinus Ponderosa) In Managed Stands In Eastern Oregon, Sharon Marie Stanton

Dissertations and Theses

Dwarf mistletoes (Arceuthobium spp.) are native flowering plants that parasitize a range of conifer species throughout western North America. Dwarf mistletoes are considered destructive forest pathogens, but recent research indicates that mistletoes play a key role in structuring plant communities by increasing structural diversity and providing wildlife habitat. The primary objective of my research is to quantify the structural and functional differences between infected and uninfected forest communities.

I investigated the effects of mistletoe (Arceuthobium campylopodum ) on host community dynamics and the interaction between mistletoe infection and fire in old-growth ponderosa pine (Pinus ponderosa) forests. …

Nest Reuse By Eastern Kingbirds: Adaptive Behavior Or Ecological Constraint?, Lucas J. Redmond, Michael T. Murphy, Amy C. Dolan

Biology Faculty Publications and Presentations

The reuse of old nests by open-cup nesting passerines is a seemingly rare but potentially adaptive behavior if, as a consequence, females begin to breed earlier, lay larger clutches, or fledge more young. We report an unusually high rate of nest reuse (~10% of 341 nests) for Eastern Kingbirds (Tyrannus tyrannus) breeding at Malheur National Wildlife Refuge, Oregon. We found no difference in availability of nesting habitat or food abundance in territories in which nests were and were not reused. We also found no support for the hypotheses that kingbirds benefited from nest reuse by breeding earlier, laying …

Avian Affairs: A Study Of The Occurrence And Benefits Of Extra-Pair Breeding Behavior In Eastern Kingbirds (Tyrannus Tyrannus), Amy Catherine Dolan

Dissertations and Theses

Over three consecutive breeding seasons I examined the breeding system of Eastern Kingbirds in Malheur National Wildlife Refuge in SE, Oregon. To assess genetic paternity, I optimized seven microsatellite markers and determined that extra pair paternity was common. Extra-pair young were present in approximately 60% of nests, representing 47% of young. I examined implications of extra-pair paternity from three perspectives.

First, I examined the impact of extra-pair paternity on the opportunity for sexual selection within a socially monogamous system and identified correlates of male reproductive success. Some males were successful at the expense of others, and 24% of males did …

Cultivation Of Methanogens From Shallow Marine Sediments At Hydrate Ridge, Orego, Melissa Kendall, David R. Boone

Biology Faculty Publications and Presentations

Little is known about the methanogenic degradation of acetate, the fate of molecular hydrogen and formate or the ability of methanogens to grow and produce methane in cold, anoxic marine sediments. The microbes that produce methane were examined in permanently cold, anoxic marine sediments at Hydrate Ridge (44°35' N, 125°10' W, depth 800 m). Sediment samples (15 to 35 cm deep) were collected from areas of active methane ebullition or areas where methane hydrates occurred. The samples were diluted into enrichment medium with formate, acetate or trimethylamine as catabolic substrate. After 2 years of incubation at 4 °C to 15 …

Contributions Of Heterosis And Epistasis To Hybrid Fitness, Mitchell B. Cruzan

Biology Faculty Publications and Presentations

Early-generation hybrid fitness is difficult to interpret because heterosis can obscure the effects of hybrid breakdown. We used controlled reciprocal crosses and common garden experiments to distinguish between effects of heterosis and nuclear and cytonuclear epistasis among morphotypes and advanced-generation hybrid derivative populations in the Piriqueta caroliniana (Turneraceae) plant complex. Seed germination, growth, and sexual reproduction of first-generation hybrids, inbred parental lines, and outbred parental lines were compared under field conditions. Average vegetative performance was greater for hybrids than for inbred lines, and firstseason growth was similar for hybrids and outbred parental lines. Hybrid survival surpassed that of inbred lines …

The Subsystems Approach To Genome Annotation And Its Use In The Project To Annotate 1000 Genomes, Ross Overbeek, Tadhg Begley, Ralph M. Butler, Jomuna V. Choudhuri, Han-Yu Chuang, Matthew Cohoon, Valérie De Crécy-Lagard, Naryttza Diaz, Terry Disz, Robert Edwards, Michael Fonstein, Ed D. Frank, Svetlana Gerdes, Elizabeth M. Glass, Alexander Goesmann, Andrew Hanson, Dirk Iwata-Reuyl, Roy Jensen, Neema Jamshidi, Lutz Krause, Michael Kubal, Niels Larsen, Burkhard Linke, Alice C. Mchardy, Folker Meyer, Heiko Neuweger, Gary Olsen, Robert Olson, Andrei Osterman, Vasiliy Portnoy, Gordon D. Pusch, Dmitry A. Rodionov, Christian Rückert, Jason Steiner, Rick Stevens, Ines Thiele, Olga Vassieva, Yuzhen Ye, Olga Zagnitko, Veronika Vonstein

Chemistry Faculty Publications and Presentations

The release of the 1000^th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high through put annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by …

Patterns Of Fitness And Fluctuating Asymmetry Across A Broad Hybrid Zone, Mitchell B. Cruzan

Biology Faculty Publications and Presentations

We estimated levels of developmental instability in leaves, as indicated by fluctuating asymmetry (i.e., random deviations from perfect bilateral symmetry), across a broad hybrid zone between two taxa in the Piriqueta caroliniana complex. Previous studies have indicated that this hybrid zone was initiated in southern Florida and has expanded northward. We found that plants from the hybrid zone generally had higher levels of leaf developmental instability than plants from allopatric regions, but the increase in asymmetry was not substantial. Although it is usually assumed that developmental instability is associated with lower fitness, these Piriqueta hybrids from central Florida are similar …

Woodland Amphibian Distribution In Parks And Greenspaces Of The Portland, Oregon Metropolitan Area: A Multiple Scale Investigation, Laura A. Roberts

Dissertations and Theses

Loss of biodiversity due to habitat fragmentation is worldwide problem. With growing human populations and increasing urbanization, it is a necessity to conduct studies on wildlife occurring in urban areas. Currently there is a deficit of research investigating woodland amphibians in urban environments. My objectives were to describe amphibian species richness and abundance in the Portland, Oregon, Metropolitan region, and relate patterns of variation to variables at three increasingly large spatial scales: 1) local microenvironmental (i.e. amphibian/substrate interaction), (2) macrohabitat/patch (i.e. park or greenspace), and 3) landscape (surrounding parks and greenspaces). Environmental variables occurring within the three spatial scales were …

Rare, Threatened And Endangered Species Of Oregon (2004), James S. Kagan, Sue Vrilakas, Eleanor P. Gaines, Cliff Alton, Fern Mcarthur, Kuuipo Walsh, Eric Scheuering, John A. Christy, Jon Hak, Claudine Tobalske, Annie Weiland, Theresa Koloszar, Oregon Natural Heritage Information Center

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 cause of this phenomenon is large-scale destruction of native habitats, which has increased since European settlement began in the mid 1800's - in Oregon and throughout the New 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 …

The Hyperthermophilic Archaeon Sulfolobus: From Exploration To Exploitation, Stan J.J. Brouns, Thijs J.G. Ettema, Kenneth M. Stedman, Jasper Walther, Hauke Smith, Ambrosius P.L. Snijders, Mark Young, Rolf Bernander, Phillip C. Wright, Betina Siebers, John Van Der Oost

Biology Faculty Publications and Presentations

In the early 1970s, Sulfolobus was first isolated by Thomas Brock and co-workers from sulfur-rich acidic hot springs in Yellowstone National Park. Sulfolobus became one of the model organisms of Archaea in general, and of Crenarchaea in particular. Many of its unusual physiological characteristics have been investigated, and several of its thermostable enzymes have been studied in considerable detail. For fundamental reasons, and because of its potential for industrial applications, Sulfolobus has been selected for a genome sequence project. The recent completion of the Sulfolobus solfataricus genome has set the stage for a series of postgenome research lines that will …

Comparative Studies Of Evolutionary Responses To Light Environments In Arabidopsis, Massimo Pigliucci, Heidi Pollard, Mitchell B. Cruzan

Biology Faculty Publications and Presentations

In this article, we compare the reaction norms to foliage shade (changes in light quality, spatially fine-grained environmental variation) and photoperiod (day length, spatially coarse-grained environmental variation) in several haplotypes of Arabidopsis thaliana from Scandinavia. We found that both across-environment means and phenotypic plasticities evolved continuously and very rapidly within this group. Both character means and trait plasticities were highly integrated, in part as predicted by the adaptive plasticity hypothesis for response to foliage shade (the so-called shade-avoidance syndrome). We found that a significant but small fraction of the variance in across-treatment trait means and plasticities in response to one …