Life Sciences Commons^™

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 …

Environmental Controls On The Landscape-Scale Biogeography Of Stream Bacterial Communities, Noah Fierer, Jennifer L. Morse, Sean T. Berthrong, Emily S. Bernhardt, Robert B. Jackson

Environmental Science and Management Faculty Publications and Presentations

We determined the biogeographical distributions of stream bacteria and the biogeochemical factors that best explained heterogeneity for 23 locations within the Hubbard Brook watershed, a 3000-ha forested watershed in New Hampshire, USA. Our goal was to assess the factor, or set of factors, responsible for generating the biogeographical patterns exhibited by microorganisms at the landscape scale. We used DNA fingerprinting to characterize bacteria inhabiting fine benthic organic matter (FBOM) because of their important influence on stream nutrient dynamics. Across the watershed, streams of similar pH had similar FBOM bacterial communities. Streamwater pH was the single variable most strongly correlated with …

Interview With Anthony Boutard, Ayers Creek Farm, 2007 (Audio), Anthony Boutard

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Interview of Anthony Boutard by Magda Gaytan at Ayers Creek Farm on August 10th, 2007.

The interview index is available for download.

Interview With Dan J. Wilson, Sudan Farms, 2007 (Audio), Dan J. Wilson

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Interview of Dan J. Wilson by Jason Keaton at Canby, Oregon on August 10th, 2007.

The interview index is available for download.

Interview With Trevor Baird, Baird Family Orchard, 2007 (Audio), Trevor Baird

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Interview of Trevor Baird by Adam Hopfe at Portland State University on August 7th, 2007.

The interview index is available for download.

Interview With Melissa & Rod Volbeda, Willamette Valley Cheese, 2007 (Audio), Melissa Volbeda, Rod Volbeda

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Interview of Melissa and Rod Volbeda by Magda Gaytan on August 6th, 2007.

Willamette Valley Cheese Company tour photos available for download.

Interview With Dianne Stefani-Ruff, Portland Farmers Market, 2007 (Audio), Dianne Stefani-Ruff

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Interview of Dianne Stefani-Ruff by Jennifer Bennett on July 31st, 2007.

The interview index is available for download.

Interview With Roger Allen Konka, Springwater Farm, 2007 (Audio), Roger Allen Konka

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Interview of Roger Allen Konka by Michael Schott on July 29th, 2007.

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Interview With Lyle N. Stanley, Gee Creek Farm, 2007 (Audio), Lyle N. Stanley

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Interview of Lyle N. Stanley by Aaron Veal at Portland State University on July 28th, 2007.

The interview index is available for download.

Interview With Kathy & Matt Unger, Unger Farms, 2007 (Audio), Kathy Unger, Matt Unger

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Interview of Kathy and Matt Unger by Alix Lefler at Cornelius, Oregon on July 25th, 2007.

The interview index is available for download.

Green Crab Management: Reduction Of A Marine Invasive Population, Catherine E. De Rivera, Edwin D. Grosholz, Greg Ruiz, Amy A. Larson, Rebecca L. Kordas, Mark Sytsma

Environmental Science and Management Faculty Publications and Presentations

The overall goal of this study is to develop and demonstrate the capacity for local eradication of adult Carcinus maenas, European green crabs. This represents a conceptual shift in development of management options to address established invasions in marine systems, extending and exploring the application of terrestrial successes in this area. Specifically, this project tests the effects of removing green crabs from Bodega Harbor on the green crab population and on native shore crabs eaten by green crabs.

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 …

Multiplex Snp Discrimination, Daniel J. Fish, M. Todd Horne, Robert P. Searles, Greg P. Brewood, Albert S. Benight

Chemistry Faculty Publications and Presentations

Multiplex hybridization reactions of perfectly matched duplexes and duplexes containing a single basepair mismatch (SNPs) were investigated on DNA microarrays. Effects of duplex length, G-C percentage, and relative position of the SNP on duplex hybridization and SNP resolution were determined. Our theoretical model of multiplex hybridization accurately predicts observed results and implicates target concentration as a critical variable in multiplex SNP detection.

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 …

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 …

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. …

The Structure And Function Of Small Nucleolar Ribonucleoproteins, Steve Reichow, Tomoko Hamma, Adrian R. Ferré-D’Amaré, Gabriele Varani

Chemistry Faculty Publications and Presentations

Eukaryotes and archaea use two sets of specialized ribonucleoproteins (RNPs) to carry out sequencespecific methylation and pseudouridylation of RNA, the two most abundant types of modifications of cellular RNAs. In eukaryotes, these protein–RNA complexes localize to the nucleolus and are called small nucleolar RNPs (snoRNPs), while in archaea they are known as small RNPs (sRNP). The C/D class of sno(s)RNPs carries out ribose- 20-O-methylation, while the H/ACA class is responsible for pseudouridylation of their RNA targets. Here, we review the recent advances in the structure, assembly and function of the conserved C/D and H/ACA sno(s)RNPs. Structures of each of the …

Spatial Symmetry Groups As Sensorimotor Guidelines, Gin Mccollum

Gin McCollum

While some aspects of neuroanatomical organization are related to packing and access rather than to function, other aspects of anatomical/physiological organization are directly related to function. The mathematics of symmetry groups can be used to determine logical structure in projections and to relate it to function. This paper reviews two studies of the symmetry groups of vestibular projections that are related to the spatial functions of the vestibular complex, including gaze, posture, and movement. These logical structures have been determined by finding symmetry groups of two vestibular projections directly from physiological and anatomical data. Logical structures in vestibular projections are …

Habitat And Distribution Of The Ruffed Lemur, "Varecia", North Of The Bay Of Antongil In Northeastern Madagascar, Evon R. Hekkala, Marius Rakotondratsima, Natalie Vasey

Anthropology Faculty Publications and Presentations

Here we present information on the conservation status of ruffed lemurs (Varecia) north of the Bay of Antongil in northeastern Madagascar. Two contiguous protected areas were recently established that traverse this region via blocks of forest connected by narrow forest corridors: the Masoala National Park, which expands further to the east, and the Makira Protected Area, which expands further to the west and northwest. The two extant ruffed lemurs, Varecia variegata and V. rubra, overlapped in this region historically and, on rare occasions, hybridized. As such, land north of the Bay of Antongil is a critical part …

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 …

Dna Multiplex Hybridization On Microarrays And Thermodynamic Stability In Solution: A Direct Comparison, Daniel J. Fish, M. Todd Horne, Greg P. Brewood, Jim P. Goodarzi, Saba Alemayehu, Ashwini Bhandiwad, Robert P. Searles, Albert S. Benight

Chemistry Faculty Publications and Presentations

Hybridization intensities of 30 distinct short duplex DNAs measured on spotted microarrays, were directly compared with thermodynamic stabilities measured in solution. DNA sequences were designed to promote formation of perfect match, or hybrid duplexes containing tandem mismatches. Thermodynamic parameters DeltaH degrees , DeltaS degrees and DeltaG degrees of melting transitions in solution were evaluated directly using differential scanning calorimetry. Quantitative comparison with results from 63 multiplex microarray hybridization experiments provided a linear relationship for perfect match and most mismatch duplexes. Examination of outliers suggests that both duplex length and relative position of tandem mismatches could be important factors contributing to …