Life Sciences Commons^™

Reconstructability Analysis Of Epistasis, Martin Zwick

Systems Science Faculty Publications and Presentations

The literature on epistasis describes various methods to detect epistatic interactions and to classify different types of epistasis. Reconstructability analysis (RA) has recently been used to detect epistasis in genomic data. This paper shows that RA offers a classification of types of epistasis at three levels of resolution (variable-based models without loops, variable-based models with loops, state-based models). These types can be defined by the simplest RA structures that model the data without information loss; a more detailed classification can be defined by the information content of multiple candidate structures. The RA classification can be augmented with structures from related …

Accelerated Erosion Of Saltmarshes Infested By The Non-Native Burrowing Crustacean Sphaeroma Quoianum, Timothy Mathias Davidson, Catherine E. De Rivera

Environmental Science and Management Faculty Publications and Presentations

Lateral erosion of saltmarshes is affected by many abiotic and biotic factors. While abiotic factors are typically regarded as primary drivers of erosion, biotic influences such as burrowing or bioturbating taxa can also extensively modify the physical structure of this marine habitat. Many estuaries on the Pacific coast of North America have been invaded by populations of the burrowing non-native isopod Sphaeroma quoianum, which are thought to exacerbate the erosion of saltmarshes. We conducted a mensurative experiment to examine the relationship between populations of S. quoianum and lateral erosion rate of saltmarshes in Coos Bay, Oregon, USA. After 1 …

Scoring Function To Predict Solubility Mutagenesis, Ye Tian, Christopher Deutsch, Bala Krishnamoorthy

Chemistry Faculty Publications and Presentations

Background: Mutagenesis is commonly used to engineer proteins with desirable properties not present in the wild type (WT) protein, such as increased or decreased stability, reactivity, or solubility. Experimentalists often have to choose a small subset of mutations from a large number of candidates to obtain the desired change, and computational techniques are invaluable to make the choices. While several such methods have been proposed to predict stability and reactivity mutagenesis, solubility has not received much attention. Results: We use concepts from computational geometry to define a three body scoring function that predicts the change in protein solubility due to …

Structure Of The Cholera Toxin Secretion Channel In Its Closed State, Steve Reichow, Konstantin V. Korotkov, Wim Gj Hol, Tamir Gonen

Chemistry Faculty Publications and Presentations

The type II secretion system (T2SS) is a macromolecular complex spanning the inner and outer membranes of Gram-negative bacteria. Remarkably, the T2SS secretes folded proteins including multimeric assemblies like cholera toxin and heat-labile enterotoxin from Vibrio cholerae and enterotoxigenic Escherichia coli, respectively. The major outer membrane T2SS protein is the “secretin” GspD. Electron cryomicroscopy reconstruction of the V. cholerae secretin at 19 Å resolution reveals a dodecameric structure reminiscent of a barrel with a large channel at its center that appears to contain a closed periplasmic gate. The GspD periplasmic domain forms a vestibule with a conserved constriction, and binds …

Cooperative Interaction Of Transcription Termination Factors With The Rna Polymerase Ii C-Terminal Domain, Bradley M. Lunde, Steve Reichow, Minkyu Kim, Hyunsuk Suh, Thomas C. Leeper, Fan Yang, Hannes Mutschler, Stephen Buratowski, Anton Meinhart, Gabriele Varani

Chemistry Faculty Publications and Presentations

Phosphorylation of the C-terminal domain of RNA polymerase II controls the co-transcriptional assembly of RNA processing and transcription factors. Recruitment relies on conserved CTDinteracting domains that recognize different CTD phosphoisoforms during the transcription cycle, but the molecular basis for their specificity remains unclear. We show that the CTD-interacting domains of two transcription termination factors, Rtt103 and Pcf11, achieve high affinity and specificity both by specifically recognizing the phosphorylated CTD and by cooperatively binding to neighboring CTD repeats. Single amino acid mutations at the protein-protein interface abolish cooperativity and affect recruitment at the 3′-end processing site in vivo. We suggest that …

The Effectiveness Of Vertebrate Passage And Prevention Structures: A Study Of Boeckman Road In Wilsonville, Catherine E. De Rivera, Leslie L. Bliss-Ketchum

Environmental Science and Management Faculty Publications and Presentations

One of the most obvious impacts roads have on the natural world is direct mortality to individual animals that attempt to cross roads. A less obvious but likely more important impact of roads on many species is habitat fragmentation. The ability for individuals to travel between subpopulations is the key to genetic diversity as well as ultimately the survival of the species. Considering these impacts and management goals to increase habitat connectivity, increased attention has been given to creating road design that reduces wildlife collisions. Most studies, however, have been in other countries or regions and most focus on connectivity …

Virus Silicification Under Simulated Hot Spring Conditions, James R. Laidler, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Silicification of organisms in silica-depositing environments can impact both their ecology and their presence in the fossil record. Although microbes have been silicified under laboratory and environmental conditions, viruses have not. Bacteriophage T4 was successfully silicified under laboratory conditions that closely simulated those found in silica-depositing hot springs. Virus morphology was maintained, and a clear elemental signature of phosphorus was detected by energy-dispersive X-ray spectrophotometry (EDS).

Symmetries Of The Central Vestibular System: Forming Movements For Gravity And A Three-Dimensional World, Gin Mccollum, Douglas Hanes

Mathematics and Statistics Faculty Publications and Presentations

Intrinsic dynamics of the central vestibular system (CVS) appear to be at least partly determined by the symmetries of its connections. The CVS contributes to whole-body functions such as upright balance and maintenance of gaze direction. These functions coordinate disparate senses (visual, inertial, somatosensory, auditory) and body movements (leg, trunk, head/neck, eye). They are also unified by geometric conditions. Symmetry groups have been found to structure experimentally-recorded pathways of the central vestibular system. When related to geometric conditions in three-dimensional physical space, these symmetry groups make sense as a logical foundation for sensorimotor coordination.

Are Biotechnology And Sustainable Agriculture Compatible?, David E. Ervin, Leland L. Glenna, Raymond Adelard Jussaume

Economics Faculty Publications and Presentations

Agricultural biotechnology has been largely opposed by advocates in the sustainable agriculture movement, despite claims by the technology’s proponents that it holds the promise to deliver both production (economic) and environmental benefits, two legs of the sustainability stool. We argue in this paper that participants in this polarized debate are talking past each other because assumptions about biotechnology and sustainability remain simplistic and poorly defined. Genetically engineered (GE) herbicide-resistant and insect-resistant crop varieties are the most visible current forms of agricultural biotechnology, and thus the form of biotechnology that many in the sustainability movement react to. However, these crops represent …

Interview With Steve Jones, Us Forest Service, 2010 (Audio), Steve Jones

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Interview of Steve Jones by Scott Swenson at Hood River, Oregon on May 25th, 2010.

The interview index is available for download.

Interview With Judy Combs, Kaiser Permanente, 2010 (Audio), Judy Combs

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Interview of Judy Combs by Nazer Frias at Clackamas, Oregon on May 17th, 2010.

The interview index is available for download.

Interview With Jeff Luebbers, Us Forest Service, 2010 (Audio), Jeff Luebbers

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Interview of Jeff Luebbers by Chelsea Saurman on May 13th, 2010.

The interview index is available for download.

Complex Interactions Between Regional Dispersal Of Native Taxa And An Invasive Species, Angela L. Strecker, Shelley E. Arnott

Environmental Science and Management Faculty Publications and Presentations

In the event of an environmental disturbance, dispersal of native taxa may provide species and genetic diversity to ecosystems, increasing the likelihood that there will be species and genotypes present that are less vulnerable to the disturbance. This may allow communities to maintain functioning during a disturbance and may be particularly important when the perturbation is novel to the system, such as the establishment of an invasive species. We examined how dispersal of native species may influence crustacean zooplankton communities in freshwater lakes invaded by the invertebrate predator, Bythotrephes longimanus. Using large enclosures, we experimentally tested the effect of …

Predicting Global Change Effects On Forest Biomass And Composition In South-Central Siberia, Eric J. Gustafson, Anatoly Z. Shvidenko, Brian R. Sturtevant, Robert M. Scheller

Environmental Science and Management Faculty Publications and Presentations

Multiple global changes such as timber harvesting in areas not previously disturbed by cutting and climate change will undoubtedly affect the composition and spatial distribution of boreal forests, which will, in turn, affect the ability of these forests to retain carbon and maintain biodiversity. To predict future states of the boreal forest reliably, it is necessary to understand the complex interactions among forest regenerative processes (succession), natural disturbances (e.g., fire, wind, and insects), and anthropogenic disturbances (e.g., timber harvest). We used a landscape succession and disturbance model (LANDIS-II) to study the relative effects of climate change, timber harvesting, and insect …

Exploring Mitigation Options To Reduce Vehicle-Caused Mortality For The Oregon Silverspot Butterfly, Speyeria Zerene Hippolyta, Along Highway 101 At The Siuslaw National Forest, Sara B. Zielin

Environmental Science and Management Professional Master's Project Reports

The Oregon Silverspot Butterfly (OSB), Speyeria zerene hippolyta, is federally listed as "threatened." It historically inhabited coastal regions of Washington, Oregon, and California (USFWS 2001). OSB populations only remain at five sites, four of which are in Oregon; one remaining population is in California, and none exist in Washington state as they have been extirpated (BFCI 2009; USFWS 2001). The site selected for this study was Rock Creek-Big Creek, adjacent to the Siuslaw National Forest. At this site OSB habitat is bisected by Highway 101; butterflies are observed to use both sides of the highway throughout their life cycle. …

Interview With Susan Stelljes, Woodlawn Community Garden, 2010 (Audio), Susan Stelljes

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Interview of Susan Stellijess by Stephanie Mackey on March 6th, 2010.

The interview index is available for download.

Interview With Sonja Andreas, Mccoy Gardens, 2010 (Audio), Sonja Andreas

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Interview of Sonja Andreas by Ian McCreary in Portland, Oregon on March 5, 2010.

The interview index is available for download.

Interview With John Witte, Tenino Farms, 2010 (Audio), John Witte

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Interview of John Witte by Steve Rosin at Portland, Oregon on March 1st, 2010.

The interview index is available for download.

Forest Restoration In A Mixed-Ownership Landscape Under Climate Change, Catherine Ravenscroft, Robert M. Scheller, David J. Mladenoff, Mark A. White

Environmental Science and Management Faculty Publications and Presentations

The article presents a study regarding forest management associated with climate change. It mentions that preservation endeavors and restoration schemes should diminish current threats like unsuited forest management and development while integrating possible effects of climate change. It also stresses that an adaptive approach to management can be the most efficient strategy of forest restoration given the doubts of climate change impacts.

Quasispecies-Like Behavior Observed In Catalytic Rna Populations Evolving In A Test Tube, Carolina Diaz Arenas, Niles Lehman

Chemistry Faculty Publications and Presentations

Background: During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous.

Results: Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen …

Interview With Jacquin Dole, Riverside Farms, 2010 (Audio), Jacquin Dole

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Interview of Jacquin Dole by Paul Hopper at Riverside Farm McMinnville, Oregon on February 28th, 2010.

The interview index is available for download.

Interview With Bernard Smith, Full Of Life Farms, 2010 (Audio), Bernard Smith

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Interview of Bernard Smith by Kyle Dykstra on February 28th, 2010.

The interview index is available for download.

Interview With Katy Kolker, Portland Fruit Tree Project, 2010 (Audio), Katy Kolker

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Interview of Katy Kolker by Dan Stillinger in Portland, Oregon on February 27th, 2010.

The interview index is available for download.

Interview With Allejandro Tecum, Adelante Mujeres, 2010 (Audio), Allejandro Tecum

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Interview of Allejandro Tecum by Adam Villareal at Forest Grove, Oregon on February 25th, 2010.

The interview index is available for download.

Interview With David Beller, Mercy Corp Nw, 2010 (Audio), David Beller

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Interview of David Beller by Kyle Koonce at Mercy Corp Portland, Oregon on February 25th, 2010.

The interview index is available for download.

Interview With Darrell Sanders, Cully Community Garden, 2010 (Audio), Darrell Sanders

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Interview of Darrell Sanders by Jeremy Cohen in Portland, Oregon on February 20th, 2010.

The interview index is available for download.

Symmetries Of The Central Vestibular System: Forming Movements For Gravity And A Three-Dimensional World, Gin Mccollum, Douglas A. Hanes

Gin McCollum

Intrinsic dynamics of the central vestibular system (CVS) appear to be at least partly determined by the symmetries of its connections. The CVS contributes to whole-body functions such as upright balance and maintenance of gaze direction. These functions coordinate disparate senses (visual, inertial, somatosensory, auditory) and body movements (leg, trunk, head/neck, eye). They are also unified by geometric conditions. Symmetry groups have been found to structure experimentally-recorded pathways of the central vestibular system. When related to geometric conditions in three-dimensional physical space, these symmetry groups make sense as a logical foundation for sensorimotor coordination.

Phase-Linking And The Perceived Motion During Off-Vertical Axis Rotation, Jan E. Holly, Scott J. Wood, Gin Mccollum

Gin McCollum

Human off-vertical axis rotation (OVAR) in the dark typically produces perceived motion about a cone, the amplitude of which changes as a function of frequency. This perception is commonly attributed to the fact that both the OVAR and the conical motion have a gravity vector that rotates about the subject. Little-known, however, is that this rotating-gravity explanation for perceived conical motion is inconsistent with basic observations about self-motion perception: (a) that the perceived vertical moves toward alignment with the gravito-inertial acceleration (GIA) and (b) that perceived translation arises from perceived linear acceleration, as derived from the portion of the GIA …

Phase-Linking And The Perceived Motion During Off-Vertical Axis Rotation, Jan Holly, Scott Wood, Gin Mccollum

Mathematics and Statistics Faculty Publications and Presentations

Human off-vertical axis rotation (OVAR) in the dark typically produces perceived motion about a cone, the amplitude of which changes as a function of frequency. This perception is commonly attributed to the fact that both the OVAR and the conical motion have a gravity vector that rotates about the subject. Little-known, however, is that this rotating-gravity explanation for perceived conical motion is inconsistent with basic observations about self-motion perception: (a) that the perceived vertical moves toward alignment with the gravito-inertial acceleration (GIA) and (b) that perceived translation arises from perceived linear acceleration, as derived from the portion of the GIA …