http://hdl.handle.net/1957/6762 2013-05-24T23:21:18Z 2013-05-24T23:21:18Z Gustafson, Adam M. Allen, Edwards Givan, Scott Smith, Daniel Carrington, James C. Kasschau, Kristin D. http://hdl.handle.net/1957/18509 2010-09-27T23:54:38Z 2005-01-01T00:00:00Z

ASRP: the Arabidopsis Small RNA Project Database Gustafson, Adam M.; Allen, Edwards; Givan, Scott; Smith, Daniel; Carrington, James C.; Kasschau, Kristin D. ABSTRACT Eukaryotes produce functionally diverse classes of small RNAs (20–25 nt). These include microRNAs (miRNAs), which act as regulatory factors during growth and development, and short-interfering RNAs (siRNAs), which function in several epigenetic and post-transcriptional silencing systems. The Arabidopsis Small RNA Project (ASRP) seeks to characterize and functionally analyze the major classes of endogenous small RNAs in plants. The ASRP database provides a repository for sequences of small RNAs cloned from various Arabidopsis genotypes and tissues. Version 3.0 of the database contains 1920 unique sequences, with tools to assist in miRNA and siRNA identification and analysis. The comprehensive database is publicly available through a web interface at http://asrp.cgrb.oregonstate.edu. This is a peer-reviewed pre-copy-editing, author-produced PDF of an article accepted for publication in Nucleic Acids Research. The definitive publisher-authenticated version [Gustafson, A. M., Allen, E., Givan, S., Smith, D., Carrington, J. C., & Kasschau, K. D. (2005). ASRP: the Arabidopsis Small RNA Project Database. Nucleic Acids Research, 33. doi: 10.1093/nar/gki127] is available online at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540081/.

2005-01-01T00:00:00Z Thomas, William J. Chang, Jeff Thireault, Caitlin A. Kimbrel, Jeffrey http://hdl.handle.net/1957/18385 2011-03-24T07:05:40Z 2009-08-06T00:00:00Z

Recombineering and stable integration of the Pseudomonas syringae pv. syringae 61 hrp/hrc cluster into the genome of the soil bacterium Pseudomonas fluorescens Pf0-1 Thomas, William J.; Chang, Jeff; Thireault, Caitlin A.; Kimbrel, Jeffrey SUMMARY Many Gram-negative bacteria use a type III secretion system (T3SS) to establish associations with their hosts. The T3SS is a conduit for direct injection of type-III effector proteins into host cells, where they manipulate the host for the benefit of the infecting bacterium. For plant-associated pathogens, the variations in number and amino acid sequences of type-III effectors, as well as their functional redundancy, make studying type-III effectors challenging. To mitigate this challenge, we developed a stable delivery system for individual or defined sets of type-III effectors into plant cells. We used recombineering and Tn5-mediated transposition to clone and stably integrate, respectively, the complete hrp/hrc region from Pseudomonas syringae pv. syringae 61 into the genome of the soil bacterium Pseudomonas fluorescens Pf0-1. We describe our development of Effector-to-Host Analyzer (EtHAn), and demonstrate its utility for studying effectors for their in planta functions.

2009-08-06T00:00:00Z Johnson, Eric M. Rosenberg, Daniel K. http://hdl.handle.net/1957/16207 2011-03-24T07:30:44Z 2006-07-14T00:00:00Z

Granary-Site Selection by Acorn Woodpeckers in the Willamette Valley, Johnson, Eric M.; Rosenberg, Daniel K. The acorn woodpecker is among the most common primary cavity nesting bird of the Oregon white oak woodlands. In most of their range, acorn woodpeckers are dependent on granaries for acorn storage, yet little is known about their selection of granary sites. We compared habitat characteristics within 12 m of granary and non-granary trees at 20 acorn woodpecker colonies in Benton County, Oregon during the winter of 2001. Compared to non-granaries, granary plots consistently had greater oak basal area and shorter shrub height, and granary trees were of larger diameter. Within each of the 20 sites, oak basal area was greater near granary than non-granary trees. This, together with the selection for larger diameter granaries, suggests acorn woodpeckers are more likely to locate granaries in the immediate area of high acorn production. Increased acorn production in the vicinity of granaries is likely beneficial to the birds because minimal effort is expended in caching maximum forage. Our results shed light on granary selection at the spatial scale of the immediate area surrounding granaries and suggest factors associated with acorn woodpecker distribution at the landscape scale. © 2006 by the Northwest Scientific Association

2006-07-14T00:00:00Z McKenney, Melissa A. Rao, Sujaya Stephen, William P. http://hdl.handle.net/1957/16200 2011-03-22T17:48:45Z 2009-01-01T00:00:00Z

Pollination in Cranberries on the South Oregon Coast: Honeybees McKenney, Melissa A.; Rao, Sujaya; Stephen, William P. Many cranberry growers on the Oregon coast are well aware that good pollination is necessary for quality fruit set. Multiple visits to the flower deliver more pollen, which can increase the percentage fruit set, number of seeds per berry, and mature berry weight. The better a bee is at delivering pollen to the flower, the fewer the number of visits required for adequate pollination. Typically growers rent hives of the European honeybee for cranberry pollination. However, honeybees have exhibited a general preference for lotus, gorse, other weeds and native plants over cranberry flowers. As a result, growers must bring in enough hives to saturate the surrounding area so that at least some of the honeybees will have no choice but to forage in cranberry beds. In addition, honeybees forage primarily in fair weather. Multiple studies have shown (and many people have observed) that honeybees will retreat to their hives once it begins to rain. Often, they will retreat even when the skies become overcast, which is not ideal behavior for working in stormy coastal weather. Further, with the recent concerns about Colony Collapse Disorder, attack by mites and other diseases, the supply of available hives has decreased. This shortage brings to light the need for an alternate pollinator—a native species that is not susceptible to the ills of honeybees. In the Pacific Northwest, there are over 200 species of native bees. Those species native to Oregon are acclimated to Oregon weather. Several species of bumblebees begin foraging hours before honeybees are active, and cease foraging at dusk when the honeybees have already been inactive for an hour or two. The advantages of having bees forage longer hours are obvious—the more time they spend foraging, the more flowers they will pollinate. In addition, Oregon's native bee species are often sighted foraging when it is drizzling while the warm-weather preferring honeybees are in their hives. Currently, little is known about the number and diversity of bee species present on the southern Oregon coast. This information is required for determining whether a better pollinator than honey bees is available for cranberries. By determining which species are present during bloom it will be possible to select a species that flies during bloom, and one that is also loyal to cranberries.

2009-01-01T00:00:00Z