Index Catalog // ScholarsArchive@OSU

Improving Best Management Practices for Potato Production in the Columbia Basin : An Evaluation of Essential Oils for Control of Verticillium Wilt and the Fate of Chloride in the System

Creator:: Light, Sarah Elizabeth
Abstract:: Although the potato (Solanum tuberosum L.) is a global crop, few growing regions rival the high yields of the Columbia Basin of Eastern Oregon and Washington. Two research projects were conducted in Hermiston, OR to contribute to best management practices for the region. The first project evaluated the efficacy of...
Resource Type:: Masters Thesis
Full Text:: : ______________________________________________________________________________ Dan M. Sullivan Philip B. Hamm Although the potato

The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases

Creator:: Givan, Scott A., Sullivan, Christopher M., and Carrington, James C.
Abstract:: Background: Large molecular sequence databases are fundamental resources for modern bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often advantageous to maintain smaller sequence databases. However, this is usually not an easy task for the average bench scientist. Results: We present the Personal Sequence Database (PSD),...
Resource Type:: Article
Full Text:: * - givans@cgrb.oregonstate.edu; Christopher M Sullivan - sullivan@cgrb.oregonstate.edu; James C Carrington

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Creator:: Kasschau, Kristin D., Fahlgren, Noah, Chapman, Elisabeth J., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., and Carrington, James C.
Abstract:: Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants...
Resource Type:: Article
Full Text:: . Sullivan 1,2 , Jason S. Cumbie 1,2 , Scott A. Givan 1,2 , James C. Carrington 1,2* 1 Center for Genome

High-Throughput Sequencing of Arabidopsis microRNAs : Evidence for Frequent Birth and Death of MIRNA Genes

Creator:: Fahlgren, Noah, Howell, Miya D., Kasschau, Kristin D., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., Law, Theresa F., Grant, Sarah R., Dangl, Jeffrey L., and Carrington, James C.
Abstract:: In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep...
Resource Type:: Article
Full Text:: . Kasschau1, Elisabeth J. Chapman1,2, Christopher M. Sullivan1, Jason S. Cumbie1, Scott A. Givan1, Theresa F

Identification of MIR390a precursor processing defective mutants in Arabidopsis by direct genome sequencing

Creator:: Cuperus, Josh T., Montgomery, Taiowa A., Fahlgren, Noah, Burke, Russell T., Townsend, Tiffany, Sullivan, Christopher M., and Carrington, James C.
Abstract:: Transacting siRNA (tasiRNA) biogenesis in Arabidopsis is initiated by microRNA (miRNA) –guided cleavage of primary transcripts. In the case of TAS3 tasiRNA formation, ARGONAUTE7 (AGO7)– miR390 complexes interact with primary transcripts at two sites, resulting in recruitment of RNA-DEPENDENT RNA POLYMERASE6 for dsRNA biosynthesis. An extensive screen for Arabidopsis mutants...
Resource Type:: Article
Full Text:: variants using mapping quality scores. Genome Res 18:1851–1858. 29. Sarin S, Prabhu S, O'Meara MM, Pe'er I

Computational and analytical framework for small RNA profiling by high-throughput sequencing

Creator:: Fahlgren, Noah, Sullivan, Christopher M., Kasschau, Krisitin D., Chapman, Elisabeth J., Cumbie, Jason S., Montgomery, Taiowa A., Gilbert, Sunny D., Dasenko, Mark, Backman, Tyler W. H., Givan, Scott A., and Carrington, James C.
Abstract:: The advent of high-throughput sequencing (HTS) methods has enabled direct approaches to quantitatively profile small RNA populations. However, these methods have been limited by several factors, including representational artifacts and lack of established statistical methods of analysis. Furthermore, massive HTS data sets present new problems related to data processing and...
Resource Type:: Article
Full Text:: framework for small RNA profiling by high-throughput sequencing NOAH FAHLGREN,1,2 CHRISTOPHER M. SULLIVAN

Serpentine and non-serpentine edaphic ecology and the recovery of Lomatium cookii (Apiaceae), an endangered endemic of southwest Oregon

Creator:: Silvernail, Ian S.
Abstract:: The role of unusual geologies in plant distribution and form is well-known. Serpentine (ultramafic) soils exert a particularly strong influence on plants, as evidenced by a high level of endemism and the morphological and physiological traits displayed in adaptation to the extraordinary chemistry of these substrates. Adaptation may lead to...
Resource Type:: Masters Thesis
Full Text:: Ian S. Silvernail for the degree of Master of Science in Botany and Plant Pathology presented on

The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications

Creator:: Fischer, Sylvia E. J., Montgomery, Taiowa A., Zhang, Chi, Fahlgren, Noah, Breen, Peter C., Hwang, Alexia, Sullivan, Christopher M., Carrington, James C., and Ruvkun, Gary
Abstract:: Endogenous small interfering RNAs (siRNAs) are a class of naturally occuring regulatory RNAs found in fungi, plants, and animals. Some endogenous siRNAs are required to silence transposons or function in chromosome segregation; however, the specific roles of most endogenous siRNAs are unclear. The helicase gene eri-6/7 was identified in the...
Resource Type:: Article

Population viability analysis of endangered plant species : an evaluation of stochastic methods and an application to a rare prairie plant

Creator:: Kaye, Thomas N.
Abstract:: Transition matrix models are one of the most widely used tools for assessing population viability. The technique allows inclusion of environmental variability, thereby permitting estimation of probabilistic events, such as extinction. However, few studies use the technique to compare the effects of management treatments on population viability, and fewer still...
Resource Type:: Dissertation
Full Text:: Rare Prairie Plant. Abstract Abstract approved: David A Patricia S. Muir Transition matrix models

Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

Creator:: Fahlgren, Noah, Bollmann, Stephanie R., Kasschau, Kristin D., Cuperus, Josh T., Press, Caroline M., Sullivan, Christopher M., Chapman, Elisabeth J., Hoyer, J. Steen, Gilbert, Kerrigan B., Grunwald, Niklaus J., and Carrington, James C.
Abstract:: In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora...
Resource Type:: Article

ScholarsArchive@OSU

Improving Best Management Practices for Potato Production in the Columbia Basin : An Evaluation of Essential Oils for Control of Verticillium Wilt and the Fate of Chloride in the System

The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

High-Throughput Sequencing of Arabidopsis microRNAs : Evidence for Frequent Birth and Death of MIRNA Genes

Identification of MIR390a precursor processing defective mutants in Arabidopsis by direct genome sequencing

Computational and analytical framework for small RNA profiling by high-throughput sequencing

Serpentine and non-serpentine edaphic ecology and the recovery of Lomatium cookii (Apiaceae), an endangered endemic of southwest Oregon

The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications

Population viability analysis of endangered plant species : an evaluation of stochastic methods and an application to a rare prairie plant

Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

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