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:: siRNAs Kristin D. Kasschau 1,2 , Noah Fahlgren 1,2,3 , Elisabeth J. Chapman 1,2,3 , Christopher M

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:: microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes Noah Fahlgren1,2, Miya D. Howell1, Kristin D

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:: defects (Fig. 1 C and D). These 193 plants with general tasiRNA defects comprised class II mutants

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

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
Full Text:: . Bollmann3, Kristin D. Kasschau2, Josh T. Cuperus2¤a, Caroline M. Press3, Christopher M. Sullivan2

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
Full Text:: . Bars are color coded according to the most abundant size class of small RNAs within each interval. (D

Seeing Genes: Multiscale Phenotyping Reveals Gene Functions in Maize Pollen

Creator:: Warman, Cedar D.
Abstract:: Plant sexual reproduction requires a broad array of molecular mechanisms to proceed successfully. Some of these mechanisms are well-studied, but our knowledge of them as a whole is fundamentally incomplete. Pollen tube growth is a key part of this process, facilitating the delivery of the sperm cells to the female...
Resource Type:: Dissertation
Full Text:: Trans Syst Man Cybern 9:62–66 Palanivelu R, Preuss D (2006) Distinct short-range ovule signals

Pyrenophora tritici-repentis : investigation of factors that contribute to pathogenicity

Creator:: Holman, Thomas W.
Abstract:: Pyrenophora tritici-repentis (Ptr) is the necrotrophic fungus responsible for tan spot of wheat (Triticum aestivum). Ptr causes disease on susceptible wheat cultivars through the production and secretion of host-selective toxins (HSTs). HSTs are compounds that are only known to be produced by fungi and considered to be primary determinants of...
Resource Type:: Masters Thesis
Full Text:: . 2006. Nature. 444:323–329. S tr en g th o f d ef en se r es p o n se R-Avr Strong

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

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

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

Seeing Genes: Multiscale Phenotyping Reveals Gene Functions in Maize Pollen

Pyrenophora tritici-repentis : investigation of factors that contribute to pathogenicity

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