Index Catalog // ScholarsArchive@OSU

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

Reconsidering Relationships among Stem and Crown Group Pinaceae: Oldest Record of the Genus Pinus from the Early Cretaceous of Yorkshire, United Kingdom

Creator:: Ryberg, Patricia E., Rothwell, Gar W., Stockey, Ruth A., Hilton, Jason, Mapes, Gene, and Riding, James B.
Abstract:: This study describes a specimen that extends the oldest fossil evidence of Pinus L. to the Early Cretaceous Wealden Formation of Yorkshire, UK (131-129 million years ago), and prompts a critical reevaluation of criteria that are employed to identify crown group genera of Pinaceae from anatomically preserved seed cones. The...
Resource Type:: Article
Full Text:: CRETACEOUS OF YORKSHIRE, UNITED KINGDOM Patricia E. Ryberg,* Gar W. Rothwell,1,y,z Ruth A. Stockey,y,§ Jason

Population Density and Phenology of Tetranychus urticae (Acari: Tetranychidae) in Hop is Linked to the Timing of Sulfur Applications

Creator:: Woods, J. L., Dreves, A. J., Fisher, Glenn C., James, David G., Wright, Larry C., and Gent, D. H.
Abstract:: The twospotted spider mite, Tetranychus urticae Koch, is a worldwide pest of numerous agronomic and horticultural plants. Sulfur fungicides are known to induce outbreaks of this pest on several crops, although mechanisms associated with sulfur-induced mite outbreaks are largely unknown. Studies were conducted during 2007–2009 in Oregon and Washington hop...
Resource Type:: Article
Full Text:: urticae (Acari: Tetranychidae) in Hop is Linked to the Timing of Sulfur Applications J. L. WOODS,1 A. J

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

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:: processing- defective mutants in Arabidopsis by direct genome sequencing Josh T. Cuperusa,b, Taiowa A

Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants

Creator:: Carbonell, Alberto, Fahlgren, Noah, Garcia-Ruiz, Hernan, Gilbert, Kerrigan B., Montgomery, Taiowa A., Nguyen, Tammy, Cuperus, Josh T., and Carrington, James C.
Abstract:: In RNA-directed silencing pathways, ternary complexes result from small RNA-guided ARGONAUTE (AGO) associating with target transcripts. Target transcripts are often silenced through direct cleavage (slicing), destabilization through slicer-independent turnover mechanisms, and translational repression. Here, wild-type and active-site defective forms of several Arabidopsis thaliana AGO proteins involved in posttranscriptional silencing were...
Resource Type:: Article
Full Text:: ARGONAUTES Using Slicer-Defective MutantsW OA Alberto Carbonell,a Noah Fahlgren,a Hernan Garcia-Ruiz,a

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:: A. Montgomery1, Chi Zhang1, Noah Fahlgren2, Peter C. Breen1, Alexia Hwang1, Christopher M

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:: ,1,2 KRISTIN D. KASSCHAU,1,2 ELISABETH J. CHAPMAN,1,2,3 JASON S. CUMBIE,1,2 TAIOWA A. MONTGOMERY,1,2

Distinct Argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline

Creator:: Gu, Weifeng, Shirayama, Masaki, Conte Jr., Darryl, Vasale, Jessica, Batista, Pedro J., Claycomb, Julie M., Moresco, James J., Youngman, Elaine, Keys, Jennifer, Stoltz, Matthew J., Chen, Chun-Cheih G., Chaves, Daniel A., Duan, Shenghua E., Kasschau, Krisitin D., Fahlgren, Noah, Yates III, John R., Mitani, Shohei, Carrington, James C., and Mello, Craig C.
Abstract:: Endogenous small RNAs (endo-siRNAs) interact with Argonaute (AGO) proteins to mediate sequence-specific regulation of diverse biological processes. Here, we combine deep-sequencing and genetic approaches to explore the biogenesis and function of endo-siRNAs in C. elegans. We describe conditional alleles of the dicer-related helicase, drh-3, that abrogate both RNA interference and...
Resource Type:: Article
Full Text:: , Matthew J. Stoltz1, Chun-Chieh G. Chen1, Daniel A. Chaves1,5, Shenghua E. Duan1, Kristen D. Kasschau6

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

Creator:: Ohm, Robin A., Feau, Nicolas, Henrissat, Bernard, Schoch, Conrad L., Horwitz, Benjamin A., Barry, Kerrie W., Condon, Bradford J., Copeland, Alex C., Dhillon, Braham, Glaser, Fabian, Hesse, Cedar N., Kosti, Idit, LaButti, Kurt, Lindquist, Erika A., Lucas, Susan, Salamov, Asaf A., Bradshaw, Rosie E., Ciuffetti, Lynda, Hamelin, Richard C., Kema, Gert H. J., Lawrence, Christopher, Scott, James A., Spatafora, Joseph W., Turgeon, B. Gillian, de Wit, Pierre J. G. M., Zhong, Shaobin, Goodwin, Stephen B., and Grigoriev, Igor V.
Abstract:: Correction 5 Mar 2013: Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, et al. (2013) Correction: Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi. PLOS Pathogens 9(3): 10.1371/annotation/fcca88ac-d684-46e0-a483-62af67e777bd
Resource Type:: Article
Full Text:: Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi Robin A. Ohm1*, Nicolas Feau2, Bernard

ScholarsArchive@OSU

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

Reconsidering Relationships among Stem and Crown Group Pinaceae: Oldest Record of the Genus Pinus from the Early Cretaceous of Yorkshire, United Kingdom

Population Density and Phenology of Tetranychus urticae (Acari: Tetranychidae) in Hop is Linked to the Timing of Sulfur Applications

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

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

Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants

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

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

Distinct Argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

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