Index Catalog // ScholarsArchive@OSU

Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes

Creator:: Filichkin, Sergei A. and Mockler, Todd C.
Abstract:: Background: Recent mapping of eukaryotic transcriptomes and spliceomes using massively parallel RNA sequencing (RNA-seq) has revealed that the extent of alternative splicing has been considerably underestimated. Evidence also suggests that many pre-mRNAs undergo unproductive alternative splicing resulting in incorporation of in-frame premature termination codons (PTCs). The destinies and potential functions...
Resource Type:: Article
Full Text:: splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes Sergei A Filichkin1

Improved DNase‑seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana

Creator:: Cumbie, Jason S., Filichkin, Sergei A., and Megraw, Molly
Abstract:: Background: Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high throughput sequencing to identify regions of regulatory DNA on a genome-wide scale. While this method was...
Resource Type:: Article
Full Text:: *Correspondence: megrawm@science.oregonstate.edu †Jason S. Cumbie and Sergei A. Filichkin have contributed

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

Creator:: Filichkin, Sergei A., Breton, Ghislain, Priest, Henry D., Dharmawardhana, Palitha, Jaiswal, Pankaj, Fox, Samuel E., Michael, Todd P., Chory, Joanne, Kay, Steve A., and Mockler, Todd C.
Abstract:: BACKGROUND: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day. Synchronized...
Resource Type:: Article

Expression, Splicing, and Evolution of the Myosin Gene Family in Plants

Creator:: Peremyslov, Valera V., Mockler, Todd C., Filichkin, Sergei A., Fox, Samuel E., Jaiswal, Pankaj, Makarova, Kira S., Koonin, Eugene V., and Dolja, Valerian V.
Abstract:: Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
Resource Type:: Article

Mechanistic Insight into Peroxydisulfate Reactivity: Oxidation of the cis,cis-[Ru(bpy)₂(OH₂)]₂O⁴⁺ "Blue Dimer"

Creator:: Hurst, James K., Roemeling, Margo D., and Lymar, Sergei V.
Abstract:: One-electron oxidation of the μ-oxo dimer (cis,cis-[Ruᴵᴵᴵ(bpy)₂(OH₂)]₂O⁴⁺, {3,3}) to {3,4} by S₂O₈²⁻ can be described by three concurrent reaction pathways corresponding to the three protic forms of {3,3}. Free energy correlations of the rate constants, transient species dynamics determined by pulse radiolysis, and medium and temperature dependencies of the alkaline...
Resource Type:: Article

Registration of the TCAP FAC-WIN6 Barley Panel for Genomewide Association Studies

Creator:: Belcher, Araby R., Graebner, Ryan C., Cuesta-Marcos, Alfonso, Fisk, Scott, Filichkin, Tanya, Smith, Kevin P., Blake, Victoria C., and Hayes, Patrick M.
Abstract:: Facultative/winter six-row malting barley is a distinct elite germplasm pool and a valuable resource that may prove useful in meeting the challenges of climate change. To preserve its diversity and make it accessible to the research and agricultural communities, the Oregon State University and University of Minnesota barley breeding programs...
Resource Type:: Article
Full Text:: Association Studies Belcher, A. R., Graebner, R. C., Cuesta-Marcos, A., Fisk, S., Filichkin, T., Smith, K. P

Multiple mantle plume components involved in the petrogenesis of subduction-related lavas from the northern termination of the Tonga Arc and northern Lau Basin: Evidence from the geochemistry of arc and backarc submarine volcanics

Creator:: Falloon, Trevor J., Danyushevsky, Leonid V., Crawford, Tony J., Maas, Roland, Woodhead, Jon D., Eggins, Stephen M., Bloomer, Sherman H., Wright, Dawn J., Zlobin, Sergei K., and Stacey, Andrew R.
Abstract:: New seafloor mapping and sampling demonstrates that the eruption of the high-Ca boninites is clearly associated with rifting of the northern Tonga ridge and the northern Lau Basin at the northern termination of the Tonga Trench. There is very strong evidence for OIB plume related mantle sources involved in the...
Resource Type:: Article
Full Text:: @dusk.geo.orst.edu) Sergei K. Zlobin Vernadsky Institute of Geochemistry and Analytical Chemistry, Russian

Multiple mantle plume components involved in the petrogenesis of subduction-related lavas from the northern termination of the Tonga Arc and northern Lau Basin: Evidence from the geochemistry of arc and backarc submarine volcanics

Creator:: Falloon, Trevor J., Danyushevsky, Leonid V., Crawford, Tony J., Maas, Roland, Woodhead, Jon D., Eggins, Stephen M., Bloomer, Sherman H., Wright, Dawn J., Zlobin, Sergei K., and Stacey, Andrew R.
Abstract:: We report new geochemical data for boninites and backarc basin-type basalts recovered from the northern termination of the Tonga trench and Lau Basin. Boninitic pillow lavas, ranging from high-Mg compositions to andesites and dacites, have been erupted within large submarine volcanic edifices (calderas and volcanoes) associated with active rifting of...
Resource Type:: Article
Full Text:: @dusk.geo.orst.edu) Sergei K. Zlobin Vernadsky Institute of Geochemistry and Analytical Chemistry, Russian Academy

Application of marker-assisted selection and genome-wide association scanning to the development of winter food barley germplasm resources

Creator:: Chutimanitsakun, Yada, Cuesta-Marcos, Alfonso, Chao, Shiaoman, Corey, Ann, Filichkin, Tanya, Fisk, Scott, Kolding, Mathias, Meints, Brigid, Ong, Yee-Ling, Rey, Juan Ignacio, Ross, Andrew S., and Hayes, Patrick M.
Abstract:: Barley (Hordeum vulgare) is an important component of heart-healthy whole grain diets because it contains β-glucan. All current US barley varieties with high β-glucan are spring habit and have waxy starch. Winter varieties have agronomic advantages but require low-temperature tolerance (LTT). Vernalization sensitivity (VS) is associated with higher levels of...
Resource Type:: Article

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

Creator:: Dharmawardhana, Palitha, Ren, Liya, Amarasinghe, Vindhya, Monaco, Marcela, Thomason, Jim, Ravenscroft, Dean, McCouch, Susan, Ware, Doreen, and Jaiswal, Pankaj
Abstract:: Background: Functional annotations of large plant genome projects mostly provide information on gene function and gene families based on the presence of protein domains and gene homology, but not necessarily in association with gene expression or metabolic and regulatory networks. These additional annotations are necessary to understand the physiology, development...
Resource Type:: Article
Full Text:: (Filichkin, Breton et al. 2011b; Xu, Yang et al. 2011; Michael, Mockler et al. 2008), a major proportion of

ScholarsArchive@OSU

Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes

Improved DNase‑seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana

Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules

Expression, Splicing, and Evolution of the Myosin Gene Family in Plants

Mechanistic Insight into Peroxydisulfate Reactivity: Oxidation of the cis,cis-[Ru(bpy)₂(OH₂)]₂O⁴⁺ "Blue Dimer"

Registration of the TCAP FAC-WIN6 Barley Panel for Genomewide Association Studies

Multiple mantle plume components involved in the petrogenesis of subduction-related lavas from the northern termination of the Tonga Arc and northern Lau Basin: Evidence from the geochemistry of arc and backarc submarine volcanics

Multiple mantle plume components involved in the petrogenesis of subduction-related lavas from the northern termination of the Tonga Arc and northern Lau Basin: Evidence from the geochemistry of arc and backarc submarine volcanics

Application of marker-assisted selection and genome-wide association scanning to the development of winter food barley germplasm resources

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

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