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

JaiswalPankajBotanyPlantPathologyGlobalProfilingRice.pdf

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...
Full Text:: and cis-Regulatory Modules Sergei A. Filichkin1, Ghislain Breton2¤a, Henry D. Priest1, Palitha

JaiswalPankajBotanyPlantPathologyGlobalProfilingRice_SupportingInformation.zip

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...

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

JaiswalPankajBotanyPlantPathologyExpressionSplicingEvolution.pdf

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...
Full Text:: , Sergei A. Filichkin, Samuel E. Fox, Pankaj Jaiswal, Kira S. Makarova, Eugene V. Koonin, and Valerian V

JaiswalPankajBotanyPlantPathologyExpressionSplicingEvolution_TableS1.pdf

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...

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

Growth, specific gravity, and chemical composition of quaking aspen on different soil types

Creator:: Forest Products Laboratory (U.S.), Wilde, Sergei A., and Paul, Benson H.
Abstract:: Information reviewed and reaffirmed 1965. Original report dated January 1959.
Resource Type:: Technical Report
Full Text:: DIFFERENT SOIL TYPES– By SERGEI A. WILDE/ Professor of Soils University of Wisconsin and BENSON H. PAUL

RoemelingMargoBiochemBiophysicsMechanisticInsightPeroxydisulfateSupportingInfo.pdf

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...
Full Text:: (bpy)2(OH2)]2O4+ “Blue Dimer” James K. Hurst,† Margo Roemeling,‡ and Sergei V. Lymar

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

JaiswalPankajBotanyPlantPathologyGlobalProfilingRice.pdf

JaiswalPankajBotanyPlantPathologyGlobalProfilingRice_SupportingInformation.zip

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

JaiswalPankajBotanyPlantPathologyExpressionSplicingEvolution.pdf

JaiswalPankajBotanyPlantPathologyExpressionSplicingEvolution_TableS1.pdf

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

Growth, specific gravity, and chemical composition of quaking aspen on different soil types

RoemelingMargoBiochemBiophysicsMechanisticInsightPeroxydisulfateSupportingInfo.pdf

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