Plant Science

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    Protocols in Current Issue
    Investigation of Transposon DNA Methylation and Copy Number Variation in Plants Using Southern Hybridisation
    Authors:  Vivek Hari Sundar G. and P. V. Shivaprasad, date: 06/05/2022, view: 713, Q&A: 0
    [Abstract]

    Plant genomes are pronouncedly enriched in repeat elements such as transposons. These repeats are epigenetically regulated by DNA methylation. Whole genome high-depth sequencing after bisulfite treatment remains an expensive and laborious method to reliably profile the DNA methylome, especially when considering large genomes such as in crops.

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    Application of Cadaverine to Inhibit Biotin Biosynthesis in Plants
    Authors:  Nicole M. Gibbs, Shih-Heng Su and Patrick H. Masson, date: 04/20/2022, view: 668, Q&A: 0
    [Abstract]

    Biotin is an essential vitamin in plants. However, characterization of biotin deficiency has been limited by embryo lethality in mutants, which can only be rescued by supplementation of biotin. Here, we describe a protocol to characterize biotin deficiency in Arabidopsis thaliana through application of the polyamine cadaverine. Cadaverine

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    Isolation of Plant Nuclei Compatible with Microfluidic Single-nucleus ATAC-sequencing
    Authors:  Sandra B. Thibivilliers, Dirk K. Anderson and Marc Y. Libault, date: 12/05/2021, view: 1819, Q&A: 0
    [Abstract]

    Gene expression depends on the binding of transcription factors with DNA regulatory sequences. The level of accessibility for these sequences varies between cells and cell types. Until recently, using the Tn5 assay for transposase-accessible chromatin for sequencing (ATAC-seq) technology allowed assessing the profiles of chromatin from an entire

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    Split-luciferase Complementation Imaging Assay to Study Protein-protein Interactions in Nicotiana benthamiana
    Authors:  Liping Wang, Gang Yu, Alberto P. Macho and Rosa Lozano-Durán, date: 12/05/2021, view: 2438, Q&A: 0
    [Abstract]

    The experimental identification of protein-protein interactions (PPIs) is critical to understand protein function. Thus, a plethora of sensitive and versatile approaches have been developed to detect PPIs in vitro or in vivo, such as protein pull-down, yeast two-hybrid (Y2H), co-immunoprecipitation (co-IP), and bimolecular fluorescence

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    Enrichment of Cytoplasmic RNA Granules from Arabidopsis Seedlings
    Authors:  Zhen Lei, Eun Yu Kim and Jungnam Cho, date: 11/05/2021, view: 1480, Q&A: 0
    [Abstract]

    RNA granules (RGs) are membraneless intracellular compartments that play important roles in the post-transcriptional control of gene expression. Stress granules (SGs) are a type of RGs that form under environmental challenges and/or internal cellular stresses. Stress treatments lead to strong mRNAs translational inhibition and storage in SGs until

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    Histone modification ChIP-seq on Arabidopsis thaliana Plantlets
    Authors:  Juan S. Ramirez-Prado, David Latrasse and Moussa Benhamed, date: 11/05/2021, view: 2039, Q&A: 1
    [Abstract]

    Characterizing the molecular mechanisms regulating gene expression is crucial for understanding the regulatory processes underlying physiological responses to environmental and developmental signals in eukaryotes. The covalent modification of histones contributes to the compaction levels of chromatin, as well as the recruitment of the

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    Quantitative Analysis of RNA Editing at Specific Sites in Plant Mitochondria or Chloroplasts Using DNA Sequencing
    Authors:  Yang Yang and Weixing Shan, date: 09/20/2021, view: 1403, Q&A: 0
    [Abstract]

    Cytidine-to-uridine (C-to-U) RNA editing is one of the most important post-transcriptional RNA processing in plant mitochondria and chloroplasts. Several techniques have been developed to detect the RNA editing efficiency in plant mitochondria and chloroplasts, such as poisoned primer extension (PPE) assays, high-resolution melting (HRM) analysis,

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    U2.3 Precursor Small Nuclear RNA in vitro Processing Assay
    Authors:  Chan Lin, Yujie Feng, Xueyan Peng, Jiaming Wu, Weili Wang and Yunfeng Liu, date: 09/05/2021, view: 1094, Q&A: 0
    [Abstract]

    Small nuclear RNAs (snRNAs) are vital for eukaryotic cell activities and play important roles in pre-mRNA splicing. The molecular mechanism underlying the transcription of snRNA, regulated via upstream/downstream cis-elements and relevant trans-elements, has been investigated in detail using cell-free extracts. However, the processing of precursor

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    A Novel Method to Map Small RNAs with High Resolution
    Authors:  Kun Huang, Feray Demirci, Blake C. Meyers and Jeffrey L. Caplan, date: 08/20/2021, view: 2071, Q&A: 0
    [Abstract]

    Analyzing cellular structures and the relative location of molecules is essential for addressing biological questions. Super-resolution microscopy techniques that bypass the light diffraction limit have become increasingly popular to study cellular molecule dynamics in situ. However, the application of super-resolution imaging techniques to detect

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    A Fast and Easy Method to Study Ralstonia solanacearum Virulence upon Transient Gene Expression or Gene Silencing in Nicotiana benthamiana Leaves
    Authors:  Wenjia Yu and Alberto P. Macho, date: 08/05/2021, view: 2154, Q&A: 0
    [Abstract]

    Ralstonia solanacearum is a devastating soil-borne bacterial pathogen that causes disease in multiple host plants worldwide. Typical assays to measure virulence of R. solanacearum in laboratory conditions rely on soil-drenching inoculation followed by observation and scoring of disease symptoms. Here, we describe a novel inoculation protocol to

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