Plant Science

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    Protocols in Current Issue
    Real-time PCR Analysis of PAMP-induced Marker Gene Expression in Nicotiana benthamiana
    Authors:  Fan Liu, Yuanpeng Xu, Yan Wang and Yuanchao Wang, date: 10/05/2018, view: 3040, Q&A: 0
    [Abstract] Perception of pathogen-associated molecular patterns (PAMPs) often triggers various innate immune responses in plants. The transcriptional changes of defense-related genes are often used as a marker to assay PAMP-triggered plant immune response. Here we described a protocol to monitor the relative expression level of marker genes in Nicotiana ...
    In planta Transcriptome Analysis of Pseudomonas syringae
    Authors:  Tatsuya Nobori and Kenichi Tsuda, date: 09/05/2018, view: 4040, Q&A: 0
    [Abstract] Profiling bacterial transcriptome in planta is challenging due to the low abundance of bacterial RNA in infected plant tissues. Here, we describe a protocol to profile transcriptome of a foliar bacterial pathogen, Pseudomonas syringae pv. tomato DC3000, in the leaves of Arabidopsis thaliana at an early stage of ...
    Extraction of RNA from Recalcitrant Tree Species Paulownia elongata
    Authors:  Niveditha Ramadoss and Chhandak Basu, date: 07/20/2018, view: 2789, Q&A: 0
    [Abstract] Isolation of pure RNA is the basic requisite for most molecular biology work. Plants contain polyphenols and polysaccharides, which can interfere with isolation of pure RNA from them. Especially hardwood tree species like Paulownia elongata have surplus amount of RNA-binding alkaloids, proteins and secondary metabolites that can further ...
    RNA Purification from the Unicellular Green Alga, Chromochloris zofingiensis
    Authors:  Sean D. Gallaher and Melissa S. Roth, date: 04/05/2018, view: 3412, Q&A: 0
    [Abstract] Chromochloris zofingiensis is a unicellular green alga that is an emerging model species for studies in fields such as biofuel production, ketocarotenoid biosynthesis and metabolism. The recent availability of a high-quality genome assembly facilitates systems-level analysis, such as RNA-Seq. However, cells of this alga have a tough cell ...
    Isolation of Nuclei in Tagged Cell Types (INTACT), RNA Extraction and Ribosomal RNA Degradation to Prepare Material for RNA-Seq
    [Abstract] Gene expression is dynamically regulated on many levels, including chromatin accessibility and transcription. In order to study these nuclear regulatory events, we describe our method to purify nuclei with Isolation of Nuclei in TAgged Cell Types (INTACT). As nuclear RNA is low in polyadenylated transcripts and conventional pulldown methods would ...
    In vitro RNA-dependent RNA Polymerase Assay Using Arabidopsis RDR6
    Authors:  Kyungmin Baeg, Yukihide Tomari and Hiro-oki Iwakawa, date: 01/05/2018, view: 4672, Q&A: 0
    [Abstract] RNA-dependent RNA polymerases (RdRPs) in eukaryotes convert single-stranded RNAs into double-stranded RNAs, thereby amplifying small interfering RNAs that play crucial roles in the regulation of development, maintenance of genome integrity and antiviral immunity. Here, we describe a method of in vitro RdRP assay using recombinant ...
    Trimolecular Fluorescence Complementation (TriFC) Assay for Direct Visualization of RNA-Protein Interaction in planta
    Authors:  Jun Sung Seo and Nam-Hai Chua, date: 10/20/2017, view: 6137, Q&A: 0
    [Abstract] RNA-Protein interactions play important roles in various eukaryotic biological processes. Molecular imaging of subcellular localization of RNA/protein complexes in plants is critical for understanding these interactions. However, methods to image RNA-Protein interactions in living plants have not yet been developed until now. Recently, we have ...
    Single Molecule RNA FISH in Arabidopsis Root Cells
    Authors:  Susan Duncan, Tjelvar S. G. Olsson, Matthew Hartley, Caroline Dean and Stefanie Rosa, date: 04/20/2017, view: 8343, Q&A: 0
    [Abstract] Methods that allow the study of gene expression regulation are continually advancing. Here, we present an in situ hybridization protocol capable of detecting individual mRNA molecules in plant root cells, thus permitting the accurate quantification and localization of mRNA within fixed samples (Duncan et al., 2016; Rosa et al ...
    Mungbean Yellow Mosaic India Virus (MYMIV)-infection, Small RNA Library Construction and Deep Sequencing for MicroRNA Identification in Vigna mungo
    Authors:  Anirban Kundu, Sujay Paul, Amita Pal and Genotypic Technology, date: 10/20/2016, view: 6916, Q&A: 0
    [Abstract] This protocol describes small RNA library preparation from Vigna mungo total RNA followed by deep sequencing and analysis for microRNA identification.​
    Total RNA Extraction from Grape Berry Skin for Quantitative Reverse Transcription PCR and Microarray Analysis
    Authors:  Mami Suzuki and Katsuhiro Shiratake, date: 04/05/2016, view: 5483, Q&A: 0
    [Abstract] Extraction of high quality RNA is an essential step for quantitative reverse transcription PCR (qRT-PCR) and microarray analysis. However, it is not easy to extract high quality RNA from fruit materials, which contain high amounts of polysaccharides, lipids and secondary metabolites. Wan and Wilkins (1994) had developed ‘Hot Borate Method’ to ...



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