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Hypochlorous Acid Staining with R19-S in the Drosophila Intestine upon Ingestion of Opportunistic Bacteria

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Extraction and Purification of Laccases from Rice Stems

Authors: Chenna Swetha and P. V. Shivaprasad, date: 04/05/2019, view: 407, Q&A: 0

[Abstract] Laccases are found in cell walls of plants in very low amounts. This protocol provides an efficient method to purify laccases from rice stems. The method involves three steps: 1) Isolation of total protein from rice stems using buffers with high salt concentration to extract protein from cell walls; 2) Purification of laccases using concanavalin-A ...

In vitro Protein-DNA Binding Assay (AlphaScreen^® Technology)

Authors: Mika Nomoto, Yasuomi Tada and Hironaka Tsukagoshi, date: 02/05/2019, view: 1092, Q&A: 0

[Abstract] Identification of specific DNA binding sites of transcription factors is important in understanding their functions. Recent techniques allow us to investigate genome-wide in vivo binding positions by chromatin immunoprecipitation combined with high-throughput sequencing. However, to further explore the binding motifs of transcription ...

Genome-wide Estimation of Evolutionary Distance and Phylogenetic Analysis of Homologous Genes

Authors: Meixia Zhao, Biao Zhang, Jianxin Ma and Damon Lisch, date: 12/05/2018, view: 1165, Q&A: 0

[Abstract] Homologous genes, including paralogs and orthologs, are genes that share sequence homologies within or between different species. Homologous genes originate from a common origin through speciation, genetic duplication or horizontal gene transfer. Estimation of the sequence divergence of homologous genes help us to understand divergence time, which ...

Using Arabidopsis Mesophyll Protoplasts to Study Unfolded Protein Response Signaling

Authors: Yan Bao and Diane C. Bassham, date: 12/05/2018, view: 1081, Q&A: 0

[Abstract] Various environmental stresses or artificial reagents can trigger unfolded protein accumulation in the endoplasmic reticulum (ER) due to the folding capacity of the ER being exceeded. This is termed ER stress, and triggers the unfolded protein response (UPR). Assays for activation of the UPR in plants include Tunicamycin (Tm)- or dithiothreitol ...

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: 1464, 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: 2133, 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 ...

Tethered Chromosome Conformation Capture Sequencing in Triticeae: A Valuable Tool for Genome Assembly

Authors: Axel Himmelbach, Ines Walde, Martin Mascher and Nils Stein, date: 08/05/2018, view: 1754, Q&A: 0

[Abstract] Chromosome conformation capture sequencing (Hi-C) is a powerful method to comprehensively interrogate the three-dimensional positioning of chromatin in the nucleus. The development of Hi-C can be traced back to successive increases in the resolution and throughput of chromosome conformation capture (3C) (Dekker et al., 2002). The basic ...

High Resolution Melting Temperature Analysis to Identify CRISPR/Cas9 Mutants from Arabidopsis

Authors: Cynthia Denbow, Sonia Carole Ehivet and Sakiko Okumoto, date: 07/20/2018, view: 1832, Q&A: 0

[Abstract] CRISPR/Cas9 made targeted mutagenesis and genome editing possible for many plant species. One of the ways that the endonuclease is used for plant genetics is the creation of loss-of-function mutants, which typically result from erroneous DNA repair through non-homologous end joining (NHEJ) pathway. The majority of erroneous repair events results ...

Extraction of RNA from Recalcitrant Tree Species Paulownia elongata

Authors: Niveditha Ramadoss and Chhandak Basu, date: 07/20/2018, view: 1469, 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 ...

Separation of Thylakoid Protein Complexes with Two-dimensional Native-PAGE

Authors: Marjaana Rantala, Virpi Paakkarinen and Eva-Mari Aro, date: 07/05/2018, view: 2204, Q&A: 0

[Abstract] The hierarchical composition and interactions of the labile thylakoid protein complexes can be assessed by sequential 2D-native gel-electrophoresis system. Mild non-ionic detergent digitonin is used to solubilize labile protein super-and megacomplexes, which are then separated with first-dimension blue native polyacrylamide gel electrophoresis ...

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