Plant Protein Secretion : Methods and Protocols /
edited by Liwen Jiang.
Bok Engelsk 2017 · Electronic books.
| Medvirkende | Jiang, Liwen. (editor.)
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|---|---|
| Omfang | 1 online resource (XI, 285 p. 68 illus., 60 illus. in color.)
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| Utgave | 1st ed. 2017.
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| Opplysninger | Intro -- Preface -- Contents -- Contributors -- Chapter 1: An Overview of Protein Secretion in Yeast and Animal Cells -- 1 A General Description of the Secretory Transport Pathway in Yeast and Animal Cells -- 2 Anterograde Transport from the ER to the Golgi -- 3 Intra-Golgi Transport -- 4 Export of Proteins Out of the Golgi -- 5 Post-Golgi Trafficking of Secretory Proteins En Route to the Plasma Membrane -- References -- Chapter 2: An Overview of Protein Secretion in Plant Cells -- 1 Conventional Protein Secretion in Plants -- 1.1 Endoplasmic Reticulum-The Port of Entry to the Secretory Pathway -- 1.2 ER-to-Golgi Anterograde Transport in Plants-Vesicles Versus Tubules? -- 1.3 Intra-Golgi Transport in Plants -- 1.4 Post-Golgi Trafficking of Secretory Proteins to the Plasma Membrane in Plants -- 2 Unconventional Protein Secretion in Plants -- 2.1 Conventional vs. Unconventional Protein Secretion in Plants -- 2.2 Direct Translocation of LSP Across the Plasma Membrane via a Golgi-Bypass Pathway -- 2.3 UPS via Vacuole- and Multivesicular Bodies-Plasma Membrane Fusion -- 2.4 Exocyst-Positive Organelle (EXPO)-Mediated Secretion Pathway -- 2.5 Techniques and Approaches for Future UPS Studies -- References -- Chapter 3: Bioinformatics Analysis of Protein Secretion in Plants -- 1 Introduction -- 2 Materials -- 3 Methods -- 3.1 Signal Peptide Sequence Prediction -- 3.2 Protein Subcellular Localization Prediction -- 3.3 Transmembrane Feature Prediction -- 3.4 Combine the Omics Data Tools -- 4 Notes -- References -- Chapter 4: Proteomic Analysis of Secreted Proteins from Cell Microenvironment -- 1 Introduction -- 2 Materials -- 2.1 Cell Culture -- 2.2 Collection of Secreted Proteins from Conditioned Media -- 2.3 Protein Digestion -- 2.4 Desalting -- 2.4.1 SPE Column Desalting -- 2.4.2 StageTip Desalting -- 2.5 High pH Reversed Phase Fractionation -- 2.6 LC-MS.. - 2.7 Database Search -- 3 Methods -- 3.1 Cell Culture -- 3.2 Collection of Conditioned Media -- 3.3 Protein Precipitation -- 3.4 Protein Digestion -- 3.5 Protein Desalting -- 3.5.1 SPE Column Desalting -- 3.5.2 StageTip Desalting -- 3.6 High pH Reversed Phase StageTip-Fractionation -- 3.7 LC-MS -- 3.7.1 Column Preparation -- Precolumn -- Analytical Column -- 3.7.2 LC-MS Analysis -- 3.8 Data Analysis -- 4 Notes -- References -- Chapter 5: Using Homology Modeling to Understand the Structural Basis of Specific Interaction of a Plant-Specific AtSar1a-AtSe... -- 1 Introduction -- 2 Materials -- 2.1 Software -- 2.2 Web-Based Tools -- 3 Methods -- 3.1 Overview of Homology Modeling -- 3.2 Before You Start -- 3.3 Template Identification -- 3.4 Initial Sequence Alignment for Target Sharing > -- ~30% Identity with the Template -- 3.5 Generation of Models Using CHIMERA/MODELLER -- 3.6 Inspecting/Revising the Initial Alignment/Models for AtSar1a -- 3.7 Initial Sequence Alignment for Target Sharing < -- ~30% Identity with the Template -- 3.8 Inspecting/Revising the Initial Alignment/Models for AtSec23a -- 3.9 Modeling of AtSar1a-AtSec23a Complex by Command-Line Based MODELLER -- 3.10 Structural Basis of Pairwise Interaction of AtSar1a-AtSec23a -- 4 Notes -- References -- Chapter 6: Analysis of Golgi-Mediated Protein Traffic in Plant Cells -- 1 Introduction -- 2 Materials -- 2.1 Plant Suspension Culture Cells and Protoplasts Isolation and Transfection -- 2.2 Arabidopsis Plant Flower Dip and Crossing -- 2.3 Drug Treatment and Confocal Microscopy -- 2.4 Endoglycosidase Treatment and Western Blotting Analysis -- 3 Methods -- 3.1 Protoplast Isolation and Transfection -- 3.2 Arabidopsis Plant Floral Dip and Crossing -- 3.3 Drug Treatment and Confocal Imaging -- 3.4 Endoglycosidase Treatment and Western Blot Analysis -- 4 Notes -- References.. - 3.1 Isolation of Tobacco Mesophyll Protoplasts for Electrotransformation -- 3.2 Isolation of Protoplasts from Suspension-Cultured Arabidopsis and Tobacco BY2 Cells -- 3.3 Electrotransformation of Protoplasts -- 3.4 Harvesting of the Culture Medium and Cells -- 3.5 Analysis of the Enzymatic α-Amylase Activity and Quantification of Protein Transport -- 4 Notes -- References -- Chapter 16: A Secretion System for Cargo Protein Identification of Vacuolar Sorting Receptors -- 1 Introduction -- 2 Materials -- 2.1 Arabidopsis PSB-D Suspension Cells Transformation -- 2.2 Precipitation of Media Proteins -- 2.3 Sample Preparation for Mass Spectrometry from Culture Medium Precipitates -- 3 Methods -- 3.1 Generation of PSB-D Stable Cell Line Expressing VSRNT (See Note 1) -- 3.2 Precipitation of Media Proteins of VSRNT -- 3.3 Sample Preparation for LC MS/MS from Culture Medium Precipitates (See Note 8) -- 4 Notes -- References -- Chapter 17: Identifying Novel Regulators of Vacuolar Trafficking by Combining Fluorescence Imaging-Based Forward Genetic Scree... -- 1 Introduction -- 2 Materials -- 2.1 Reagents for EMS Mutagenesis and Transgenic Seeds Expressing a GFP-Translational Fusion of Tonoplast Protein -- 2.2 In Vitro Pollen Germination Media (for Arabidopsis Col-0) -- 3 Methods -- 3.1 EMS Mutagenesis -- 3.2 In Vitro Pollen Germination Assay (Fig. 1) -- 4 Notes -- References -- Chapter 18: Measuring Plant Protein Secretion -- 1 Introduction -- 2 Materials -- 2.1 Solutions and Buffers -- 2.2 secYFP Fluorescent Constructs -- 2.3 Software -- 3 Method 1: Transient Expression of a Secretable YFP Protein for Ratiometric Measurement of Secretion in Arabidopsis Seedling ... -- 3.1 Transformation of Arabidopsis Seedlings -- 3.2 Measuring Secretion in Transgenic Arabidopsis Roots.. - 3.2 In Vitro Arabidopsis Pollen Germination -- 3.3 Visualization and Quantification of Cytoplasmic Streaming in the Pollen Tube -- 3.4 Visualization and Quantification of YFP-ARA7-Decorated Endosomes in the Pollen Tube -- 3.5 Visualization and Quantification of YFP-RabA4b Decorated Transport Vesicles in the Pollen Tube -- 3.6 FRAP Analysis -- 4 Notes -- References -- Chapter 12: Analysis of Phragmoplast Kinetics During Plant Cytokinesis -- 1 Introduction -- 2 Materials -- 2.1 Plant Material -- 2.2 Plant Growth -- 2.3 Sample Preparation -- 2.4 Fluorescent Dyes -- 2.5 Microscope -- 2.6 Software -- 3 Methods -- 3.1 Plant Material and Growth Conditions -- 3.2 Sample Preparation -- 3.3 Microscopy and Live Cell Imaging Adjustments -- 3.4 Preparing Files for Analysis -- 3.5 Kymograph Analysis and Quantification of Expansion Rate -- 3.6 Potential Approaches and Considerations -- 3.7 Conclusions -- 4 Notes -- References -- Chapter 13: Immunofluorescence Analysis of Membrane-Associated Proteins for Clathrin-Mediated Endocytosis in Plant Root Cells -- 1 Introduction -- 2 Materials -- 2.1 Reagent Preparation -- 2.2 Antibody Solution Preparation -- 3 Methods -- 3.1 Tissue Fixation -- 3.2 Tissue Permeation -- 3.3 Blocking -- 3.4 Primary Antibody Incubation -- 3.5 Secondary Antibody Incubation -- 4 Notes -- References -- Chapter 14: In Vivo Interaction Studies by Measuring Förster Resonance Energy Transfer Through Fluorescence Lifetime Imaging M... -- 1 Introduction -- 2 Material -- 2.1 Plant Material -- 2.2 Equipment -- 3 Methods -- 3.1 Experimental Strategy -- 3.2 Recording of an Instrumental Response Function -- 3.3 Data Acquisition -- 3.4 Analysis -- 4 Notes -- References -- Chapter 15: Analysis of Nanobody-Epitope Interactions in Living Cells via Quantitative Protein Transport Assays -- 1 Introduction -- 2 Materials -- 3 Methods.. - 3.3 Ratiometric Analysis of Secretion in Arabidopsis Roots-Measuring Internal secYFP Signal in Root Epidermal Cells.. - Chapter 7: Analysis of Membrane Protein Topology in the Plant Secretory Pathway -- 1 Introduction -- 2 Materials -- 2.1 Tobacco BY-2 Cells -- 2.2 Protoplasts Transient Expression -- 2.3 Microsomes Trypsin Digestion -- 3 Methods -- 3.1 Transient Expression in Tobacco BY-2 Cells -- 3.2 Microsomes Preparation and Trypsin Digestion -- 4 Notes -- References -- Chapter 8: Semiautomatic Segmentation of Plant Golgi Stacks in Electron Tomograms Using 3dmod -- 1 Introduction -- 2 Materials -- 2.1 3D Modeling -- 3 Methods -- 3.1 Manually Drawing 3D Model Using 3dmod -- 3.2 Automatic Contouring -- 3.3 Image Stacking with Slicer View -- 4 Notes -- References -- Chapter 9: 3D Printing of Plant Golgi Stacks from Their Electron Tomographic Models -- 1 Introduction -- 2 Materials -- 2.1 3D Printing -- 3 Methods -- 3.1 Preparing the Model in 3dmod -- 3.2 Converting the File -- 3.3 Making the 3D Print -- 3.4 Postprocessing the 3D Print -- 4 Notes -- References -- Chapter 10: Transient Expression of Chimeric Fluorescent Reporter Proteins in Pollen Tubes to Study Protein Polar Secretion an... -- 1 Introduction -- 2 Materials -- 2.1 Plant Materials and Growth Conditions -- 2.2 In Vitro Pollen Tube Germination -- 2.3 Pollen Grain Harvest and Preparation -- 2.4 Particle Bombardment -- 2.5 Confocal Microscopy Imaging -- 3 Methods -- 3.1 Pollen Harvesting and Preparation for Bombardment -- 3.2 Plasmid Preparation and Gold Particle Coating -- 3.3 DNA Expression in Pollens via Particle Bombardment -- 3.4 In Vitro Pollen Tube Germination -- 3.5 Confocal Microscopy Imaging -- 4 Notes -- References -- Chapter 11: Analysis of Actin-Based Intracellular Trafficking in Pollen Tubes -- 1 Introduction -- 2 Materials -- 2.1 Plant Materials -- 2.2 Actin-Based Drugs -- 2.3 Glass Bottom Dish with Cover -- 2.4 Pollen Germination Medium (PGM) -- 3 Methods -- 3.1 Growth of Arabidopsis Plants.. - This volume aims to provide an update on recent developments in protein secretion studies in plants versus yeast and mammalian systems. This book also discusses case studies that analyze the use of plant protein secretion using various tools and systems. The chapters in this book explore topics such as the study of Golgi-mediated protein traffic in plant cells; actin-based intracellular trafficking in pollen tubes; secretion system for identification of cargo proteins of vacuolar sorting receptors; isolation of the plant exocyst complex; and plant autophagy. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and authoritative, Plant Protein Secretion: Methods and Protocols is a valuable resource for researchers interested in furthering their studies in plant protein secretion.".
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| Emner | |
| Sjanger | |
| Dewey | |
| ISBN | 1-4939-7262-6
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