Functional Glycomics

1st Edition, Volume 417 - November 21, 2006
Editor: Minoru Fukuda
Language: English
Hardback ISBN:
9 7 8 - 0 - 1 2 - 1 8 2 8 2 2 - 6
eBook ISBN:
9 7 8 - 0 - 0 8 - 0 4 6 9 0 0 - 3

In the past decade, there has been an explosion of progress in understanding the roles of carbohydrates in biological systems. This explosive progress was made with the efforts in… Read more

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In the past decade, there has been an explosion of progress in understanding the roles of carbohydrates in biological systems. This explosive progress was made with the efforts in determining the roles of carbohydrates in immunology, neurobiology and many other disciplines, examining each unique system and employing new technology. This volume represents the second of three in the Methods in Enzymology series, including Glycobiology (vol. 415) and Glycomics (vol. 416), dedicated to disseminating information on methods in determining the biological roles of carbohydrates. These books are designed to provide an introduction of new methods to a large variety of readers who would like to participate in and contribute to the advancement of glycobiology. The methods covered include structural analysis of carbohydrates, biological and chemical synthesis of carbohydrates, expression and determination of ligands for carbohydrate-binding proteins, gene expression profiling including micro array, and generation of gene knockout mice and their phenotype analyses.

Contributors to Volume 417
- Publisher Summary
Preface
- Publisher Summary
Contents of Previous Volumes
Section I. N-Glycan Function Revealed by Gene Inactivation
- Cytokine Sensitivity and N-Glycan Processing Mutations
  - Abstract
  - Introduction
  - Materials
  - Methods
  - Notes
  - Acknowledgments
- Phenotype Changes of Fut8 Knockout Mouse: Core Fucosylation Is Crucial for the Function of Growth Factor Receptor(s)
  - Abstract
  - Overview
  - Materials and Methods
Section II. Neural Cell Function
- Cellular and Molecular Analysis of Neural Development of Glycosyltransferase Gene Knockout Mice
  - Abstract
  - Overview
  - Acknowledgment
- Roles of Glycolipids in the Development and Maintenance of Nervous Tissues
  - Abstract
  - Overview
  - Genetic Approaches
  - Fundamental Behavior Analysis
  - Surgical Approaches for Repair Potential
  - Morphological Approaches
- Analysis of Neural Cell Functions in Gene Knockout Mice: Electrophysiological Investigation of Synaptic Plasticity in Acute Hippocampal Slices
  - Abstract
  - Overview
  - Acknowledgments
- Analysis of Neural Cell Function in Gene Knockout Mice: Behavior
  - Abstract
  - Introduction
  - Materials
  - Methods
  - Acknowledgments
- Electrophysiological Analysis of Interactions Between Carbohydrates and Transmitter Receptors Reconstituted in Lipid Bilayers
  - Abstract
  - Overview
  - Acknowledgment
Section III. Notch Signaling and Muscular Dystrophy
- Methods for Analysis of O-Linked Modifications on Epidermal Growth Factor-Like and Thrombospondin Type 1 Repeats
  - Abstract
  - Overview
  - Analysis of O-Fucose and O-Glucose Glycan Structure by Metabolic Radiolabeling Coupled with Alkali-Induced β-Elimination
  - Glycosylation Site Mapping by Mass Spectrometry
  - Acknowledgments
- Roles of O-Fucosyltransferase 1 and O-Linked Fucose in Notch Receptor Function
  - Abstract
  - Overview
  - Enzyme Assay for O-Fucosyltransferase 1 Activity
  - Downregulation of Ofut1 by Use of RNAi Techniques
  - Quantification of the O-Fucose Level
  - Cell Surface Notch Staining
  - Notch Secretion Assay
  - Western Blotting for Notch
  - Notch-Ligand Binding Assay
  - Notch–OFUT1 Binding Assay
  - Acknowledgments
- Roles of O-Fucose Glycans in Notch Signaling Revealed by Mutant Mice
  - Abstract
  - Overview
  - Glycosylation of Notch Receptors and Notch Ligands
  - Pofut1 Is an Essential Component of the Canonical Notch Signaling Pathway
  - Fringe Is a Modulator of Notch Signaling
  - β4GalT-1 Is a Novel Regulator of Notch Signaling
  - Mutations in Other Glycosyltransferase Genes
  - Acknowledgments
- Defect in Glycosylation that Causes Muscular Dystrophy
  - Abstract
  - Overview
  - Purification of α-DG
  - Method for Glycoprotein Enrichment and Western Blot Analysis (Laminin Overlay Assay)
  - Method for Laminin Overlay Assay
  - Solid-Phase Binding Assay
  - Assay for POMT and POMGnT1 Activities
  - Preparation of Membrane Fraction for Enzyme Sources from Brain
  - Preparation of GST-α-DG
  - POMT Assay
  - Expression and Enzymatic Activity of POMT1 Mutants
  - POMGnT1 Assay
  - POMGnT1 Assay
  - Expression and Enzymatic Activity of POMGnT1 Mutants
Section IV. Glycolipid Function
- Identification and Analysis of Novel Glycolipids in Vertebrate Brains by HPLC/Mass Spectrometry
  - Abstract
  - Overview
  - Isolation of PtdGlc from Developing Brains
  - Extraction of Lipids
  - Purification of PtdGlc
  - Identification of PtdGlc by Normal-phase HPLC/Electrospray Ionization Ion-trap Mass Spectrometry
- Modulation of Growth Factor Signaling by Gangliosides: Positive Or Negative?
  - Abstract
  - Overview
  - Methods
  - Results and Conclusion
  - Acknowledgments
- Activation of Natural Killer T Cells by Glycolipids
  - Abstract
  - Overview
  - Vα14i NKT Cell Isolation
  - In Vitro Antigen Presentation Assay
  - In Vivo iNKT Cell Activation Assay
  - Biochemical Assays
Section V. Glycolipid Interaction
- Determination of Glycolipid–Protein Interaction Specificity
  - Abstract
  - Overview
  - Materials
  - Methods
  - Notes
- Analysis of Carbohydrate–Carbohydrate Interactions Using Gold Glyconanoparticles and Oligosaccharide Self-Assembling Monolayers
  - Abstract
  - Overview
  - Marine Sponges
  - Synthesis of Spacer-Containing Oligosaccharides
  - Synthesis of Thiol-Spacer–Containing Oligosaccharides
  - Synthesis of Gold Nanoparticles
  - Analysis of Gold Glyconanoparticles
  - Aggregation Experiments Using TEM
  - Atomic Force Microscopy
Section VI. Galectin Function
- Galectin Interactions with Extracellular Matrix and Effects on Cellular Function
  - Abstract
  - Overview
  - Chemicals and Reagents
  - Preparation of ECM
  - T Cell–ECM Adhesion Assays
  - Cell Migration through ECM
  - Assessing Cell Death on Matrigel
  - Conclusions
  - Acknowledgments
- Galectins in Apoptosis
  - Abstract
  - Overview
  - Regulation of Apoptosis by Extracellular Galectins
  - Regulation of Apoptosis Demonstrated by Use of the Gene Transfection Approach
  - Preparation of Recombinant Galectin-3
  - Overexpression of Galectin-3 in Eukaryotic Cells
  - Acknowledgments
- On the Role of Galectins in Signal Transduction
  - Abstract
  - Overview
  - The Role of Extracellular Galectins in Signal Transduction
  - The Role of Intracellular Galectins in Signal Transduction
  - Construction of Expression Vectors
  - Binding Assays for Extracellular Galectins
  - Analyses of Phosphorylated Proteins
  - Kinase Assays
Section VII. Newly Developed Field
- Helicobacter pylori Adhesion to Carbohydrates
  - Abstract
  - Overview
  - Characterization of Bacterial Adherence by In Vitro Binding to Host Tissue
  - Glycoprotein Array for Screening and Identification of Adhesin Binding Properties
  - Analyses of Binding Capacity Based on of RIA and Scatchard Affinity Assays a Nonradioactive Alternative Based on Fluorescent Glycoconjugates
  - A Nonradioactive Alternative to Test for H. pylori Binding Properties in Solution: Fluorochrome-labeled Glycoconjugates
  - H. Pylori Binding Assay Using Fluorescent Glycoconjugates
  - Affinity Analysis by RIA According to Scatchard
  - ELISA Analysis of H. pylori Binding to Immobilized Lewis b Glycoconjugate
  - Receptor Activity–directed Affinity Tagging (Retagging) Technique for Adhesin Protein Identification
  - Phylogenetic Methods for Detecting Adaptive Change
  - Knock-out of Adhesin Gene: General Strategy for Genetic Constructions by PCR without Recombinant DNA Cloning
  - Identification of Bacterial Clones with Rare and/or Induced Receptor Binding Properties by Use of Glycoprobes
  - Characterization of Spatial Expression of H. pylori Virulence Products in Gastric Mucosa by In Situ Hybridization
  - Application of Laser Tweezers Technique for Analyzes of Binding Strength
  - Analyses of Nonopsonic Bacterial–Cell Interactions by Chemiluminescence Measurements of Released Oxidative Burst Metabolites
  - Acknowledgments
- Caenorhabditis elegans Carbohydrates in Bacterial Toxin Resistance
  - Abstract
  - Overview
  - Procedure for EMS Mutagenesis
  - Isolation of Glycosphingolipids from C. elegans by Svennerholm Partitioning
  - Analysis of Glycolipids by Thin Layer Chromatography
  - Isolation of Specific Glycosphingolipid Components
- N-Glycans Are Involved in the Response of Caenorhabditis elegans to Bacterial Pathogens
  - Abstract
  - Overview
  - The Biology of Caenorhabditis elegans
  - The Structure and Biosynthesis of GlcNAcβ1-N-Asn Glycans (N-Glycans) in C. elegans
  - The Function of N-Glycans in C. elegans
  - Experimental
  - Results
  - Effects of Pseudomonas aeruginosa Strain 14 on PGS Medium on the Survival of C. elegans
  - Production of gly-13 and gly-14 Phenotypes by RNA-mediated Interference (RNAi)
  - Rescue of the Mutant gly-13 Phenotype by a Wild-type gly-13 Extrachromosomal Array
  - Discussion
  - Acknowledgments
- Detection of Cytoplasmic Glycosylation Associated with Hydroxyproline
  - Abstract
  - Overview
  - In Vivo Detection of HyPro-dependent Glycosylation by M_r-Shift Analysis
  - Detection of Cytoplasmic Glycosyltransferases
Author Index
- Publisher Summary
Subject Index
- Publisher Summary

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Functional Glycomics

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