Glycolipids: Methods and Protocols

Preface
Contents
Contributors
Chapter 1: Immunomodulatory Functions of α-GalCer and a Derivative, α-Carba-GalCer
	1 Introduction
	2 Materials
		2.1 Mice
		2.2 Cell Culture
		2.3 Glycolipid Antigen
		2.4 Flow Cytometric Analysis
		2.5 Immunization
	3 Methods
		3.1 Activation of NKT Cells with α-GalCer-Coated Plates
		3.2 NKT Cell Activation with α-GalCer-Loaded APCs
		3.3 Detection of NKT Cells with α-GalCer/CD1d Tetramer Using Flow Cytometry
		3.4 Detection of Cytokine-Producing NKT Cells Using Flow Cytometry
		3.5 In Vivo NKT Cell Activation
		3.6 NKT Cell Activation Using a Th1-Skewing α-GalCer Derivative, α-Carba-GalCer, in an In Vivo Experimental Autoimmune Uveoret...
	4 Notes
	References
Chapter 2: Chemical Synthesis and Molecular Interaction Analysis of α-Galactosyl Ceramide Derivatives as CD1d Ligands
	1 Introduction
		1.1 Chemical Synthesis
		1.2 Binding Assay of CD1d and the Ligand
	2 Materials
	3 Methods
	4 Notes
	References
Chapter 3: Immunomodulatory Functions of Glycolipids from Pathogens
	1 Introduction
	2 Materials
		2.1 Extracting Glycolipids from Microorganisms/Delipidating
		2.2 Reporter Cell Assay
		2.3 Generation and Measuring Activation of BMDCs
		2.4 In Vitro Adjuvant Activity Using T Cells and BMDC Co-cultures
	3 Methods
		3.1 Extracting Glycolipids from Microorganisms/Delipidating
		3.2 Reporter Cell Assay
		3.3 Generation and Measuring Activation of BMDCs
		3.4 In Vitro Adjuvant Activity Using T Cells
	4 Notes
	References
Chapter 4: Chemical Synthesis and Immunomodulatory Functions of Bacterial Lipid As
	1 Introduction
		1.1 Immune Stimulation Induced by Bacterial Components
		1.2 Bacterial Lipid A: An Innate Immune Stimulant
		1.3 Molecular Basis of TLR4-Mediated Immune Activation
	2 Materials
		2.1 Structure-Activity Relationship of Lipid A with a Focus on Phosphate and Acyl Groups
		2.2 Development of MPLs as Adjuvants
		2.3 Structure-Activity Relationship of Lipid A with a Focus on Kdo
		2.4 Lipid A Adjuvant Development Based on Bacterial-Host Chemical Ecology
		2.5 Generals in Chemical Synthesis
		2.6 Generals in Immunological Assays
	3 Methods
		3.1 Chemical Synthesis
		3.2 Immunological Assay
	4 Notes
	References
Chapter 5: Innovative Vaccine Strategy: Self-Adjuvanting Conjugate Vaccines
	1 Introduction
	2 Vaccine Adjuvants
	3 Self-Adjuvanting Conjugate Vaccines
		3.1 TLR2 Ligand-Conjugated Vaccines
		3.2 TLR4 Ligand-Conjugated Vaccines
		3.3 CD1d Ligand-Conjugated Vaccines
		3.4 Vaccines Conjugated with Other Adjuvants
	4 Conclusion
	5 Notes
	References
Chapter 6: Chemical Synthesis of Phosphatidylglucoside
	1 Introduction
	2 Materials
		2.1 Equipment
		2.2 Reagents and Solutions
	3 Methods
	4 Notes
	References
Chapter 7: Sialidase-Resistant Ganglioside GM3 Analogues: Evaluation of Biological Activity
	1 Introduction
	2 Materials
		2.1 Cell Culture
		2.2 EGFR Autophosphorylation Analysis
	3 Methods
		3.1 Inhibitory Effect of GM3 and Its Analogues on EGF-Induced EGFR Autophosphorylation
		3.2 Promoting Effect of GM3 and Its Analogues on Had-1 Cell Proliferation
	4 Notes
	References
Chapter 8: Chemical Synthesis of Gangliosides
	1 Introduction
	2 Synthetic Strategies for Gangliosides
		2.1 Late-Stage Ceramide Coupling Strategy
		2.2 GlcCer Cassette Strategy
		2.3 Late-Stage Sialylation Strategy
	3 Conclusion
	References
Chapter 9: Sialyltransferase Activity Assay for Ganglioside GM3 Synthase
	1 Introduction
	2 Materials
		2.1 Reagents and Materials for Preparation of Enzyme Source
		2.2 GM3S Enzyme Reaction
		2.3 Separation of Enzymatic Products by HPLC
	3 Methods
		3.1 Preparation of Microsomal Membrane Proteins
			3.1.1 Preparation of HEK/GM3S KO Cells Transfected with GM3S Vector (HEK/GM3S KO + GM3S) (See Note 1)
			3.1.2 Preparation of Microsomal Membranes from Cells or Mouse Brain Tissue
		3.2 GM3S Enzyme Reaction
		3.3 Separation of Enzymatic Products by HPLC
	4 Notes
	References
Chapter 10: Construction of Sphingolipid Remodeled Cells by Genome Editing
	1 Introduction
	2 Materials
		2.1 Plasmid Construction and Mutation Analysis
		2.2 Cell Culture and Transfection
		2.3 Metabolic Labeling of Sphingolipids
	3 Methods
		3.1 Construction of sgRNA- and Cas9-Expression Plasmid
			3.1.1 Digestion of Plasmid and Formation of the Double-Stranded Oligos for sgRNA
			3.1.2 Ligation, Transformation, and Purification of the Plasmids
		3.2 Construction of KO Cells
			3.2.1 Transfection
			3.2.2 Genomic Mutation Check
		3.3 Metabolic Labeling of Sphingolipids
			3.3.1 Pulse Labeling with Radioactive Serine or Galactose
			3.3.2 Lipid Purification Using the Bligh and Dyer Method
			3.3.3 TLC Analysis
	4 Notes
	References
Chapter 11: Mass Spectrometry of Neutral Glycosphingolipids
	1 Introduction
	2 Materials
		2.1 TLC-MALDI/MS
		2.2 LC-ESI/MS with Reversed Phase Chromatography
		2.3 LC-MS with MRM Analysis
	3 Methods
		3.1 Structural Characterization
			3.1.1 TLC-MALDI/MS
			3.1.2 LC-ESI/MS with Reversed Phase Chromatography
		3.2 Determination of Neutral GSL Contents by LC-ESI/MS with MRM
	4 Notes
	References
Chapter 12: Structural Analyses of the Glycolipids in Lipid Rafts
	1 Introduction
	2 Materials
	3 Methods
		3.1 Cell Culture of Murine 3T3-L1 Preadipocytes
		3.2 Lipid Raft Fractionation (Sucrose Gradient Centrifugation) of Cultured 3T3-L1 Preadipocytes
		3.3 Detergent Removal Using 1,2-dichloroethane and Confirmation of the Removal/Recovery Ratio for the Detergents/Glycolipids
		3.4 Applications of 1,2-DCE Washing for Glycolipid Analysis
	4 Notes
	References
Chapter 13: Extraction, Purification, and Chemical Degradation of LPS from Gut Microbiota Strains
	1 Introduction
	2 Materials
		2.1 Preliminary Manipulations and Check
			2.1.1 Cell Wash Solvents and Components
		2.2 Ultracentrifugation
		2.3 Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) on Cells
			2.3.1 Gel Preparation
			2.3.2 Sample Preparation and Set-Up Electrophoretic System
			2.3.3 Gel Staining with Silver Nitrate
		2.4 Extraction Methods
			2.4.1 PCP Extraction Reagents and Components
			2.4.2 Hot Phenol/Water Extraction Reagents and Components
		2.5 Purification and Qualitative Analyses
			2.5.1 Enzymatic Digestion Reagents and Components
			2.5.2 Low-Pressure Chromatography: Size-Exclusion Chromatography (SEC)
		2.6 SDS-PAGE on  LPS
			2.6.1 Sample Preparation Proteinase K Solution (5 mg/mL)
			2.6.2 Gel Staining
			2.6.3 Gel Staining-Alcian  Blue
			2.6.4 Gel Staining-Coomassie Blue Staining
		2.7 Chemical Degradations
			2.7.1 Acid Hydrolysis of LPS: Reagents and Components
			2.7.2 Deacylation of LPS: Reagents and Components
				O-Deacylation
				N-Deacylation
	3 Methods
		3.1 Preliminary Manipulations and Check
			3.1.1 Cell  Wash
			3.1.2 Ultracentrifugation of Cells
			3.1.3 SDS-PAGE of Digested Cells
				Preparation of the  Gel
				Preparation of the Samples (See Fig. 2)
				Silver Nitrate Staining of the Gel
		3.2 Extraction of the R-LPS and S-LPS (See Note 12)
			3.2.1 PCP Extraction (See Note 13)
			3.2.2 Hot Water/Phenol Extraction (See Note 18)
		3.3 Purification and Qualitative Analyses
			3.3.1 Enzymatic Digestion of the  LPS
			3.3.2 Ultracentrifugation of the LPS (See Note 24)
			3.3.3 Low-Pressure Chromatography: Size-Exclusion Chromatography (SEC) (See Note 26)
			3.3.4 SDS-PAGE of  LPS
				Preparation of the Sample
				Staining of the Gel-Alcian Blue
				Staining of the Gel-Coomassie Brilliant Blue (See Note 29)
		3.4 Chemical Treatments
			3.4.1 Acid Hydrolysis
			3.4.2 Deacylation Treatment
				O-Deacylation
				N-Deacylation (See Note 33)
	4 Notes
	References
Chapter 14: NMR Analysis of Mammalian Glycolipids
	1 Introduction
	2 Materials
	3 Methods
		3.1 Sample Preparation
		3.2 One-Dimensional 1H-NMR
		3.3 Two-Dimensional NMR to Identify Intraresidue Connectivity
		3.4 Two-Dimensional NMR to Identify Interresidue Connectivity
	4 Notes
	References
Chapter 15: Distribution of Glycolipids in the Plasma Membrane Monitored by Specific Probes in Combination with Sodium Dodecyl...
	1 Introduction
	2 Materials
		2.1 Equipment
		2.2 Chemicals
		2.3 Consumables
	3 Methods
		3.1 Plasma Membrane Staining of PtdGLc with Specific Antibody in Suspension Cells, Followed by Transmission Electron Microscop...
		3.2 Plasma Membrane Staining of PtdGLc with Specific Antibody in Adherent Cells, Followed by TEM
		3.3 Double Labeling of PtdGlc and GM1 with Specific Antibody and Biotinylated Cholera Toxin B Subunit
		3.4 Cluster Analysis of Gold Distributions in the Electron Micrographs
	4 Notes
	References
Chapter 16: Biochemical and Microscopic Analyses for Sphingolipids and Its Related Molecules in Phagosomes
	1 Introduction
	2 Materials
		2.1 Disposables
		2.2 Equipment
		2.3 Reagents
		2.4 Antibodies
		2.5 Cell Culture
		2.6 Bacterial Culture
		2.7 Labeling of Mycobacteria with Alexa Fluor  Dye
	3 Methods
		3.1 Isolation of Phagosomes
		3.2 Lipid Extraction from Phagosomes
		3.3 Immunoprecipitation with Anti-LacCer IgM Huly M-13 from Phagosome Lysates
		3.4 Immunostaining of Phagocytosing Neutrophils with Anti-LacCer IgM T5A7 and Lysenin
		3.5 Observation of LacCer-Enriched Microdomains and SM on Phagosome Using  STED
		3.6 Concluding Remarks
	4 Notes
	References
Chapter 17: Single-Molecule Imaging of Ganglioside Probes in Living Cell Plasma Membranes
	1 Introduction
	2 Single-Molecule Imaging at High-Temporal Resolution
	3 Dual-Color Single-Molecule Observation of Ganglioside Probes and GPI-Anchored Proteins
	4 Examination of Transbilayer Lipid Coupling of Ganglioside Probes
	5 Summary
	References
Chapter 18: Assays and Utilization of Enzymes Involved in Glycolipid Metabolism in Bacteria and Fungi
	1 Introduction
	2 Hydrolysis of GSLs by Endoglycoceramidases (EGCases)
		2.1 Introduction
		2.2 Materials
		2.3 Methods
			2.3.1 Hydrolysis of GSLs in the Presence of Detergents
			2.3.2 Hydrolysis of GSLs Assisted with Activator Protein (In Vitro)
			2.3.3 Hydrolysis of Cellular GSLs Assisted with Activator Protein (In Vivo)
		2.4 Notes
	3 Assay of Glycosidases Capable of Hydrolyzing GlcCer and Steryl Glucosides
		3.1 Introduction
		3.2 Materials and Equipment
		3.3 Preparation of Reagents and Cell Lysates
		3.4 Methods
			3.4.1 Assay for GlcCer-Hydrolyzing Enzymes (EGCrP1 and EGCrP2)
			3.4.2 Assay of Steryl Glucoside-Hydrolyzing Enzyme (EGCrP2, Egh1, or Sgl1)
		3.5 Notes
	4 Preparation of Deacylated GSLs (Lyso-GSLs) by Sphingolipid Ceramide N-Deacylase (SCDase) in the Aqueous-Organic Biphasic Sys...
		4.1 Introduction
		4.2 Materials
		4.3 Methods
			4.3.1 Hydrolysis of GSLs by SCDase in the Aqueous-Organic Biphasic System (Microliter Scale)
			4.3.2 Hydrolysis of GSLs by SCDase in the Aqueous-Organic Biphasic System (Milliliter Scale)
		4.4 Notes
	5 Assay of Bacterial Glucuronosylceramide and Galactosylceramide Synthases
		5.1 Introduction
		5.2 Materials
		5.3 Methods
			5.3.1 Preparation of Fluorescent Ceramide Liposomes
			5.3.2 Assay of Bacterial Glycosphingolipid Synthases
		5.4 Notes
	References
Chapter 19: Molecular Dynamics of Glycolipids in Liposomes
	1 Introduction
		1.1 Fluorescence Intensity I(t) and Lifetimes
		1.2 Multicomponent Fitting of Time-Dependent Fluorescence Decays
	2 Materials
		2.1 Synthesis and Purification of  tPA
			2.1.1 Materials for tPA Synthesis
			2.1.2 Five-Step Synthesis of tPA Probe from Linolenic Acid for Fluorescence Lifetime Experiment
		2.2 Vesicle Preparation
			2.2.1 Reagents and Supplies for Vesicle Preparation
			2.2.2 Equipment for Vesicle Preparation
	3 Methods
		3.1 Preparation of Multilamellar Vesicles (MLVs)
		3.2 Instrument and Measurement Conditions for Time-Resolved Fluorescence
		3.3 Results
			3.3.1 Interpretation of the Result of tPA Lifetime in the Case to Examine the LacCer Gel Domain
			3.3.2 tPA-LacCer Lifetime to Probe LacCer Gel Domain
	4 Notes
	References
Chapter 20: Inhibitors of Glucosylceramide Synthase
	1 Introduction
	2 Cell-Free Glucosylceramide Synthase Activity Assay
		2.1 Background and Assay Principles
		2.2 Materials
		2.3 Reagents
		2.4 Methods
			2.4.1 Preparation of the Membrane Fraction of MDCK Cells
			2.4.2 Liposome Preparation
			2.4.3 GCS Assay in the Presence of or Absence of Specific Enzyme Inhibitors
		2.5 Notes
	3 MDCK Cell Assay for Reduction in Glucosylceramide
		3.1 Materials
		3.2 Reagents
			3.2.1 Solutions for Whole Cellular Lipid Extraction
			3.2.2 Solutions for Quantitation of Total Lipid Phosphate
			3.2.3 Solutions for Neutral Glycosphingolipid Extraction
			3.2.4 Solutions for TLC Glucosylceramide Analysis by High-Performance Thin-Layer Chromatography
		3.3 Methods
			3.3.1 Extraction of Cellular Lipids from Whole Cells
			3.3.2 Colorimetric Determination of Inorganic Phosphate (Pi) in Lipid Extracts
			3.3.3 Extraction of Neutral Glycosphingolipids from Lipid Extracts
			3.3.4 Thin-Layer Chromatography (TLC) Separation of Glycosphingolipids
		3.4 Notes
	References
Chapter 21: Comprehensive Glycan Analysis of Sphingolipids in Human Serum/Plasma
	1 Introduction
	2 Materials
		2.1 Glucose Oxidation
		2.2 Ethanol Precipitation
		2.3 GSL-Glycan Preparation
		2.4 Purification of GSL-Glycans by Glycoblotting
		2.5 aoWR-Labeled Glycan Purification
		2.6 In-Solution Sialyl Linkage-Specific Amide Derivatization of Esterified Glycans
		2.7 MALDI-TOF MS Analysis
	3 Methods
		3.1 Glucose Oxidation
		3.2 Ethanol Precipitation
		3.3 GSL-Glycan Preparation
		3.4 Glycoblotting for Aminolysis-SALSA
		3.5 aoWR-Labeled Glycan Purification
		3.6 Glycoblotting for LEAD-SALSA
		3.7 Sialyl Linkage- and Structure-Specific Amide Derivatization
		3.8 MALDI-TOF MS Analysis
	4 Notes
	References
Index