Handbook of Glycomics

Copyright Page
......Page 2
List of Contributors......Page 3
Preface......Page 6
Acknowledgments......Page 9
Glycoconjugate Structural Analysis......Page 10
Introduction......Page 11
Chemical Release......Page 12
Enzymatic Release......Page 13
Solid-Phase Extraction......Page 14
Other Purification Protocols......Page 15
Capillary Electrophoresis-Based Approaches......Page 17
Capillary Electrochromatography-Based Approaches......Page 24
Liquid Chromatography-Based Approaches......Page 28
Mass Spectrometry of Native N-Glycans......Page 30
Mass Spectrometry of Derivatized N-Glycans......Page 33
Mass Spectrometry of N-Glycans Derivatized with Stable Isotopes......Page 36
Tandem Mass Spectrometry......Page 39
Conclusions......Page 45
References......Page 46
Introduction......Page 52
O-Mannose Initiated......Page 53
O-Fucose Initiated......Page 54
O-Galactose Initiated......Page 55
Release......Page 56
Mass Spectrometry of Derivatized O-Glycans......Page 57
Quantitative Mass Spectrometry Approaches......Page 58
Conclusions......Page 60
References......Page 61
Introduction......Page 65
Isolation of GAGs......Page 67
Purification of Individual GAGs......Page 69
Molecular Weight Analysis of GAGs......Page 70
Disaccharide Analysis......Page 71
Oligosaccharide Mapping and Analysis......Page 74
Sequence Analysis......Page 75
Conformational Analysis......Page 78
Conclusion......Page 79
References......Page 80
Glycotranscriptomics......Page 87
Introduction......Page 88
Overall Strategy of Isotope Labeling of Glycans for Quantitative Glycomics......Page 89
Isotope-Coded Reagents for Glycan Analyses and Analytical Approaches......Page 91
Acknowledgments......Page 96
References......Page 97
Introduction......Page 99
Overview of Glycan Biosynthesis in Animal Systems......Page 101
Identification of Genes Involved in Glycan Biosynthesis......Page 108
Overview of Transcript Analysis and Gene Expression Methods......Page 112
Analysis of Gene Expression Data......Page 121
Examples of Correlation of Transcript Analysis Data with Protein and Structural Data......Page 122
Acknowledgments......Page 124
References......Page 125
Protein–Glycan Interactions......Page 140
Introduction......Page 141
Construction of Glycan Microarrays......Page 142
Overall Strategy of Glycan Arrays: the Big Picture......Page 147
Methods for Detecting Binding of GBPs to Glycan Arrays......Page 148
Collection and Presentation of Data from a Large Glycan Microarray......Page 152
Use of Glycan Arrays to Investigate Specificity of Glycan-Binding Proteins......Page 153
Virus Binding to Glycan Arrays......Page 156
Limitations of Glycan Arrays......Page 158
References......Page 159
Basic Approaches to Structural Glycomics......Page 163
The use of Lectins in Structural Glycomics......Page 166
Methods for Interaction Analysis of Lectins and Glycans: A Basis of Lectin Study......Page 167
Frontal Affinity Chromatography......Page 168
Lectin Microarray......Page 172
References......Page 174
Glycobioinformatics......Page 179
The Structural Complexity of Glycans......Page 180
The Complexity of Glycan Biosynthesis......Page 181
The Explosion of Glycomics Data......Page 182
Formal Specification of an Ontology......Page 183
The GlycO Ontology......Page 184
The ReactO Ontology......Page 188
Structural Data Exchange Protocols......Page 189
Workflows for Processing Glycomics Data......Page 190
Web Services......Page 191
GlycoBrowser......Page 192
Qrator......Page 194
Conclusions......Page 195
References......Page 196
Introduction......Page 197
Metabolic Pathway Maps......Page 198
Glycan Structure Maps......Page 199
Genes Related to Glycan Biosynthesis......Page 200
Orthologous Information for the Pathway and the Structure Maps......Page 201
Tools for Structure Search and Drawing Glycans......Page 203
From Genomic Information to Chemical Information......Page 204
Predicting Glycan Structures from Gene Expression Data......Page 205
Capturing Complex Patterns in Glycans using Data Mining Techniques......Page 206
Concluding Remarks......Page 208
References......Page 209
Introduction......Page 211
Complex Carbohydrate Structure Database (CCSD, CarbBank)......Page 213
CFG Glycan Database......Page 215
Other Carbohydrate-Related Databases and Resources......Page 216
EUROCarbDB—Development of an Infrastructure for Storage of Carbohydrate Structure and Analytical Data......Page 217
GlycomeDB—Integration of Carbohydrate Structure Databases......Page 219
Case Study 1—A Search for Species-Specific Carbohydrates......Page 222
Case Study 2—Searching for Carbohydrate 3D Structures and Their Protein Interactions......Page 224
Conclusion and Outlook......Page 227
References......Page 230
Glycomes......Page 234
Glycosylation in the Immune System......Page 235
Mammalian Lectins of the Immune System......Page 236
Current Approaches in the Study of Immune Cell Glycomes......Page 237
Neutrophils......Page 240
Eosinophils......Page 242
Macrophages......Page 243
Dendritic Cells......Page 244
T Lymphocytes......Page 246
T Lymphocyte Development in the Thymus......Page 247
T Lymphocyte Activation: the Expansion and Contraction Phases of the Adaptive Immune Response......Page 250
B Lymphocytes......Page 254
References......Page 255
The Consortium for Functional Glycomics......Page 260
Interpretation of Glycomic Data......Page 261
Mouse Brain......Page 263
Key Features......Page 265
Mouse Colon......Page 266
Key Features......Page 270
Key Features......Page 273
Mouse Liver......Page 274
Mouse Lung......Page 276
Key Features......Page 277
Key Features......Page 278
Mouse Small Intestine......Page 279
Key Features......Page 280
Key Features......Page 282
Key Features......Page 284
Mouse Thymus......Page 285
Key Features......Page 286
Summary of the Mouse Glycome......Page 287
Key Features......Page 288
Human Colon......Page 291
Human Heart......Page 297
Key Features......Page 298
Key Features......Page 299
Key Features......Page 301
Key Features......Page 304
Human Lung......Page 305
Key Features......Page 306
Key Features......Page 308
Human Small Bowel......Page 310
Key Features......Page 312
Key Features......Page 313
Glycome Comparisons......Page 315
Human vs. Mouse Variation......Page 316
Differences Among Tissue Glycomes......Page 317
Variation in Single Tissues of Single Species......Page 318
Data Repositories......Page 319
Current Limitations and the Future......Page 320
References......Page 321
Introduction, Overview, and Scope......Page 325
N-Linked Glycoprotein Glycans......Page 326
O-Linked Glycoprotein Glycans......Page 330
Glycosphingolipid Glycans......Page 332
Summary and Perspective......Page 335
References......Page 336
Introduction......Page 342
Life Cycle......Page 343
The Sporozoite (first recognition event)......Page 344
Erythrocyte Invasion (Second Recognition Event)......Page 347
Development in the Vector—Third and Fourth Recognition Events......Page 348
Disease Pathology (Fifth Recognition Event)......Page 349
Malaria in Pregnancy (Sixth Recognition Event)......Page 350
Experimental Conditions and Assays......Page 351
Conclusion......Page 352
Overall Summary......Page 353
References......Page 354
Introduction......Page 362
Glycan Structures in Helminths......Page 363
Cestodes......Page 365
Schistosomes......Page 368
Fasciola hepatica......Page 370
Glycan Antigens in Nematodes......Page 371
Parasite Glycans are Key Players in Helminth-Induced Immune Regulation......Page 375
Secretion of Lectins by Parasitic Helminths......Page 378
Anti-Glycan Humoral Responses......Page 379
Conclusions and Future Prospects......Page 380
References......Page 381
Disease Glycomes......Page 392
Introduction......Page 393
Analysis of Glycans on Specific Glycoproteins......Page 397
Comparative Glycoproteomics of Serum to Identify Potential Tumor Markers......Page 398
Glycans Released from Serum Glycoproteins......Page 401
Use of Targeted Glycoproteomics to Identify Changes in Glycoprotein Expression in Cancer Serum......Page 404
Comparison of O-Linked Glycans in Cancer Serum and on Cancer Cells......Page 406
Comparative Glycoproteomic Analysis of Cancer Cells and Tissues......Page 408
Antibody Arrays to Detect Glycan Variation on Glycoprotein Markers......Page 411
Conclusion......Page 412
References......Page 414
Brief History and Nomenclature......Page 424
Glycobiologists, Clinicians, and Geneticists Collaborate in Patient Diagnosis......Page 427
N-Glycan Defects......Page 428
Animal Models of N-Glycosylation Disorders......Page 431
Congenital Muscular Dystrophies......Page 434
Defects in Glycosphingolipid and Glycosylphosphaditylinositol Biosynthesis......Page 438
Defects in O-Fucose-Linked Glycans......Page 439
Defects in Glycosaminoglycan Synthesis......Page 440
Opportunities......Page 442
Possible Therapies for CDG-Ia?......Page 443
Some Unanswered Questions......Page 444
Conclusions......Page 445
References......Page 446
C......Page 458
D......Page 459
G......Page 460
H......Page 462
L......Page 463
M......Page 464
S......Page 465
Z......Page 466