Cummings / Pierce Handbook of Glycomics

1. Auflage 2009
ISBN: 978-0-08-092005-4
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, 512 Seiten

This handbook provides the first comprehensive overview of the emerging field of glycomics, defined as the study of all complex carbohydrates in an organism or cell ('the glycome'). Beginning with analytic approaches and bioinformatics, this work provides a detailed discussion of relevant databases, data integration, and analysis. It then moves on to a discussion of specific model organism and pathogen glycomes followed by therapeutic approaches to human disorders of glycosylization. Structure and function of glycomes are included along with state-of-the-art technologies and systems approaches to the analysis of glycans.
* Synthesizes contributions from experts in biology, chemistry, bioinformatics, biotechnology, and medicine
* Highlights chapters devoted to chemical synthesis, cancer glycomics and immune cell glycomics
* Includes discussions of proteomics, mass spectrometry, NMR, array technology, and transcriptomics analytic approaches

Autoren/Hrsg.

Cummings, Richard D.

Pierce, J. Michael

Inhaltsverzeichnis

1;Front Cover;1
2;Handbook of Glycomics;4
3;Copyright Page;5
4;Contents;6
5;List of Contributors;8
6;Preface;12
7;Acknowledgments;16
8;Section I: Glycoconjugate Structural Analysis;18
8.1;Chapter 1. High-Sensitivity Analytical Approaches to the Analysis of N-Glycans;20
8.1.1;Introduction;20
8.1.2;Release of N-Glycans from Glycoproteins;21
8.1.3;Purification of N-Glycans;23
8.1.4;Analysis of Glycan Mixtures;26
8.1.5;Conclusions;54
8.1.6;References;55
8.2;Chapter 2. O-Glycan Complexity and Analysis;62
8.2.1;Introduction;62
8.2.2;O-Glycan Complexity;63
8.2.3;Analysis of Released O-Glycans;66
8.2.4;Analysis of O-Glycopeptides;70
8.2.5;Conclusions;70
8.2.6;References;71
8.3;Chapter 3. Glycosaminoglycans;76
8.3.1;Introduction;76
8.3.2;Isolation of GAGs;78
8.3.3;Purification of Individual GAGs;80
8.3.4;Structure Analysis;81
8.3.5;Conclusion;90
8.3.6;References;91
9;Section II: Glycotranscriptomics;98
9.1;Chapter 4. Isotopic Labeling of Glycans for Quantitative Glycomics;100
9.1.1;Introduction;100
9.1.2;Overall Strategy of Isotope Labeling of Glycans for Quantitative Glycomics;101
9.1.3;Isotope-Coded Reagents for Glycan Analyses and Analytical Approaches;103
9.1.4;Concluding Remarks;108
9.1.5;References;109
9.2;Chapter 5. Glycotranscriptomics;112
9.2.1;Introduction;112
9.2.2;Overview of Glycan Biosynthesis in Animal Systems;114
9.2.3;Identification of Genes Involved in Glycan Biosynthesis;121
9.2.4;Overview of Transcript Analysis and Gene Expression Methods;125
9.2.5;Analysis of Gene Expression Data;134
9.2.6;Examples of Correlation of Transcript Analysis Data with Protein and Structural Data;135
9.2.7;Future Directions;137
9.2.8;References;138
10;Section III: Protein–Glycan Interactions;154
10.1;Chapter 6. Glycan-Binding Proteins and Glycan Microarrays;156
10.1.1;Introduction;156
10.1.2;Construction of Glycan Microarrays;157
10.1.3;Overall Strategy of Glycan Arrays: the Big Picture;162
10.1.4;Methods for Detecting Binding of GBPs to Glycan Arrays;163
10.1.5;Collection and Presentation of Data from a Large Glycan Microarray;167
10.1.6;Use of Glycan Arrays to Investigate Specificity of Glycan-Binding Proteins;168
10.1.7;Virus Binding to Glycan Arrays;171
10.1.8;Limitations of Glycan Arrays;173
10.1.9;Concluding Remarks;174
10.1.10;References;174
10.2;Chapter 7. Chromatographic and Mass Spectrometric Techniques;178
10.2.1;Current Status of Understanding about Glycans;178
10.2.2;Basic Approaches to Structural Glycomics;178
10.2.3;The Use of Lectins in Structural Glycomics;181
10.2.4;Methods for Interaction Analysis of Lectins and Glycans: A Basis of Lectin Study;182
10.2.5;Concluding Remarks;189
10.2.6;References;189
11;Section IV: Glycobioinformatics;194
11.1;Chapter 8. Integration of Glycomics Knowledge and Data;196
11.1.1;Background and Motivation;196
11.1.2;Bioinformatic Approaches to Glycobiology;199
11.1.3;Conclusions;211
11.1.4;References;212
11.2;Chapter 9. KEGG GLYCAN for Integrated Analysis of Pathways, Genes, and Glycan Structures;214
11.2.1;Introduction;214
11.2.2;Glycan Biosynthesis and Metabolism;215
11.2.3;Genes Related to Glycan Biosynthesis;217
11.2.4;Glycan Structures;220
11.2.5;Bioinformatics Approach to Glycomics Research;221
11.2.6;Algorithms for Feature Extraction of Glycan Structures;223
11.2.7;Concluding Remarks;225
11.2.8;References;226
11.3;Chapter 10. Carbohydrate Structure Databases;228
11.3.1;Introduction;228
11.3.2;Current Established Carbohydrate Structure Databases;230
11.3.3;New Database Initiatives;234
11.3.4;Case Studies;239
11.3.5;Conclusion and Outlook;244
11.3.6;References;247
12;Section V: Glycomes;252
12.1;Chapter 11. Glycomics of the Immune System;254
12.1.1;Glycosylation in the Immune System;254
12.1.2;Mammalian Lectins of the Immune System;255
12.1.3;Current Approaches in the Study of Immune Cell Glycomes;256
12.1.4;Cellular Glycomes of the Innate Immune System;259
12.1.5;Cellular Glycomes of the Adaptive Immune System;265
12.1.6;Conclusions;274
12.1.7;References;274
12.2;Chapter 12. Mouse and Human Glycomes;280
12.2.1;Introduction;280
12.2.2;Mouse Glycomics;283
12.2.3;Human Glycomics;308
12.2.4;Glycome Comparisons;335
12.2.5;Data Repositories;339
12.2.6;Current Limitations and the Future;340
12.2.7;References;341
12.3;Chapter 13. Genetic and Structural Analysis of the Glycoprotein and Glycolipid Glycans of Drosophila melanogaster;346
12.3.1;Introduction, Overview, and Scope;346
12.3.2;N-Linked Glycoprotein Glycans;347
12.3.3;O-Linked Glycoprotein Glycans;351
12.3.4;Glycosphingolipid Glycans;353
12.3.5;Summary and Perspective;356
12.3.6;References;357
12.4;Chapter 14. Malaria;364
12.4.1;Introduction;364
12.4.2;Life Cycle;365
12.4.3;Glycobiology of P. falciparum;366
12.4.4;Experimental Results;366
12.4.5;Direct Glycosylation by the Parasite;373
12.4.6;Conclusion;374
12.4.7;Overall Summary;375
12.4.8;References;376
12.5;Chapter 15. Glycomics in Unraveling Glycan-Driven Immune Responses by Parasitic Helminths;384
12.5.1;Introduction;384
12.5.2;Glycan Structures in Helminths;385
12.5.3;Recognition of Parasite Glycans by Collectins of the Innate Immune System;397
12.5.4;Parasite Glycans are Key Players in Helminth-Induced Immune Regulation;397
12.5.5;Secretion of Lectins by Parasitic Helminths;400
12.5.6;Anti-Glycan Humoral Responses;401
12.5.7;Diagnostic Approaches Employing Helminth Glycans;402
12.5.8;Conclusions and Future Prospects;402
12.5.9;References;403
13;Section VI: Disease Glycomes;414
13.1;Chapter 16. Cancer Glycomics;416
13.1.1;Introduction;416
13.1.2;Analysis of Glycans on Specific Glycoproteins;420
13.1.3;Comparative Glycoproteomics of Serum to Identify Potential Tumor Markers;421
13.1.4;Glycans Released from Serum Glycoproteins;424
13.1.5;Use of Targeted Glycoproteomics to Identify Changes in Glycoprotein Expression in Cancer Serum;427
13.1.6;Comparison of O-Linked Glycans in Cancer Serum and on Cancer Cells;429
13.1.7;Comparative Glycoproteomic Analysis of Cancer Cells and Tissues;431
13.1.8;Antibody Arrays to Detect Glycan Variation on Glycoprotein Markers;434
13.1.9;Antibodies to Glycan Epitopes Expressed in Cancer Tissues;435
13.1.10;Conclusion;435
13.1.11;References;437
13.2;Chapter 17. Introduction to Human Glycosylation Disorders;448
13.2.1;Introduction;448
13.2.2;Brief History and Nomenclature;448
13.2.3;Glycobiologists, Clinicians, and Geneticists Collaborate in Patient Diagnosis;451
13.2.4;Spectrum of Disorders;452
13.2.5;N-Glycan Defects;452
13.2.6;Animal Models of N-Glycosylation Disorders;455
13.2.7;Congenital Muscular Dystrophies;458
13.2.8;Defects in Glycosphingolipid and Glycosylphosphaditylinositol Biosynthesis;462
13.2.9;Defects in O-GalNAc Glycan Biosynthesis;463
13.2.10;Defects in O-Fucose-Linked Glycans;463
13.2.11;Defects in Glycosaminoglycan Synthesis;464
13.2.12;Opportunities;466
13.2.13;Possible Therapies for CDG-Ia?;467
13.2.14;Some Unanswered Questions;468
13.2.15;Conclusions;469
13.2.16;References;470
14;Index;482
14.1;A;482
14.2;B;482
14.3;C;482
14.4;D;483
14.5;E;484
14.6;F;484
14.7;G;484
14.8;H;486
14.9;I;487
14.10;K;487
14.11;L;487
14.12;M;488
14.13;N;489
14.14;O;489
14.15;P;489
14.16;Q;489
14.17;R;489
14.18;S;489
14.19;T;490
14.20;U;490
14.21;W;490
14.22;Z;490
15;Color Plates;492