Glycosaminoglycans : methods and protocols

著者

    • Balagurunathan, Kuberan
    • Nakato, Hiroshi
    • Desai, Umesh R.
    • Saijoh, Yukio

書誌事項

Glycosaminoglycans : methods and protocols

edited by Kuberan Balagurunathan ... [et al.]

(Methods in molecular biology / John M. Walker, series editor, 2303)(Springer protocols)

Humana Press, 2022 [i.e. 2021]

2nd ed

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注記

Other editors: Hiroshi Nakato, Umesh Desai, Yukio Saijoh

Previous ed.: 2015

Includes bibliographical references and index

内容説明・目次

内容説明

This second edition volume expands on the previous edition with new information on the structural analysis of glycosaminoglycans (GAGs); chemical and enzymatic synthesis of GAGs; biophysical, biochemical, and computational analysis of GAG-protein interactions; molecular and genetic approaches to manipulating GAG cell biology; and molecular and genetic methods involving animal models and organoids. This volume also offers insight and guidance to non-glycoscience researchers who are performing advanced experiments on GAGs. 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. \ Cutting-edge and authoritative, Glycosaminoglycans: Methods and Protocols, Second Edition is a valuable experimental manual for practicing researchers including graduate and post-doctoral fellows, and provides them with the latest methodologies and practical tips to overcoming barriers in understanding the chemistry and biology of GAGs.

目次

Dedication... Preface... Table of Contents... Contributing Authors... Part I GAG Structures 1. One-Pot Enzymatic Synthesis of Heparin from N-Sulfoheparosan Li Fu and Robert J. Linhardt 2. Solution NMR Spectroscopy for Characterizing Protein-Glycosaminoglycan Interactions Prem Raj B. Joseph, Krishna Mohan Sepuru, Krishna Mohan Poluri, and Krishna Rajarathnam 3. Metabolic Labeling of Proteoglycans and Analysis of Their Synthesis and Sorting in Filter-Grown and Polarized Epithelial Cells Kristian Prydz and Ravi Adusumalli 4. Fluorous-Tag Assisted Synthesis of GAG-Like Oligosaccharides Jose L. de Paz and Pedro M. Nieto 5. Aqueous Molecular Dynamics for Understanding Glycosaminoglycan Recognition by Proteins Balaji Nagarajan and Umesh R. Desai 6. A Non-Radioactive Method to Measure Hyaluronan Synthase Activity Davide Vigetti, Evgenia Karousou, Manuela Viola, and Alberto Passi 7. A Glycoproteomic Approach to Identify Novel Proteoglycans Fredrik Noborn, Mahnaz Nikpour, Andrea Persson, Carina Sihlbom, Jonas Nilsson, and Goeran Larson 8. Analysis of Protein-Glycosaminoglycan Interactions using Traveling Wave Ion Mobility Mass Spectrometry Robert V. Williams and I. Jonathan Amster 9. Ascidian (Chordata-Tunicata) Glycosaminoglycans: Extraction, Purification, Biochemical, and Spectroscopic Analysis Felipe C. O. B. Teixeira and Mauro S. G. Pavao 10. Quantitative Disaccharide Profiling of Glycosaminoglycans from Two Different Preparations by PMP and Deuterated PMP Labeling Meng Zhang, Yi An, and Lijuan Zhang 11. Preparation and Characterization of Heparan Sulfate Derived Oligosaccharides to Investigate Protein-GAG Interaction and HS Biosynthesis Enzyme Activity Cedric Laguri, Rabia Sadir, Evelyne Gout, Romain R. Vives, and Hugues Lortat-Jacob 12. Heparan Sulfate Structure: Methods to Study N-sulfation and NDST Action Anders Dagalv, Anders Lundequist, Beata Filipek-Gorniok, Tabea Dierker, Inger Eriksson, and Lena Kjellen 13. Methods for the Production of Recombinant Heparosan: A Critical Heparin Precursor, from Non-Pathogenic E.coli Strains Anindita Roy, Varun Garg, Sai K Mehta, Alessandro Rossi, and Balagurunathan Kuberan 14. De novo Sequencing of Heparin/Heparan Sulfate Oligosaccharides by Chemical Derivatization and LC-MS/MS Quntao Liang and Joshua S. Sharp 15. Production and HPLC-Based Disaccharide Analysis of Xyloside-Primed Glycosaminoglycans Andrea Persson, Emil Tykesson, Ulf Ellervik, and Katrin Mani 16. Nuclear Magnetic Resonance Methods in Structural Characterization of Glycosaminoglycans Vitor H. Pomin and Barbara Mulloy 17. Aggrecan: Approaches to Study Biophysical and Biomechanical Properties Hadi Tavakoli Nia, Christine Ortiz, and Alan Grodzinsky 18. Chromatographic Molecular Weight Measurements for Heparin: Its Fragments and Fractions, and Other Glycosaminoglycans Barbara Mulloy and John Hogwood 19. Mass Spectrometric Methods for the Analysis of Heparin and Heparan Sulfate Miroslaw Lech, Ishan Capila, and Ganesh V. Kaundinya 20. Affinity Purification of Glycosylphosphatidylinositol-Anchored Proteins by Alpha-Toxin Kevin Huang and Sungjin Park 21. Thermodynamic Affinity and Nature of Forces Defining Glycosaminoglycan: Protein Systems Using Fluorescence Spectroscopy Rio S. Boothello and Umesh R. Desai 22. Isolation and Characterization of Heparan Sulfate Containing Amyloid Precursor Protein Degradation Products Katrin Mani 23. Chemical Approaches to Prepare Modified Heparin and Heparosan Polymers for Biological Studies Karthik Raman and Sailaja Arungundram 24. Glycosaminoglycan Quality Control by Monosaccharide Analysis Yiran Zhang, Xuexiao Ma, and Lijuan Zhang 25. Characterizing Thermodynamics of Protein-Glycosaminoglycan Interactions using Isothermal Titration Calorimetry Amit K. Dutta, Krishna M. Sepuru, Joerg Roesgen, and Krishna Rajarathnam 26. Automated Synthesis of Chondroitin Sulfate Oligosaccharides Chien-Fu Liang, Heung Sik Hahm, Narayana Murthy Sabbavarapu, and Peter H. Seeberger 27. Capillary Electrophoretic Analysis of Isolated Sulfated Polysaccharides to Characterize Pharmaceutical Products Zachary Shriver and Ram Sasisekharan 28. Preparation of Isotope Enriched Heparan Sulfate Precursors for Structural Biology Studies Victor V. Xylophone, My Vu Tran, Balagurunathan Kuberan, and Thao Kim Nu Nguyen 29. Methods for Measuring Exchangeable Protons in Glycosaminoglycans Consuelo N. Beecher and Cynthia K. Larive 30. Advances in Studying Glycosaminoglycan-Protein Interactions Using Capillary Electrophoresis Aiye Liang and Umesh R. Desai 31. anexVis: A Transcriptome Tool to Visualize Organ/Tissue-Specific Glycosaminoglycan Biosynthetic and Catabolic Pathways in Human Health and Diseases Kishan Thambu and Balagurunathan Kuberan Part II GAG Functions 32. Molecular Genetic Techniques for the Proteoglycan Functions in Drosophila Nanako Bowden, Masahiko Takemura, and Hiroshi Nakato 33. Measuring Sulfatase Expression and Invasion in Glioblastoma Anna Wade, Jane R. Engler, Vy My Tran, and Joanna J. Phillips 34. Analyzing the Role of Heparan Sulfate Proteoglycans in Axon Guidance In Vivo in Zebrafish Fabienne E. Poulain 35. Regulation of 3-O-Sulfation of Heparan Sulfate during Transition from the Naive to the Primed State in Mouse Embryonic Stem Cells Hayato Ota and Shoko Nishihara 36. Analysis of Human Hyaluronan Synthase Gene Transcriptional Regulation and Downstream Hyaluronan Cell Surface Receptor Mobility in Myofibroblast Differentiation Adam C. Midgley and Timothy Bowen 37. Methods to Analyze the Effect of Diet-Derived Metabolites on Endothelial Inflammation and Cell Surface Glycosaminoglycans Brett Ronald Cutler, Jie Shi Chua, Balagurunathan Kuberan, and Pon Velayutham Anandh Babu 38. Assays for Evaluation of Substrates for and Inhibitors of -1,4-Galactosyltransferase 7 Emil Tykesson, Andrea Persson, Katrin Mani, and Ulf Ellervik 39. Enzymatic Alteration of ECM to Explore Muscle Function and Motor Control of a Learned Behavior Caitlin Mencio, Balagurunathan Kuberan, and Franz Goller 40. Procedures to Evaluate the Role of Heparan Sulfate in the Reactivity of Resistance and Conductance Arteries Ex Vivo Jae Min Cho, Kellsey Ly, Steven Ly, Seul-Ki Park, Pon Velayutham Anandh Babu, Balagurunathan Kuberan, and J. David Symons 41. Computerized Molecular Modeling for Discovering Promising Glycosaminoglycan Oligosaccharides that Modulate Protein Function Nehru Viji Sankaranarayanan and Umesh R. Desai 42. Imaging Glycosaminoglycan Modification Patterns In Vivo Hannes E. Bu low 43. Isolation and Purification of Versican and Analysis of Versican Proteolysis Simon J. Foulcer, Anthony J. Day, and Suneel S. Apte 44. Identification of Cell Autonomous and Non-Cell Autonomous Functions of Heparan Sulfate Glycosaminoglycan Chains by Creating Chimeric Mouse Embryos Isao Matsuo and Chiharu Kimura-Yoshida 45. Methods for Assessing the Effects of Xylosides on Angiogenesis Jie Shi Chua, Geethu Muruganandam, Yukio Saijoh, and Balagurunathan Kuberan 46. Role of HSPGs in Systemic Bacterial Infections Rafael S. Aquino, Kazutaka Hayashida, Atsuko Hayashida, and Pyong Woo Park 47. Generation of Drosophila Heparan Sulfate Mutant Cell Lines from Existing Fly Strains Eriko Nakato, Nanako Bowden, and Hiroshi Nakato 48. Application of a Mutant Cell Library to Determine the Structure-Function Relationship of Heparan Sulfate in Facilitating FGF-FGFR Signaling John Faulkner, Xuehong Song, and Lianchun Wang 49. Manipulation of Glycosaminoglycans using Synthetic Xylosides to Study their Roles in Lung Branching Morphogenesis in Ex Vivo Lung Bud Culture System Jie Shi Chua, Balagurunathan Kuberan, and Yukio Saijoh 50. Informatics Ecosystems to Advance the Biology of Glycans Lewis J. Frey 51. Analysis of 3'-phosphoadenosine 5'-phosphosulfate Transporters: Transporter Activity Assay, Real-Time Reverse Transcription Polymerase Chain Reaction, and Immunohistochemistry Hideo Egawa and Shoko Nishihara 52. Preparation of Nanosensors for Detecting the Activity of Glycosaminoglycan Cleaving Enzymes Mausam Kalita, April Joice, Khoi Dang Le, Yiling Bi, Gurusankar Ramamoorthy, Orlando Antelope, Anindita Roy, and Balagurunathan Kuberan 53. The Detection of Glycosaminoglycans in Pancreatic Islets and Lymphoid Tissues Marika Bogdani,Charmaine Simeonovic, Nadine Nagy, Pamela Y. Johnson, Christina K. Chan, and Thomas N. Wight 54. Histochemical Analysis of Heparan Sulfate 3-O-sulfotransferase Expression in Mouse Brain Tomio Yabe and Nobuaki Maeda 55. Mapping Proteoglycan Functions Using Novel Genetic Strategies Mauricio Cortes, Leslie K. Cortes, and Nancy B. Schwartz 56. Xyloside Derivatives as Molecular Tools to Selectively Inhibit Heparan Sulfate and Chondroitin Sulfate Proteoglycan Biosynthesis Caitlin Mencio, Balagurunathan Kuberan, and Mamoru Koketsu 57. A Strategic Approach to Identification of Selective Inhibitors of Cancer Stem Cells Nirmita Patel, Somesh Baranwal, and Bhaumik B. Patel 58. Applications of Xylosides in the Manipulation of Stem Cell Niche to Regulate Human Neural Stem Cell Differentiation and Neurite Outgrowth Jie Shi Chua, Geethu Muruganandam, Daeun Sung, Yukio Saijoh, and Balagurunathan Kuberan 59. Murine Models in the Evaluation of Heparan Sulfate-Based Anticoagulants Bassem M. Mohammed, Qiufang Cheng, Ivan S. Ivanov, and David Gailani 60. Investigating the Roles of Heparan Sulfate Structures in Alpha-Synuclein Aggregation in Cell Culture Models Anindita Roy, Akila V. Chalapathi, and Balagurunathan Kuberan Subject Index List...

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詳細情報

  • NII書誌ID(NCID)
    BC11334072
  • ISBN
    • 9781071613979
  • 出版国コード
    us
  • タイトル言語コード
    eng
  • 本文言語コード
    eng
  • 出版地
    New York
  • ページ数/冊数
    xxi, 829 p.
  • 大きさ
    27 cm
  • 分類
  • 件名
  • 親書誌ID
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