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  • 1
    Online Resource
    Online Resource
    San Diego :Elsevier Science & Technology,
    Keywords: Biochemistry. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (240 pages)
    Edition: 1st ed.
    ISBN: 9780128023570
    Series Statement: Issn Series
    DDC: 547.78
    Language: English
    Note: Front Cover -- Advances in Carbohydrate Chemistry and Biochemistry -- Copyright -- Contents -- Contributors -- Preface -- Reference -- Robert John (Robin) Ferrier -- Bibliography -- Chapter Two: Synthetic Approaches to l-Iduronic Acid and l-Idose: Key Building Blocks for the Preparation of Glycosaminog... -- 1. Introduction -- 1.1. Background -- 2. Epimerization at C-5 of d-Glucose Derivatives -- 2.1. SN2 Displacement of Sulfonates -- 2.2. The Mitsunobu Reaction -- 2.3. Epimerization via Generation of a C-5 Radical -- 3. Homologation of Tetroses and Pentoses -- 3.1. The Mukaiyama-Type Aldol Reaction -- 3.2. Diastereoselective Cyanohydrin Formation -- 3.3. Addition of Organometallic Reagents -- 3.4. Homologation Using 2-(Trimethylsilyl)thiazole -- 4. Isomerization of Unsaturated Sugars -- 4.1. Diastereoselective Hydroboration of exo-Glycals -- 4.2. From Delta4-Uronates -- 4.3. From 4-Deoxypentenosides -- 4.4. From d-Glucuronic Acid Glycal -- 5. Miscellaneous Methods -- 5.1. Diastereoselective Tishchenko Reaction -- 5.2. Homologation with 5,6-Dihydro-1,4-dithiin-2-yl[(4-methoxybenzyl)oxy]methane -- 5.3. C-H Activation of 6-Deoxy-l-hexoses -- 6. Conclusions -- Acknowledgments -- References -- Chapter Three: Glycosylation of Cellulases: Engineering Better Enzymes for Biofuels -- 1. Introduction -- 2. Glycosylation of Cellulose-Degrading Enzymes -- 2.1. Introduction -- 2.2. Glycan Structures Found on TrCel7A and Additional Secreted Cellulases -- 2.3. Implications of N-Glycosylation of the TrCel7A Catalytic Domain -- 2.4. Implications of O-Glycosylation of TrCel7A Linker Domain -- 2.5. Implications of O-Glycosylation of the CBM -- 3. Recombinant Expression of Fungal Cellulases -- 3.1. Expression of T. reesei Cellulases in Saccharomyces cerevisiae -- 3.2. Glycoengineered Strains of and Heterologous Protein Expression in Pichia pastoris. , 3.3. Glycosylation and Engineering of Expressed Proteins in Aspergillus Species -- 4. Modifications by Glycan-Trimming Enzymes -- 4.1. Introduction -- 4.2. Secreted Glycan-Active α-Mannosidases from T. reesei -- 4.3. Secreted α-Mannosidases from Additional Fungi -- 4.4. endo-β-N-Acetylglucosaminidases Secreted by Fungi -- 5. Summary and Future Perspectives -- Acknowledgments -- Appendix 1. Molecular Dynamics Simulation of a Linker Interacting with Crystalline Cellulose -- References -- Chapter Four: Human Milk Oligosaccharides (HMOS): Structure, Function, and Enzyme-Catalyzed Synthesis -- 1. Introduction -- 2. Structures of HMOS -- 2.1. HMOS Monosaccharide Building Blocks, Core Structures, and Glycosidic Linkages -- 2.2. HMOS Structures -- 3. Biosynthesis of HMOS -- 4. Functions of HMOS -- 4.1. Neutral Non-Fucosylated HMOS -- 4.2. Fucosylated HMOS -- 4.3. Sialylated HMOS -- 5. Production of HMOS by Enzyme-Catalyzed Processes -- 5.1. 2FL -- 5.2. 3SL and 3SLN -- 5.3. 6SL and 6SLN -- 5.4. LNT2, LNnT, LNnH, LNnO, LNnD, LSTd, and Disialyl Oligosaccharides -- 5.5. Fucα1-2LNnT -- 5.6. LNFP III, LNnFP V, and LNnDFH -- 5.7. LNT -- 5.8. 3FL, LDFT, LNFP II, Lea Tetrasaccharide, and LeX Tetrasaccharide -- 5.9. LNFP I and LNDFH I -- 5.10. Other Oligosaccharides -- 6. Perspectives -- Acknowledgments -- References -- Author Index -- Subject Index -- Back Cover.
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  • 2
    Online Resource
    Online Resource
    San Diego :Elsevier Science & Technology,
    Keywords: Carbohydrates. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (196 pages)
    Edition: 1st ed.
    ISBN: 9780128171486
    Series Statement: Issn Series
    DDC: 547.78
    Language: English
    Note: Front Cover -- Sialic Acids, Part II: Biological and Biomedical Aspects -- Copyright -- Contents -- Contributors -- Preface -- References -- Chapter One: Sialic Acids in Neurology -- 1. Introduction -- 2. History, Definition, and Occurrence -- 2.1. History -- 2.2. Definition of Oligo/PolySia -- 2.3. Occurrence -- 3. Analytical Methods -- 3.1. Biochemical Probes -- 3.1.1. Antibodies -- 3.1.2. Enzymes -- 3.2. Chemical Detection Method -- 3.2.1. Fluorometric C7/C9 Analysis -- 3.2.2. Mild Acid Hydrolysis-Fluorescent Anion-Exchange HPLC Analysis -- 3.2.3. Conventional Chemical Methods -- 3.2.4. Chemical Biological Approaches -- 4. Biosynthesis -- 4.1. Common Features -- 4.2. Oligo/PolySia-Biosynthesizing Enzymes: ST8Sia2, ST8Sia4, and ST8Sia3 -- 4.3. Di/TriSia-Synthesizing Enzymes: ST8Sia1, ST8Sia5, and ST8Sia6 -- 5. Phenotypes of PolySia-Impaired Animals -- 6. Biochemical Features of Di/Oligo/PolySia and Their Functions -- 6.1. Repulsive Field of PolySia -- 6.2. Attractive Field of PolySia -- 6.2.1. Neurotrophic Factors -- 6.2.2. Growth Factors -- 6.2.3. Neurotransmitters and Ions -- 6.2.4. Cytokines -- 6.2.5. Transcription Factors -- 6.3. Regulatory Role for Receptors -- 6.3.1. Ion and Ion Channel -- 6.3.2. Siglecs -- 6.3.3. Other Molecules -- 7. Related Diseases -- 7.1. Mental Disorders and Neurodegenerative Diseases -- 7.2. Cancer -- 8. Perspectives -- Acknowledgments -- References -- Chapter Two: Sialic Acids in Nonenveloped Virus Infections -- 1. Sialic Acids as Viral Receptors-One Term, Many Functions -- 2. Identification of Sialic Acid as a Determinant of Infection -- 2.1. Hemagglutination Assays -- 2.2. Neuraminidase Treatment -- 2.3. Inhibition of Glycosylation -- 2.4. Sialic Acid-Deficient Cell Lines -- 2.5. Discrepancies Between In Vivo and In Vitro ``Receptors´´ -- 2.6. Other Experiments. , 3. Identification of Specific Sialylated Receptor Candidates -- 3.1. Glycan Arrays for Verification of Receptor Glycan Specificity -- 3.2. STD NMR Spectroscopy for Verification of Receptor Glycan Specificity -- 3.3. Affinity Measurements -- 3.4. Differentiating Between Glycolipids and Glycoproteins -- 4. Atomic Resolution Structures of Sialic Acid-Virus Interactions and Structure-Based Inhibitor Design -- 4.1. General Aspects of Virus-Glycan Structural Biology -- 4.2. Single Virus Families -- 4.2.1. Polyomaviruses -- 4.2.2. Reoviruses -- 4.2.3. Adenoviruses -- 4.2.4. Picornaviruses -- 4.3. Structure-Based Inhibitors -- 5. Outlook: The Microbiome in Enteric Virus Infections -- Acknowledgments -- References -- Chapter Three: The Biology of Gangliosides -- 1. Ganglioside Structures, Distribution, and Biosynthesis -- 2. Ganglioside Functions: cis Regulation and trans Recognition -- 3. Gangliosides Regulate Receptor Tyrosine Kinases -- 4. Gangliosides Impact Human Proteinopathies -- 5. Gangliosides Are Cell-Surface Receptors for Bacterial Toxins -- 6. Gangliosides Are Cell-Surface Receptors for Myelin-Associated Glycoprotein -- 7. Intellectual Disability and Seizures in Humans and Mice With Altered Ganglioside Biosynthetic Genes -- 8. Gangliosides in Human Disease -- Acknowledgments -- References -- Author Index -- Subject Index -- Back Cover.
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  • 3
    Online Resource
    Online Resource
    San Diego :Elsevier Science & Technology,
    Keywords: Biochemistry. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (288 pages)
    Edition: 1st ed.
    ISBN: 9780128121801
    Series Statement: Issn Series
    DDC: 547.78
    Language: English
    Note: Front Cover -- Advances in Carbohydrate Chemistry and Biochemistry -- Copyright -- Contents -- Contributors -- Preface -- Chapter One: Hyaluronan and Hyaluronan Fragments -- 1. Introduction -- 2. HA in the Solid State and at Surfaces -- 3. HA in Dilute and in Crowded Solutions -- 4. HA Self-association -- 5. HA Size and Why It Matters -- 5.1. High-Molecular-Mass HA Is the Physiological Protector of Cells -- 5.2. Low-Molecular-Mass HA Stimulates Defensive Cellular Responses -- 5.3. Mechanisms for HA Degradation -- 5.3.1. Hyaluronidases -- 5.3.2. Degradation of HA by ROS/RNS -- 5.3.3. Degradation of HA by Other Chemical and Physical Means -- 6. Experimental Determination of HA Content and Size In Vivo -- 6.1. Isolation Methods -- 6.2. Specific Quantification Methods -- 6.3. Methods for Molecular Mass Analysis -- 6.4. Experimental Findings on HA Content and Size -- 6.4.1. HA in Biological Fluids -- 6.4.2. HA in Tissues -- 7. Diagnostic and Therapeutic Applications -- 7.1. Exogenous HA -- 7.2. HA-Based Medical Diagnostics -- 7.3. Therapeutic Modulation of HA Signaling -- Acknowledgments -- References -- Chapter Two: Application of Porous Materials to Carbohydrate Chemistry and Glycoscience -- 1. Introduction -- 2. Glycoproteins, Glycans, and Glycosylation -- 3. Characteristics of Porous Materials -- 4. Methods for Characterizing Porous Materials -- 5. Glycan and Carbohydrate Enrichment -- 6. Mesoporous Silica and Related Materials -- 6.1. Basic Aspects of Mesoporous Silicas -- 6.2. General Applications of Mesoporous and Porous Silica to Glycans -- 6.3. Mesoporous and Porous Silicas Modified for Boronate Affinity Applications -- 6.4. Carbon-Mesoporous Silica Composites -- 6.5. Lectin-Modified Porous Silica -- 6.6. Controlled Release Applications Involving Mesoporous Silica and Glycans -- 7. Porous Alumina -- 8. Porous Titania -- 9. Mesoporous Carbon. , 10. Porous Graphitic Carbon -- 11. Porous Polymers Interacting With or Modified by Carbohydrates -- 11.1. Boronate-Modified Porous Polymers -- 11.2. Hydrophilic Interactions on Porous Polymers -- 11.3. Glycan Release by Enzyme-Modified Porous Polymers -- 11.4. Porous Polymers Modified by or Interacting With Lectins -- 12. Nanoporous Gold -- 13. Future Directions -- Acknowledgments -- References -- Chapter Three: The Synthesis and Biological Characterization of Acetal-Free Mimics of the Tumor-Associated Carbohydrate A ... -- 1. Introduction -- 2. Cancer and Immunotherapy -- 2.1. Overview -- 2.2. TACAs in Cancer -- 3. Synthesis of the Natural TACAs: Historical Overview -- 3.1. Tn Antigen -- 3.2. TF Antigen -- 3.3. sTn Antigen -- 4. Synthetic TACA Antigens as Potential Immunotherapeutics -- 4.1. Overview of Current State of TACA Therapies -- 4.2. Challenges in TACA Vaccine Preparation -- 4.3. Acetal-Free Carbohydrate Antigens -- 5. Synthesis of Carbasugars -- 5.1. Overview -- 5.2. Diels-Alder Approach -- 5.2.1. McCasland Synthesis -- 5.2.2. Ogawa Synthesis -- 5.3. Chemoenzymatic Processes -- 5.4. Ring-Closing Metathesis -- 5.5. Ferrier Type II Rearrangements -- 5.6. Radical Cyclization -- 6. Synthesis of C-Glycosides -- 6.1. Cross-Coupling -- 6.1.1. Heck Reaction -- 6.1.2. Suzuki-Miyaura Coupling -- 6.1.3. Negishi Coupling -- 6.2. Ring-Closing Metathesis -- 6.3. Radical Tethering -- 6.4. Allylation and Related Reactions -- 7. Synthesis of Acetal-Free Tn Antigens -- 8. Synthesis of Acetal-Free TF Antigens -- 9. Synthesis of Acetal-Free sTn Antigens -- 10. Partial Synthesis of Acetal-Free Sialyl Lewis Antigens -- 11. Biological Conjugation and Biological Evaluation of Acetal-Free Mimics -- 11.1. Tn Antigen -- 11.2. TF Antigen -- 11.3. sTn Antigen -- 12. Conclusions and Perspectives -- Acknowledgments -- References -- Author Index -- Subject Index. , Back Cover.
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  • 4
    Online Resource
    Online Resource
    San Diego :Elsevier Science & Technology,
    Keywords: Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (366 pages)
    Edition: 1st ed.
    ISBN: 9780128155363
    Series Statement: Issn Series
    DDC: 547.7
    Language: English
    Note: Front Cover -- Sialic Acids, Part I: Historical Background and Development, and Chemical Synthesis -- Copyright -- Contents -- Contributors -- Preface -- Reference -- Chapter One: Exploration of the Sialic Acid World -- 1. Introduction -- 2. Paving the Way With Ehrlich´s Aldehyde and Bial´s Orcinol Reagents -- 2.1. The First Scoutings -- 2.2. The Growing Knowledge About the Substance -- 2.3. The Expanding Network of Researchers -- 3. The First Creation of Chemical Structures -- 4. The Battle for the Stereochemistry -- 4.1. The C5, C6, C7, and C8 Chiralities -- 4.2. The C4 Chirality -- 4.3. The C2 Chirality and the Ring Form/Conformation -- 4.4. The Replacement of NH2-C5 by HO-C5 -- 5. Elucidating the O-Substitution Patterns -- 6. Different Views on the Conformation of the Glycerol Side Chain -- 6.1. X-ray Diffraction Analysis -- 6.2. NMR Spectroscopy -- 6.3. Molecular Mechanics, Molecular Dynamics, and Ab Initio Calculations -- 6.4. Final Remarks -- 7. An Impression of Analytical Techniques as Used in Sialic Acid Analysis -- 7.1. Spectrophotometric Assays -- 7.2. Chromatographic Techniques -- 7.3. Instrumental Techniques -- 7.4. Histological Methods -- 8. Sialic Acids as a Part of Glycoproteins, Glycolipids, Oligosaccharides, and Polysaccharides -- 8.1. Glycoprotein N- and O-Glycans -- 8.2. Glycolipids -- 8.3. Milk Oligosaccharides -- 8.4. Urinary Oligosaccharides and Glycopeptides -- 8.5. Capsular Polysaccharides, Lipopolysaccharides, and Lipooligosaccharides -- 8.6. General Remarks About the Structural Analysis of Glycans -- 9. Growing Interest From the Organic and Enzymatic Chemistry -- 10. Structural Variants of the Sialic Acid Backbone -- 11. Unraveling the Metabolism of Sialic Acids -- 11.1. The Biosynthesis of N-Acetylneuraminic Acid -- 11.2. The Activation of Sialic Acids -- 11.3. Sialic Acid Transfer to Glycans. , 11.4. The Regulation of Sialic Acid Biosynthesis -- 11.5. Modified Sialic Acids Different From N-Acetylneuraminic Acid -- 11.5.1. N-Glycolylneuraminic Acid -- 11.5.2. O-Acetylated Sialic Acids -- 11.5.3. Other Natural Sialic Acids -- 11.5.4. Nonnatural Sialic Acids -- 11.6. The De-esterification of O-Acetylated Sialic Acids -- 11.7. exo-, endo-, and trans-Sialidases -- 11.7.1. Sialidase Inhibitors -- 12. The Biology of Sialic Acids -- 12.1. The ``Sweet Coat of the Cell´´ -- 12.2. The Masking Role of Sialic Acids in Serum Glycoproteins and Blood Cells -- 12.3. Sialic Acids in Tumors -- 12.4. The Role of Sialic Acids in Immunology -- 12.5. Proteins Recognizing Sialic Acids -- 12.5.1. Plant and Other Lectins, and Virus Hemagglutinins -- 12.5.2. Selectins -- 12.5.3. Siglecs -- 13. Hereditary Sialic Acid Diseases -- 13.1. Sialuria -- 13.2. Salla Disease and Infantile Sialic Acid Storage Disease -- 13.3. Sialidosis -- 13.4. Galactosialidosis -- 13.5. Hereditary Inclusion Body Myopathy (GNE Myopathy) -- 14. Concluding Remarks -- Acknowledgments -- References -- Chapter Two: Chemical Synthesis of Glycosides of N-Acetylneuraminic Acid -- 1. Introduction -- 2. Chemical Synthesis of O-Sialosides -- 2.1. Modifications at C-1 -- 2.2. Modifications at C-2: Leaving Groups -- 2.2.1. Halides -- 2.2.2. S-Sialosides: Thiosialosides and Other 2-Thio Derivatives -- 2.2.3. O-Sialosides: Trifluoroacetimidates, Phosphites, and Phosphates -- 2.3. Modifications at C-3 -- 2.3.1. 3-Bromo Auxiliaries -- 2.3.2. 3-O-Acyl Auxiliaries -- 2.3.3. 3-S-Aryl (and 3-Se-Aryl) Auxiliaries -- 2.4. Modifications at C-4 -- 2.4.1. 4-O-tert-Butyldimethylsilyl Ether Derivative -- 2.4.2. 4-O-Picoloyl (and 4-O-Benzoyl) Derivatives -- 2.5. Modifications at C-5 -- 2.5.1. N-Acetylacetamido Derivatives -- 2.5.2. Azido Derivatives -- 2.5.3. Trifluoroacetamido Derivatives. , 2.5.4. N-Trichloroethoxycarbonyl Derivatives -- 2.5.5. N-Phthalimido Derivatives -- 2.5.6. Isothiocyanate Derivatives -- 2.6. Cyclic Protecting Groups -- 2.6.1. Oxazolidinone trans-Fused Ring -- 2.6.2. Miscellaneous Cyclic Substituents -- 2.7. Modifications at the Glycerol Chain -- 2.7.1. O-Benzoyl (O-Bz) Derivatives -- 2.7.2. O-Chloroacetyl (O-CA or O-ClAc) Derivatives -- 2.7.3. O-Trifluoroacetyl (O-TFA) Derivatives -- 2.7.4. O-Picoloyl (O-Pico) Derivatives -- 3. Mechanistic Studies of O-Sialylations -- 4. Conclusions -- Acknowledgments -- References -- Author Index -- Subject Index -- Back Cover.
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  • 5
    Online Resource
    Online Resource
    San Diego :Elsevier Science & Technology,
    Keywords: Biochemistry. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (358 pages)
    Edition: 1st ed.
    ISBN: 9780128099841
    Series Statement: Issn Series
    DDC: 547.78
    Language: English
    Note: Front Cover -- Advances in Carbohydrate Chemistry and Biochemistry -- Copyright -- Contents -- Contributors -- Preface -- Chapter One: Stevia Glycosides: Chemical and Enzymatic Modifications of Their Carbohydrate Moieties to Improve the Sweet- ... -- 1. Introduction -- 2. Steviol Glycoside Structures from S. rebaudiana -- 3. Steviol Variants of Glycoside Structures from S. rebaudiana -- 4. Stability of Steviol Glycosides -- 5. Structure-Sweetness Relationship -- 6. Chemical Modifications of Steviol Glycosides -- 7. Enzymatic Modifications of Steviol Glycosides -- 7.1. Cyclodextrin Glycosyl Transferase Systems -- 7.2. α-Glucosidase Transglycosylation Systems -- 7.3. β-Glucosidase Transglycosylation and Deglycosylation Systems -- 7.4. α-Galactosidase Transglycosylation Systems -- 7.5. β-Galactosidase Transglycosylation Systems -- 7.6. β-Fructosidase Transglycosylation Systems -- 7.7. β-Glycosyltransferase Glycosylation Systems Using UDP-Sugars -- 8. Patents Regarding Enzymatic Modifications of Steviol Glycosides -- 9. Concluding Remarks -- Addendum -- Acknowledgments -- References -- Chapter Two: Endoglycosidases for the Synthesis of Polysaccharides and Glycoconjugates -- 1. Introduction -- 1.1. Biological Functions of Glycans and Glycoconjugates -- 1.2. Synthetic Glycans and Glycoconjugates for Deciphering Functions -- 1.3. Enzymes as a Tool for the Synthesis of Glycans and Glycoconjugates -- 2. Endoglycosidases in the Synthesis of Natural and Artificial Polysaccharides -- 2.1. Synthesis of Artificial Cellulose and Derivatives via Enzymatic Polymerization of Glycosyl Fluorides Catalyzed by Ce ... -- 2.2. Chitinase-Catalyzed Synthesis of Artificial Chitin and Derivatives Using Sugar Oxazolines as Activated Substrates -- 2.3. Hyaluronidase-Catalyzed Construction of Glycosaminoglycans Using Sugar Oxazoline as the Activated Substrates. , 2.4. Endo-β-Xylosidase-Catalyzed Transglycosylation in the Synthesis of Proteoglycans -- 3. Endoglycosidases in the Synthesis of N-Glycopeptides and N-Glycoproteins -- 3.1. Exploration of Glycan Oxazolines as Donor Substrates for ENGase-Catalyzed Synthesis of Complex Glycopeptides and Gly ... -- 3.2. Generation of ENGase-Based Glycosynthases for Transglycosylation -- 3.3. ENGase-Catalyzed Synthesis of Selected Biologically Interesting Glycopeptides and Glycoproteins -- 3.4. ENGase-Catalyzed Transglycosylation for Glycosylation Remodeling of Therapeutic Monoclonal Antibodies -- 4. Endoglycosidases for the Synthesis of Neoglycolipids and Glycosphingolipids -- 4.1. Ceramide Glycanase-Catalyzed Transglycosylation for Glycolipid Synthesis -- 4.2. Endoglycoceramidase-Based Glycosynthase for the Synthesis of Glycosphingolipids -- 5. Concluding Remarks -- Acknowledgment -- References -- Chapter Three: Recent Advances Toward Robust N-Protecting Groups for Glucosamine as Required for Glycosylation Strategies -- 1. Introduction -- 2. The Glycosylation Reaction -- 3. Acyclic N-Protecting Groups -- 3.1. The Acetyl (Ac) Group -- 3.2. The Diacetyl [-N(Ac)2] Group -- 3.3. The Chloroacetyl (ClCH2CO) Group -- 3.4. The Dichloroacetyl Group -- 3.5. The Trichloroacetyl (TCA) and Trifluoroacetyl (TFA) Groups -- 3.6. The Pent-4-enoyl Group -- 3.7. The Trichloroethoxycarbonyl (Teoc) Group -- 3.8. The 2,2,2-Trichloro-1,1-dimethylethyloxycarbonyl (TCBOC) Group -- 3.9. The Allyloxycarbonyl (AOC) Group -- 3.10. The Benzyloxycarbonyl (Cbz or Z) Group -- 3.11. The p-Nitrobenzyloxycarbonyl (PNZ) Group -- 3.12. The Methoxycarbonyl Group -- 3.13. The Ethoxycarbonyl, Chloroethyloxycarbonyl, and Phenyloxycarbonyl Groups -- 3.14. The (1,3-Dimethyl-2,4,6-(1H,3H,5H)-trioxopyrimidin-5-ylidene)methyl (DTPM) Group -- 3.15. The 4,4-Dimethyl-2,6-dioxocyclohexylidenemethyl (Dde) Group. , 3.16. The N-2,4-Dinitrophenyl (DNP) Group -- 3.17. The Diphenylphosphoryl (DPPO) and Dimethylphosphoryl (DMPO) Groups -- 3.18. The N-Alkylacetamido Groups -- 3.19. Fluorous-Protecting Groups (Froc) -- 4. Cyclic N-Protecting Groups -- 4.1. Oxazolines -- 4.1.1. Methyloxazoline -- 4.1.2. Phenyloxazoline -- 4.1.3. 2-Alkoxy Glyco-[2,1-d]-2-oxazolines -- 4.2. Nonparticipating Groups -- 4.2.1. The 2,3-Oxazolidinone Group -- 4.2.2. The 2,5-Dimethylpyrrole Group (DMP) -- 4.3. Participating Groups -- 4.3.1. Five-Membered Ring Groups -- 4.3.1.1. The Phthalimido Family -- 4.3.1.2. The Dithiasuccinyl Group (Dts) -- 4.3.1.3. The Dimethylmaleoyl (DMM) Group -- 4.3.1.3.1. Formation of β Glycosides -- 4.3.1.3.2. Transformation of N-DMM to NHAc -- 4.3.1.3.3. β-(1→4)-Mannosyl-Linked Chitobiose-Type Compounds -- 4.3.1.3.4. Glycolipid Synthesis -- 4.3.1.3.5. Glycosaminoglycan (GAG) Syntheses -- 4.3.1.3.6. N-DMM-Protected Glycosyl Iodides -- 4.3.1.3.7. N-DMM-Based Synthesis of Trehalosamines -- 4.3.1.3.8. Synthesis of Chitooligomers -- 4.3.1.3.9. Synthesis of Murin-Type Oligosaccharides -- 4.3.1.3.10. N-Glycan Syntheses -- 4.3.1.3.11. Human Milk Oligosaccharides (HMOs) -- 4.3.1.3.12. Galactofuranosyl-β-(1→4)-GlcNAc -- 4.3.1.3.13. Glycosylation of 3- and 4-OH-Free DMM-Protected d-Glucosamines and d-Allosamines -- 4.3.1.3.14. Solid-Phase Synthesis of N-Glycans and HMOs -- 4.3.1.4. The Diphenylmaleoyl (DPM) Group -- 4.3.2. Six-Membered Ring Groups -- 4.3.2.1. The Thiodiglycolyl (TDG) Group -- 4.3.2.2. The Dimethylglutaroyl (DMG) Group -- 4.3.2.3. The Diglycolyl (DG) Group -- 5. Latent Amino-Protecting Groups -- 5.1. The Azido Glycosylation Method -- 5.2. 2-Nitro Sugars -- 5.2.1. 2-Nitro Glycals -- 5.2.1.1. O-Glycosides via Michael-Type Addition -- 5.2.1.2. Synthesis of N-Nucleosides -- 5.2.1.3. Synthesis of Glycosyl Phosphonates. , 5.2.1.4. Synthesis of β-C-Glycosyl Compounds (``β-C-Glycosides´´) -- 5.2.2. 2-Nitro-1-thioglycosyl Donors -- 6. Conclusions -- Acknowledgments -- References -- Chapter Four: Carbohydrate-Processing Enzymes of the Lysosome: Diseases Caused by Misfolded Mutants and Sugar Mimetics as ... -- 1. Introduction -- 2. Carbohydrate-Processing Enzymes of the Glycosphingolipid Degradation Pathway -- 2.1. Lysosomal β-d-Galactosidase -- 2.2. Lysosomal N-Acetyl-β-d-hexosaminidase -- 2.3. Lysosomal α-d-Galactosidase -- 2.4. Arylsulfatase A -- 2.5. Lysosomal β-d-Galactocerebrosidase -- 3. Lysosomal Glycogen Degradation and Glycogen Storage Disease -- 3.1. Lysosomal α-d-Glucosidase -- 4. Enzymes of the Glycoprotein Degradation Pathway and Glycoproteinoses -- 4.1. Lysosomal α-l-Fucosidase -- 4.2. Neuraminidase 1 -- 4.3. N-Acetyl-α-d-galactosaminidase -- 4.4. Lysosomal α-d-Mannosidase -- 4.5. Lysosomal β-d-Mannosidase -- 4.6. Aspartyl-N-acetyl-d-glucosaminidase -- 5. Enzymes Involved in Mucopolysaccharide Degradation and Mucopolysaccharidoses -- 5.1. Lysosomal α-l-Iduronidase -- 5.2. Lysosomal Heparan-N-sulfatase -- 5.3. Lysosomal N-Acetyl-α-d-glucosaminidase -- 5.4. Heparin Acetyl-CoA:α-d-glucosaminide-N-acetyltransferase -- 5.5. Lysosomal N-Acetyl-d-glucosamine-6-sulfatase -- 5.6. Lysosomal N-Acetyl-d-galactosamine-6-sulfatase -- 5.7. N-Acetyl-d-galactosamine-4-sulfatase (Arylsulfatase B) -- 5.8. Lysosomal β-Glucuronidase -- 5.9. Lysosomal Hyaluronidase -- 6. Conclusions and Outlook -- References -- Author Index -- Subject Index -- Back Cover.
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  • 6
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 2047, doi:10.1038/s41467-017-01848-y.
    Description: Integrin αβ heterodimer cell surface receptors mediate adhesive interactions that provide traction for cell migration. Here, we test whether the integrin, when engaged to an extracellular ligand and the cytoskeleton, adopts a specific orientation dictated by the direction of actin flow on the surface of migrating cells. We insert GFP into the rigid, ligand-binding head of the integrin, model with Rosetta the orientation of GFP and its transition dipole relative to the integrin head, and measure orientation with fluorescence polarization microscopy. Cytoskeleton and ligand-bound integrins orient in the same direction as retrograde actin flow with their cytoskeleton-binding β-subunits tilted by applied force. The measurements demonstrate that intracellular forces can orient cell surface integrins and support a molecular model of integrin activation by cytoskeletal force. Our results place atomic, Å-scale structures of cell surface receptors in the context of functional and cellular, μm-scale measurements.
    Description: Supported by the Lillie Research award from Marine Biological Laboratory and the University of Chicago (C.M.W., T.A.S., S.M., T.T.), NIH 5R13GM085967 grant to the Physiology Course at Marine Biological Laboratory, HHMI Summer Institute at Marine Biological Laboratory (S.M.), NIH CA31798 (T.A.S., P.N., T.I.M.), NIH GM100160 (T.T., S.M.), NIH GM092802 (D.B., N.K.), NIH GM114274 (R.O., S.M.) National Center for Biological Sciences-Tata Institute of Fundamental Research (S.M., J.M.K.), J.C. Bose Fellowship and HFSP Grant RGP0027/2012 (S.M.), NHLBI Division of Intramural Research (C.M.W., V.S.), Swedish Research Council VR 524-2011-891 Fellowship (P.N.), Swedish Society for Medical Research SSMF Fellowship (P.N.), Crafoord Foundation (P.N.).
    Keywords: Actin ; Integrin signalling ; Integrins ; Molecular imaging ; Polarization microscopy
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 7
    Publication Date: 2022-01-31
    Description: Pulau Redang and Pulau Tioman have experienced huge tourism growth over the last two decades, but minimal sewage treatment may threaten the resilience of their coral reefs. This study uses stable isotope techniques to identify suitable bioindicators of sewage nutrients (δ15N) at these islands by measuring macroalgae (Lobophora spp.), gastropods (Drupella spp.), scleractinian coral (Acropora spp.), and leather coral (Sinularia spp.). At tourist hubs using seepage septic tank systems, enrichment of Acropora δ15N (Redang, +0.7‰) and Sinularia δ15N (Tioman, +0.4‰) compared to pristine background levels indicate enhanced sewage nutrient discharge. Carbon isotopes and survey data suggest that sedimentation did not confound these δ15N trends. Potential damaging effects of sewage discharge on the coral reef communities at both islands are highlighted by strong correlations between Acropora δ15N and regional variation in coral reef community structure, and exclusive occurrence of degraded reefs at regions of high sewage influence.
    Type: Article , PeerReviewed
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  • 8
    Publication Date: 2015-10-07
    Description: Background: Specific genes, such as BCAT1 and IKZF1, are methylated with high frequency in colorectal cancer (CRC) tissue compared to normal colon tissue specimens. Such DNA may leak into blood and be present as cell-free circulating DNA. We have evaluated the accuracy of a novel blood test for these two markers across the spectrum of benign and neoplastic conditions encountered in the colon and rectum. Methods: Circulating DNA was extracted from plasma obtained from volunteers scheduled for colonoscopy for any reason, or for colonic surgery, at Australian and Dutch hospitals. The extracted DNA was bisulphite converted and analysed by methylation specific real-time quantitative PCR (qPCR). A specimen was deemed positive if one or more qPCR replicates were positive for either methylated BCAT1 or IKZF1 DNA. Sensitivity and specificity for CRC were estimated as the primary outcome measures. Results: Plasma samples were collected from 2105 enrolled volunteers (mean age 62 years, 54 % male), including 26 additional samples taken after surgical removal of cancers. The two-marker blood test was run successfully on 2127 samples. The test identified 85 of 129 CRC cases (sensitivity of 66 %, 95 % CI: 57–74). For CRC stages I-IV, respective positivity rates were 38 % (95 % CI: 21–58), 69 % (95 % CI: 53–82), 73 % (95 % CI: 56–85) and 94 % (95 % CI: 70–100). A positive trend was observed between positivity rate and degree of invasiveness. The colonic location of cancer did not influence assay positivity rates. Gender, age, smoking and family history were not significant predictors of marker positivity. Twelve methylation-positive cancer cases with paired pre- and post-surgery plasma showed reduction in methylation signal after surgery, with complete disappearance of signal in 10 subjects. Sensitivity for advanced adenoma (n = 338) was 6 % (95 % CI: 4–9). Specificity was 94 % (95 % CI: 92–95) in all 838 non-neoplastic pathology cases and 95 % (95 % CI: 92–97) in those with no colonic pathology detected (n = 450). Conclusions: The sensitivity for cancer of this two-marker blood test justifies prospective evaluation in a true screening population relative to a proven screening test. Given the high rate of marker disappearance after cancer resection, this blood test might also be useful to monitor tumour recurrence.Trial registrationACTRN12611000318987.
    Electronic ISSN: 1471-2407
    Topics: Medicine
    Published by BioMed Central
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  • 9
    Publication Date: 2017-11-29
    Description: Energetic particle bursts associated with dipolarization events within Mercury's magnetosphere were first observed by Mariner 10. The events appear analogous to particle injections accompanying dipolarization events at Earth. The Energetic Particle Spectrometer (3 s resolution) aboard MESSENGER determined the particle bursts are composed entirely of electrons with energies ≤ ~300 keV. Here we use the Gamma-Ray Spectrometer high-time-resolution (10 ms) energetic electron measurements to examine the relationship between energetic electron injections and magnetic field dipolarization in Mercury's magnetotail. Between March 2013 and April 2015, we identified 2976 electron burst events within Mercury's magnetotail, 538 of which are closely associated with dipolarization events. These dipolarizations were detected on the basis of their rapid (~2 s) increase in the northward component of the tail magnetic field (Δ B z ~ 30 nT), which typically persists for ~10 s. Similar to at Earth, we find these dipolarizations appear to be low-entropy, depleted flux tubes convecting planetward following the collapse of the inner magnetotail. We find electrons experience brief, yet intense, betatron and Fermi acceleration during these dipolarizations, reaching energies ~130 keV and contributing to nightside precipitation. Thermal protons experience only modest betatron acceleration. While only ~25% of energetic electron events in Mercury's magnetotail were directly associated with dipolarization, the remaining events are consistent with the Near-Mercury Neutral Line model of magnetotail injection and eastward drift about Mercury, finding that electrons may participate in Shabansky-like closed drifts about the planet. Magnetotail dipolarization may be the dominant source of energetic electron acceleration in Mercury's magnetosphere.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
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  • 10
    Publication Date: 2016-11-19
    Description: Proteins are often engineered to have higher affinity for their ligands to achieve therapeutic benefit. For example, many studies have used phage or yeast display libraries of mutants within complementarity-determining regions to affinity mature antibodies and T cell receptors (TCRs). However, these approaches do not allow rapid assessment or evolution across the entire interface. By combining directed evolution with deep sequencing, it is now possible to generate sequence fitness landscapes that survey the impact of every amino acid substitution across the entire protein-protein interface. Here we used the results of deep mutational scans of a TCR-peptide-MHC interaction to guide mutational strategies. The approach yielded stable TCRs with affinity increases of 〉200-fold. The substitutions with the greatest enrichments based on the deep sequencing were validated to have higher affinity and could be combined to yield additional improvements. We also conducted in silico binding analyses for every substitution to compare them with the fitness landscape. Computational modeling did not effectively predict the impacts of mutations distal to the interface and did not account for yeast display results that depended on combinations of affinity and protein stability. However, computation accurately predicted affinity changes for mutations within or near the interface, highlighting the complementary strengths of computational modeling and yeast surface display coupled with deep mutational scanning for engineering high affinity TCRs.
    Print ISSN: 0021-9258
    Electronic ISSN: 1083-351X
    Topics: Biology , Chemistry and Pharmacology
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