Biochemistry Books

Book SynopsisNew and expanded for its second edition, Environmental Microbiology: From Genomes to Biogeochemistry Second Edition, is a timely update to a classic text filled with ideas, connections, and concepts that advance an in-depth understanding of this growing segment of microbiology. Core principles are highlighted with an emphasis on the logic of the science and new methods-driven discoveries. Numerous up-to-date examples and applications boxes provide tangible reinforcement of material covered. Study questions at the end of each chapter require students to utilize analytical and quantitative approaches, to define and defend arguments, and to apply microbiological paradigms to their personal interests. Essay assignments and related readings stimulate student inquiry and serve as focal points for teachers to launch classroom discussions. A companion website with downloadable artwork and answers to study questions is also available. Environmental Microbiology: From GeTable of ContentsPreface viii About the Companion Website x 1 Significance, History, and Challenges of Environmental Microbiology 1 1.1 Core concepts can unify environmental microbiology 1 1.2 Synopsis of the significance of environmental microbiology 2 1.3 A brief history of environmental microbiology 6 1.4 Complexity of our world 10 1.5 Many disciplines and their integration 13 2 Formation of the Biosphere: Key Biogeochemical and Evolutionary Events 25 2.1 Issues and methods in Earth’s history and evolution 26 2.2 Formation of early planet Earth 26 2.3 Did life reach Earth from Mars? 30 2.4 Plausible stages in the development of early life 31 2.5 Mineral surfaces in marine hydrothermal vents: the early iron/sulphur world could have driven biosynthesis 35 2.6 Encapsulation (a key to cellular life) and an alternative (nonmarine) hypothesis for the habitat of precellular life 36 2.7 A plausible definition of the tree of life’s “Last universal common ancestor” (LUCA) 37 2.8 The rise of oxygen 39 2.9 Evidence for oxygen and cellular life in the sedimentary record 39 2.10 The evolution of oxygenic photosynthesis 42 2.11 Consequences of oxygenic photosynthesis: molecular oxygen in the atmosphere and large pools of organic carbon 45 2.12 Eukaryotic evolution: endosymbiotic theory and the blending of traits from Archaea and Bacteria 48 3 Physiological Ecology: Resource Exploitation by Microorganisms 56 3.1 The cause of physiological diversity: diverse habitats provide selective pressures over evolutionary time 57 3.2 Biological and evolutionary insights from genomics 57 3.3 Fundamentals of nutrition: carbon- and energy-source utilization provide a foundation for physiological ecology 69 3.4 Selective pressures: ecosystem nutrient fluxes regulate the physiological status and composition of microbial communities 71 3.5 Cellular responses to starvation: resting stages, environmental sensing circuits, gene regulation, dormancy, and slow growth 76 3.6 A planet of complex mixtures in chemical disequilibrium 86 3.7 A thermodynamic hierarchy describing biosphere selective pressures, energy sources, and biogeochemical reactions 91 3.8 Using the thermodynamic hierarchy of half reactions to predict biogeochemical reactions in time and space 93 3.9 Overview of metabolism and the “logic of electron transport” 104 3.10 The flow of carbon and electrons in anaerobic food chains: syntrophy is the rule 105 3.11 The diversity of lithotrophic reactions 109 4 A Survey of the Earth’s Microbial Habitats 117 4.1 Terrestrial biomes 118 4.2 Soils: geographic features relevant to both vegetation and microorganisms 120 4.3 Aquatic habitats 124 4.4 Subsurface habitats: oceanic and terrestrial 131 4.5 Defining the prokaryotic biosphere: where do prokaryotes occur on Earth? 141 4.6 Life at the micron scale: an excursion into the microhabitat of soil microorganisms 145 4.7 Extreme habitats for life and microbiological adaptations 151 5 Microbial Diversity: Who is Here and How do we Know? 162 5.1 Defining cultured and uncultured microorganisms 163 5.2 Approaching a census: an introduction to the environmental microbiological “toolbox” 167 5.3 Criteria for census taking: recognition of distinctive microorganisms (species) 170 5.4 Proceeding toward census taking and measures of microbial diversity 175 5.5 The tree of life: our view of evolution’s blueprint for biological diversity 181 5.6 A Sampling of key traits of cultured microorganisms from the domains Eukarya, Bacteria, and Archaea 185 5.7 Placing the “uncultured majority” on the tree of life: what have nonculture-based investigations revealed? 205 5.8 Viruses: an overview of biology, ecology, and diversity 213 5.9 Microbial diversity illustrated by genomics, horizontal gene transfer, and cell size 220 5.10 Biogeography of microorganisms 224 6 Generating and Interpreting Information in Environmental Microbiology: Methods and Their Limitations 238 6.1 How do we know? 239 6.2 Perspectives from a century of scholars and enrichment-cultivation procedures 239 6.3 Constraints on knowledge imposed by ecosystem complexity 243 6.4 Environmental microbiology’s “Heisenberg uncertainty principle”: model systems and their risks 245 6.5 Fieldwork: being sure sampling procedures are compatible with analyses and goals 247 6.6 Blending and balancing disciplines from field geochemistry to pure cultures 253 6.7 Overview of methods for determining the position and composition of microbial communities 257 6.8 Methods for determining in situ biogeochemical activities and when they occur 276 6.9 Cloning-based Metagenomics and related methods: procedures and insights 280 6.10 cloning-free, next-generation sequencing and omics methods: procedures and insights 290 6.11 Discovering the organisms responsible for particular ecological processes: linking identity with activity 325 7 Microbial Biogeochemistry: A Grand Synthesis 356 7.1 Mineral connections: the roles of inorganic elements in life processes 357 7.2 Greenhouse gases and lessons from biogeochemical modeling 361 7.3 The “stuff of life”: identifying the pools of biosphere materials whose microbiological transformations drive the biogeochemical cycles 372 7.4 Elemental biogeochemical cycles: concepts and physiological processes 393 7.5 Cellular mechanisms of microbial biogeochemical pathways 409 7.6 Mass balance approaches to elemental cycles 418 8 Special and Applied Topics in Environmental Microbiology 432 8.1 Other organisms as microbial habitats: ecological relationships 432 8.2 Microbial residents of plants and humans 449 8.3 Biodegradation and bioremediation 461 8.4 Biofilms 489 8.5 Evolution of catabolic pathways for organic contaminants 493 8.6 Environmental biotechnology: overview and nine case studies 499 8.7 Antibiotic resistance 514 9 Future Frontiers in Environmental Microbiology 538 9.1 The influence of systems biology on environmental microbiology 538 9.2 Ecological niches and their genetic basis 546 9.3 Concepts help define future progress in environmental microbiology 551 Glossary 557 Index 564

Read more less

Book SynopsisWnt signaling in Development and Disease: Molecular Mechanisms and Biological Functions reviews the core topics in Wnt signaling, from molecular pathway mechanisms to its role in embryogenesis, adult tissue homeostasis, and chronic disease. Written by a team of expert reviewers, the book provides clear and concise coverage of the core foundations of Wnt signaling before advancing to discussion of cutting-edge scientific research. Focused on the biological insights and current scientific questions of Wnt signaling, this book will be a comprehensive and definitive resource for a wide range of researchers and students in cell signaling, cell physiology, developmental biology, and biomedical engineering, as well as anyone interested in learning more about this important and complex protein network. A definitive source of information on Wnt signaling and its role in development and disease, written by leaders in the field. Explores the role of Wnt signalingTable of ContentsContributors vii Preface xi Part 1 Molecular Signaling Mechanisms: From Pathways to Networks 1 1 Wnt Signal Production, Secretion, and Diffusion 3 Madelon M. Maurice and Hendrik C. Korswagen 2 Wnt Signaling at the Membrane 15 Gary Davidson and Christof Niehrs 3 Wnt Signal Transduction in the Cytoplasm: an Introduction to the Destruction Complex 33 Tony W. Chen, Heather A. Wallace, Yashi Ahmed, and Ethan Lee 4 An Overview of Gene Regulation by Wnt/β-Catenin Signaling 51 Chen U. Zhang and Ken M. Cadigan 5 Finding a Needle in a Genomic Haystack: Genome-Wide Approaches to Identify Wnt/TCF Transcriptional Targets 73 Chandan Bhambhani and Ken M. Cadigan 6 Introduction to β-Catenin-Independent Wnt Signaling Pathways 89 Susanne Kühl and Michael Kühl 7 Molecular Mechanisms of Wnt Pathway Specificity 101 Alexandra Schambony, Guido J.R. Zaman, and Folkert Verkaar 8 Modulation of Wnt Signaling by Endocytosis of Receptor Complexes 113 Akira Kikuchi, Shinji Matsumoto, Katsumi Fumoto, and Akira Sato 9 New Insights from Proteomic Analysis of Wnt Signaling 125 Matthew P. Walker, Dennis Goldfarb, and Michael B. Major 10 New Insights about Wnt/β-Catenin Pathway Mechanisms from Global siRNA Screens 137 Tenzin Gocha and Ramanuj DasGupta 11 Mathematical Models of Wnt Signaling Pathways 153 Michael Kühl, Barbara Kracher, Alexander Groß, and Hans A. Kestler 12 The Wnt’s Tale: On the Evolution of a Signaling Pathway 161 Jenifer C. Croce and Thomas W. Holstein Part 2 Selected Key Molecules in Wnt Signaling 177 13 Secreted Wnt Inhibitors or Modulators 179 Paola Bovolenta, Anne-Kathrin Gorny, Pilar Esteve, and Herbert Steinbeisser 14 Frizzleds as G Protein-Coupled Receptors 195 Gunnar Schulte 15 Dishevelled at the Crossroads of Pathways 207 Vítìzslav Bryja and Ondøej Bernatík 16 β-Catenin: a Key Player in Both Cell Adhesion and Wnt Signaling 217 Jonathan Pettitt 17 Evolutionary Diversification of Vertebrate TCF/LEF Structure, Function, and Regulation 225 Stefan Hoppler and Marian L. Waterman 18 Insights from Structural Analysis of Protein–Protein Interactions by Wnt Pathway Components and Functional Multiprotein Complex Formation 239 Zhihong Cheng and Wenqing Xu Part 3 Wnt Signaling in Embryonic Development and Adult Tissue Homeostasis 251 19 Wnt Signaling in Early Vertebrate Development: From Fertilization to Gastrulation 253 Eliza Zylkiewicz, Sergei Y. Sokol, and Stefan Hoppler 20 Wnt/β-Catenin Signaling in Embryonic Stem Cells: Insights into Early Mammalian Development 267 Kathryn C. Davidson 21 Wnt Signaling in Neural Development 279 Richard I. Dorsky 22 Wnt Signaling in Heart Organogenesis 293 Stefan Hoppler, Silvia Mazzotta, and Michael Kühl 23 Wnt Signaling in Kidney Organogenesis 303 Kimmo Halt and Seppo Vainio 24 Wnt Signaling Regulation of Tissue Architecture (EMT and MET) and Morphogenesis: Consequences for Colorectal and Liver Cancer 315 Theodora Fifis, Bang M. Tran, Renate H.M. Schwab, Timothy M. Johanson, Nadia Warner, Nick Barker, and Elizabeth Vincan 25 Wnt Signaling in Adult Stem Cells: Tissue Homeostasis and Regeneration 329 Frank J.T. Staal and Riccardo Fodde 26 Restoring Tissue Homeostasis: Wnt Signaling in Tissue Regeneration After Acute Injury 339 Günes Özhan and Gilbert Weidinger Part 4 Wnt Signaling in Chronic Disease 357 27 Wnt Signaling and Colorectal Cancer 359 Kevin Myant and Owen J. Sansom 28 Wnt Signaling in Melanoma 369 Jamie N. Anastas and Andy J. Chien 29 Wnt Signaling in Mood and Psychotic Disorders 379 Stephen J. Haggarty, Karun Singh, Roy H. Perlis, and Rakesh Karmacharya 30 Neuropsychiatric Disease-Associated Genetic Variation in the Wnt Pathway 393 Stephen J. Haggarty, Karun Singh, Roy H. Perlis, and Rakesh Karmacharya 31 Wnt Signaling in Dementia 411 Stephen J. Haggarty 32 Therapeutic Targeting of the Wnt Signaling Network 421 Felicity Rudge and Trevor Dale Index 445

Read more less

Book SynopsisFocuses on the aggregation of recombinant proteins in bacterial cells in the form of inclusion bodiesand on their use in biotechnological and medical applications The first book devoted specifically to the topic of aggregation in bacteria, Protein Aggregation in Bacteria: Functional and Structural Properties of Inclusion Bodies in Bacterial Cells provides a large overview of protein folding and aggregation, including cell biology and methodological aspects. It summarizes, for the first time in one book, ideas and technical approaches that pave the way for a direct use of inclusion bodies in biotechnological and medical applications. Protein Aggregation in Bacteria covers: Molecular and cellular mechanisms of protein folding, aggregation, and disaggregation in bacteria Physiological importance and consequences of aggregation for the bacterial cell Factors inherent to the protein sequence responsible for aggregation andTable of ContentsContributors vii Preface xi Introduction to the Wiley Series in Protein and Peptide Science xiii 1 Fundamentals of Protein Folding 1 Vladimir N. Uversky 2 Recruiting Unfolding Chaperones to Solubilize Misfolded Recombinant Proteins 63 Rayees U.H. Mattoo and Pierre Goloubinoff 3 Osmolytes as Chemical Chaperones to Use in Protein Biotechnology 77 Ario de Marco 4 Inclusion Bodies in the Study of Amyloid Aggregation 93 Anna Villar-Piqué and Salvador Ventura 5 Protein Aggregation in Unicellular Eukaryotes 117 Marina Caldara, Joris Winderickx, and Vanessa Franssens 6 Structural Properties of Bacterial Inclusion Bodies 151 Antonino Natalello, Diletta Ami, and Silvia Maria Doglia 7 Residue-Specific Structural Studies of Inclusion Bodies 181 Christian Wasmer, Marielle Wälti, Yongli Chen, and Lei Wang 8 Biomedical Applications of Bacterial Inclusion Bodies 203 Imma Ratera, Spela Peternel, Joaquin Seras-Franzoso, Olivia Cano-Garrido, Elena García-Fruitós, Rafael Cubarsí, Esther Vazquez, José Luis Corchero, Escarlata Rodríguez-Carmona, Jaume Veciana, and Antonio Villaverde 9 Aggregation of Recombinant Proteins: Understanding Basic Issues to Overcome Production Bottlenecks 221 Marina Lotti and Loredano Pollegioni 10 Fusion to a Pull-Down Module: Designing Enzymes to Form Biocatalytically Active Insoluble Aggregates 247 Bernd Nidetzky Index 263

Read more less

Book SynopsisLipidomics is an important aspect of personalized medicine in relation to nutrition and metabolism. This approach has become important due to the substantial presence of nutraceuticals in the market, since it gives personalized criteria on how to choose the right nutraceutical strategy for both prevention and for quality of life.Table of ContentsAbout the Authors xi Preface xiii Acknowledgments xvii Abbreviations xix Part I Molecular and Nutritional Basis of Cell Membranes and Lipidomics 1 1 Membranes for Life and Life for Membranes 3 1.1 Cell Membranes: The Role of Fatty Acids and the Exclusion of Trans Isomers 3 1.2 Organization and Homeostasis 11 1a In Depth: The Formation of a Cell Membrane 16 1b In Depth: Cholesterol and Membranes 17 1c In Depth: Lipid Rafts 19 2 Fatty Acid Families: Metabolism and Nutrition 21 2.1 Saturated Fatty Acids: Biosynthesis and Dietary Regulation 23 2.2 Monounsaturated Fatty Acids: The Importance to be cis 28 2a In Depth: The key Steps of Phospholipid Synthesis 31 2b In Depth: Biosynthesis of the Double Bond and Desaturase Features 34 2.3 Polyunsaturated Fatty Acids: The Essentiality for Human Cells 37 Concepts’ Summary 38 S1 Beware of the Nutritional Label! 38 S2 The Optimal Values of Fatty Acids in Tissues 38 S3 Structural Role of Fatty Acids 40 3 Essential Fatty Acids 41 3.1 The Omega-6 and Omega-3 Families: Cascades and Regulation 42 3a In Depth: The Definition of Omega-6 and Omega-3 48 3b The Polyunsaturated Fatty Acids in Cell Membrane Remodeling 50 3c In Depth: How do you Define an Inflammatory Pathway? 55 3.2 The Balance Between Omega-6 and Omega-3 Pathways: Nutritional and Metabolic Considerations 56 3.3 Food and Membranes: A Virtuous Cycle 60 4 Free Radicals and Lipids: Trans and Oxidized Fatty Acids 65 4.1 Trans Fatty Acids for Humans: The Nutritional Intake 66 4.2 Endogenous Sources of Trans Fatty Acids by Free Radical Stress 71 4.3 Free Radicals and Lipid Oxidation: The Threshold for Health 73 4.4 Lipoproteins and Development of Markers for Lipid Reactivity 79 4a In Depth: Oleic versus Linoleic Acid Reactivity with Free Radicals 83 Concepts’ Summary 84 S1 Fatty Acid Geometry: A “Radical” Change 84 S2 Antioxidants for Membranes 85 Part II Membrane Lipidomics for Personalized Health 87 5 What Is Lipidomics for Health 89 5.1 The Birth of the Postgenomics Era 89 5.2 Lipidomics in the Postgenomic Era 92 5.3 Fatty Acids Involved in Membrane and Mediator Lipidomics 93 5.4 Membrane Lipidomics: Cellular Stress, Turnover, and Opportunities 95 5.4.1 How Does the Stress Involve Membranes? 97 5.5 Phospholipids From Dietary Intakes to Biological Functions 100 6 Lipidomics of Erythrocyte Membranes 105 6.1 Erythrocyte as a Comprehensive Health Biomarker 107 6.2 The Optimal Value Intervals and The Membrane Unbalance Index 115 6.3 Lipid Biosynthesis and Related Indices 120 6.4 The Individuation of Molecular Indicators 122 7 Nutrilipidomics 127 7.1 When Fatty Acids Become Nutraceuticals: Membrane Therapy With Nutrilipidomics 128 7.2 Fatty Acid–Based Membrane Lipidomics and Nutrilipidomics: The Personalized Approach for Nutrition and Nutraceuticals in Health and Diseases 131 8 Lipidomic Profiles and Intervention Strategies in Prevention and Diseases 135 8.1 Lipidomics and Sport 137 8.2 Lipidomics and Pregnancy 140 8.3 Lipidomics and Aging 143 8.4 Lipidomics and Cardiovascular Health 145 8.5 Lipidomics and Overweight 148 8.6 Lipidomics and Dermatology 150 8.7 Lipidomics and Neurology 151 8.8 Lipidomics and Ophtalmology 153 8.9 Conclusive Remarks 154 9 Lipidomics and Tutorials 157 9.1 First Steps for the Lipidomic Analysis 159 9.1.1 Saturated Fatty Acid Excess 160 9.1.2 Monounsaturated Fatty Acid Excess 160 9.1.3 Omega-6 PUFA Excess 160 9.1.4 Omega-3 PUFA Deficit 161 9.2 Learning Verification 162 References and Notes 167 Index 181

Read more less

Book SynopsisThe current volume continues the tradition of providing significant and interesting procedures, which should prove worthwhile to many synthetic chemists working in increasingly diverse areas. Following precedent, there is no specific or central theme to this volume.

Read more less

Book SynopsisOxidative Stress and Antioxidant Protection: The Science of Free Radical Biology and< Disease provides an overview of the basic principles of free radical formation. The text delves into free radical formation in molecular biology and its effect on subcellular damage, as well as the role of antioxidant reserves as a protective mechanism. Oxidative Stress and Antioxidant Protection begins with a historical perspective of pioneers in oxidative stress with an introductory section that explains the basic principles related to oxidative stress in biochemistry and molecular biology, demonstrating both pathways and biomarkers. This section also covers diagnostic imaging and differential diagnostics. The following section covers psychological, physiologic, pharmacologic and pathologic correlates. This section addresses inheritance, gender, nutrition, obesity, family history, behavior modification, natural herbal-botanical products, and supplementation in the treatment oTable of ContentsList of Contributors ix Special Recognition xiii Foreword xv Preface xvii Section 1: Introduction 1 Introduction to Free Radicals, Inflammation, and Recycling 3 Donald Armstrong 2 Diagnostic Imaging and Differential Diagnosis 11 Robert D. Stratton Section 2: Clinical Correlations on Acute and Chronic Diseases 3 Free Radicals: Their Role in Brain Function and Dysfunction 23 Natan Gadoth 4 Mediators of Neuroinflammation 39 Rajiv Tikamdas, Ping Zhang, and Bin Liu 5 Oxidative and Nitrative Stress in Schizophrenia 57 Anna Dietrich-Muszalska 6 The Effects of Hypoxia, Hyperoxia, and Oxygen Fluctuations on Oxidative Signaling in the Preterm Infant and on Retinopathy of Prematurity 77 M. Elizabeth Hartnett 7 Oxidative Damage in the Retina 93 Robert D. Stratton 8 The Role of Oxidative Stress in Hearing Loss 115 Colleen G. Le Prell and Josef M. Miller 9 Disorders of Children 133 Hirokazu Tsukahara and Masato Yashiro 10 Oxidative Stress in Oral Cavity: Interplay between Reactive Oxygen Species and Antioxidants in Health, Inflammation, and Cancer 155 Maurizio Battino, Maria Greabu and Bogdan Calenic 11 Oxidative Stress and the Skin 167 Christina L. Mitchell 12 Oxidative Stress in Osteoarticular Diseases 183 María José Alcaraz, Sergio Portal-Núñez, Juan A. Ardura and Pedro Esbrit 13 Gene Therapy to Reduce Joint Inflammation in Horses 193 Patrick Colahan, Rachael Watson, and Steve Ghivizzani 14 Muscle and Oxidative Stress 205 Reza Ghiasvand and Mitra Hariri 15 Role of Oxidants and Antioxidants in Male Reproduction 221 Ashok Agarwal, Hanna Tadros, Aaron Panicker and Eva Tvrdá 16 Role of Oxidants and Antioxidants in Female Reproduction 253 Ashok Agarwal, Hanna Tadros and Eva Tvrdá 17 Reactive Oxygen Species, Oxidative Stress, and Cardiovascular Diseases 281 Fatemeh Sharifpanah and Heinrich Sauer 18 Oxidative Stress and Antioxidant Imbalance: Respiratory Disorders 307 Surinder K. Jindal 19 Oxidative Stress and Type 1 Diabetes 319 Chao Liu, Clayton E. Mathews, and Jing Chen 20 Metabolic Syndrome, Inflammation, and Reactive Oxygen Species in Children and Adults, 329 William E. Winter and Janet H. Silverstein 21 Oxidative Stress in Chronic Pancreatitis 339 Shweta Singh and Bechan Sharma 22 Wound Healing and Hyperbaric Oxygen Therapy Physiology: Oxidative Damage and Antioxidant Imbalance 347 James R. Wilcox and D. Scott Covington 23 Radiobiology and Radiotherapy 357 Justin Wray and Judith Lightsey 24 Chemotherapy-Mediated Pain and Peripheral Neuropathy: Impact of Oxidative Stress and Inflammation 367 Hassan A.N. El-Fawal, Robert Rembisz, Ryyan Alobaidi, and Shaker A. Mousa 25 Grape Polyphenol-rich Products with Antioxidant and Anti-inflammatory Properties 389 Eduarda Fernandes, Marisa Freitas, Renan C. Chisté, Elena Falqué, and Herminia Domínguez 26 Isotonic Oligomeric Proanthocyanidins 403 Hanbo Hu and Donald Armstrong 27 Superoxide Dismutase Mimics and Other Redox-active Therapeutics 415 Ines Batinic-Haberle and Artak Tovmasyan 28 Herbal Medicine: Past, Present, and Future with Emphasis on the Use of Some Common Species 471 Aneela Afzal and Mohammad Afzal 29 Ayurvedic Perspective on Oxidative Stress Management 483 Priyanka M. Jadhav 30 Clinical Trials and Antioxidant Outcomes 493 Carlos Palacio and Arshag D. Mooradian 31 Statistical Approaches to Make Decisions in Clinical Experiments 507 Albert Vexler and Xiwei Chen Index 561

Read more less

Book SynopsisThis book provides an introduction to physical chemistry that is directed toward applications to the biological sciences. Advanced mathematics is not required. This book can be used for either a one semester or two semester course, and as a reference volume by students and faculty in the biological sciences.Table of ContentsPreface to First Edition xv Preface to Second Edition xvii THERMODYNAMICS 1 1. Heat, Work, and Energy 3 1.1 Introduction 3 1.2 Temperature 4 1.3 Heat 5 1.4 Work 6 1.5 Definition of Energy 9 1.6 Enthalpy 11 1.7 Standard States 12 1.8 Calorimetry 13 1.9 Reaction Enthalpies 16 1.10 Temperature Dependence of the Reaction Enthalpy 18 References 19 Problems 20 2. Entropy and Gibbs Energy 23 2.1 Introduction 23 2.2 Statement of the Second Law 24 2.3 Calculation of the Entropy 26 2.4 Third Law of Thermodynamics 28 2.5 Molecular Interpretation of Entropy 29 2.6 Gibbs Energy 30 2.7 Chemical Equilibria 32 2.8 Pressure and Temperature Dependence of the Gibbs Energy 35 2.9 Phase Changes 36 2.10 Additions to the Gibbs Energy 39 Problems 40 3. Applications of Thermodynamics to Biological Systems 43 3.1 Biochemical Reactions 43 3.2 Metabolic Cycles 45 3.3 Direct Synthesis of ATP 49 3.4 Establishment of Membrane Ion Gradients by Chemical Reactions 51 3.5 Protein Structure 52 3.6 Protein Folding 60 3.7 Nucleic Acid Structures 63 3.8 DNA Melting 67 3.9 RNA 71 References 72 Problems 73 4. Thermodynamics Revisited 77 4.1 Introduction 77 4.2 Mathematical Tools 77 4.3 Maxwell Relations 78 4.4 Chemical Potential 80 4.5 Partial Molar Quantities 83 4.6 Osmotic Pressure 85 4.7 Chemical Equilibria 87 4.8 Ionic Solutions 89 References 93 Problems 93 CHEMICAL KINETICS 95 5. Principles of Chemical Kinetics 97 5.1 Introduction 97 5.2 Reaction Rates 99 5.3 Determination of Rate Laws 101 5.4 Radioactive Decay 104 5.5 Reaction Mechanisms 105 5.6 Temperature Dependence of Rate Constants 108 5.7 Relationship Between Thermodynamics and Kinetics 112 5.8 Reaction Rates Near Equilibrium 114 5.9 Single Molecule Kinetics 116 References 118 Problems 118 6. Applications of Kinetics to Biological Systems 121 6.1 Introduction 121 6.2 Enzyme Catalysis: The Michaelis–Menten Mechanism 121 6.3 α-Chymotrypsin 126 6.4 Protein Tyrosine Phosphatase 133 6.5 Ribozymes 137 6.6 DNA Melting and Renaturation 142 References 148 Problems 149 QUANTUM MECHANICS 153 7. Fundamentals of Quantum Mechanics 155 7.1 Introduction 155 7.2 Schrödinger Equation 158 7.3 Particle in a Box 159 7.4 Vibrational Motions 162 7.5 Tunneling 165 7.6 Rotational Motions 167 7.7 Basics of Spectroscopy 169 References 173 Problems 174 8. Electronic Structure of Atoms and Molecules 177 8.1 Introduction 177 8.2 Hydrogenic Atoms 177 8.3 Many-Electron Atoms 181 8.4 Born–Oppenheimer Approximation 184 8.5 Molecular Orbital Theory 186 8.6 Hartree–Fock Theory and Beyond 190 8.7 Density Functional Theory 193 8.8 Quantum Chemistry of Biological Systems 194 References 200 Problems 201 SPECTROSCOPY 203 9. X-ray Crystallography 205 9.1 Introduction 205 9.2 Scattering of X-Rays by a Crystal 206 9.3 Structure Determination 208 9.4 Neutron Diffraction 212 9.5 Nucleic Acid Structure 213 9.6 Protein Structure 216 9.7 Enzyme Catalysis 219 References 222 Problems 223 10. Electronic Spectra 225 10.1 Introduction 225 10.2 Absorption Spectra 226 10.3 Ultraviolet Spectra of Proteins 228 10.4 Nucleic Acid Spectra 230 10.5 Prosthetic Groups 231 10.6 Difference Spectroscopy 233 10.7 X-Ray Absorption Spectroscopy 236 10.8 Fluorescence and Phosphorescence 236 10.9 RecBCD: Helicase Activity Monitored by Fluorescence 240 10.10 Fluorescence Energy Transfer: A Molecular Ruler 241 10.11 Application of Energy Transfer to Biological Systems 243 10.12 Dihydrofolate Reductase 245 References 247 Problems 248 11. Circular Dichroism, Optical Rotary Dispersion, and Fluorescence Polarization 253 11.1 Introduction 253 11.2 Optical Rotary Dispersion 254 11.3 Circular Dichroism 256 11.4 Optical Rotary Dispersion and Circular Dichroism of Proteins 257 11.5 Optical Rotation and Circular Dichroism of Nucleic Acids 259 11.6 Small Molecule Binding to DNA 260 11.7 Protein Folding 263 11.8 Interaction of DNA with Zinc Finger Proteins 266 11.9 Fluorescence Polarization 267 11.10 Integration of HIV Genome Into Host Genome 269 11.11 α-Ketoglutarate Dehydrogenase 270 References 272 Problems 273 12. Vibrations in Macromolecules 277 12.1 Introduction 277 12.2 Infrared Spectroscopy 278 12.3 Raman Spectroscopy 279 12.4 Structure Determination with Vibrational Spectroscopy 281 12.5 Resonance Raman Spectroscopy 283 12.6 Structure of Enzyme–Substrate Complexes 286 12.7 Conclusion 287 References 287 Problems 288 13. Principles of Nuclear Magnetic Resonance and Electron Spin Resonance 289 13.1 Introduction 289 13.2 NMR Spectrometers 292 13.3 Chemical Shifts 293 13.4 Spin–Spin Splitting 296 13.5 Relaxation Times 298 13.6 Multidimensional NMR 300 13.7 Magnetic Resonance Imaging 306 13.8 Electron Spin Resonance 306 References 310 Problems 310 14. Applications of Magnetic Resonance to Biology 315 14.1 Introduction 315 14.2 Regulation of DNA Transcription 315 14.3 Protein–DNA Interactions 318 14.4 Dynamics of Protein Folding 320 14.5 RNA Folding 322 14.6 Lactose Permease 325 14.7 Proteasome Structure and Function 328 14.8 Conclusion 329 References 329 STATISTICAL MECHANICS 331 15. Fundamentals of Statistical Mechanics 333 15.1 Introduction 333 15.2 Kinetic Model of Gases 333 15.3 Boltzmann Distribution 338 15.4 Molecular Partition Function 343 15.5 Ensembles 346 15.6 Statistical Entropy 349 15.7 Helix-Coil Transition 350 References 353 Problems 354 16. Molecular Simulations 357 16.1 Introduction 357 16.2 Potential Energy Surfaces 358 16.3 Molecular Mechanics and Docking 364 16.4 Large-Scale Simulations 365 16.5 Molecular Dynamics 367 16.6 Monte Carlo 373 16.7 Hybrid Quantum/Classical Methods 373 16.8 Helmholtz and Gibbs Energy Calculations 375 16.9 Simulations of Enzyme Reactions 376 References 379 Problems 379 SPECIAL TOPICS 383 17. Ligand Binding to Macromolecules 385 17.1 Introduction 385 17.2 Binding of Small Molecules to Multiple Identical Binding Sites 385 17.3 Macroscopic and Microscopic Equilibrium Constants 387 17.4 Statistical Effects in Ligand Binding to Macromolecules 389 17.5 Experimental Determination of Ligand Binding Isotherms 392 17.6 Binding of Cro Repressor Protein to DNA 395 17.7 Cooperativity in Ligand Binding 397 17.8 Models for Cooperativity 402 17.9 Kinetic Studies of Cooperative Binding 406 17.10 Allosterism 408 References 412 Problems 412 18. Hydrodynamics of Macromolecules 415 18.1 Introduction 415 18.2 Frictional Coefficient 415 18.3 Diffusion 418 18.4 Centrifugation 421 18.5 Velocity Sedimentation 422 18.6 Equilibrium Centrifugation 424 18.7 Preparative Centrifugation 425 18.8 Density Centrifugation 427 18.9 Viscosity 428 18.10 Electrophoresis 429 18.11 Peptide-Induced Conformational Change of a Major Histocompatibility Complex Protein 432 18.12 Ultracentrifuge Analysis of Protein–DNA Interactions 434 References 435 Problems 435 19. Mass Spectrometry 441 19.1 Introduction 441 19.2 Mass Analysis 441 19.3 Tandem Mass Spectrometry (MS/MS) 445 19.4 Ion Detectors 445 19.5 Ionization of the Sample 446 19.6 Sample Preparation/Analysis 449 19.7 Proteins and Peptides 450 19.8 Protein Folding 452 19.9 Other Biomolecules 455 References 455 Problems 456 APPENDICES 457 Appendix 1. Useful Constants and Conversion Factors 459 Appendix 2. Structures of the Common Amino Acids at Neutral pH 461 Appendix 3. Common Nucleic Acid Components 463 Appendix 4. Standard Gibbs Energies and Enthalpies of Formation at 298 K, 1 atm, pH 7, and 0.25 M Ionic Strength 465 Appendix 5. Standard Gibbs Energy and Enthalpy Changes for Biochemical Reactions at 298 K, 1 atm, pH 7.0, pMg 3.0, and 0.25M Ionic Strength 467 Appendix 6. Introduction to Electrochemistry 469 A6-1 Introduction 469 A6-2 Galvanic Cells 469 A6-3 Standard Electrochmical Potentials 471 A6-4 Concentration Dependence of the Electrochemical Potential 472 A6-5 Biochemical Redox Reactions 473 References 473 Index 475

Read more less

Book SynopsisCovering a key topic due to growing research into the role of signaling mechanisms in toxicology, this book focuses on practical approaches for informatics, big data, and complex data sets. Combines fundamentals / basics with experimental applications that can help those involved in preclinical drug studies and translational research Includes detailed presentations of study methodology and data collection, analysis, and interpretation Discusses tools like experimental design, sample handling, analytical measurement techniques Table of ContentsList of Contributors xv About the Editors xvii Preface xix 1 Introduction to Cellular Signal Transduction: The Connection Between a Biological System and Its Surroundings 1Jonathan W. Boyd, Richard R. Neubig, Alice Han, and Maren Prediger 1.1 Starting Big, but Ending Small 3 1.1.1 Key Features of Signal Transduction 3 1.2 Responding to Our Environment: Sensory Perception Begins and Ends with Signal Transduction 4 1.2.1 Taste (Gustation) 4 1.2.2 Smell (Olfaction) 5 1.2.3 Sight (Vision) 6 1.2.4 Sound (Audition) 6 1.2.5 Touch (Somatosensation) 8 1.3 Primary Transport Systems Involved in Signal Transduction 8 1.3.1 Ion Channels, Transporters, and Ion Pumps 9 1.3.2 Receptors 10 1.3.3 Endocytosis 10 1.3.4 Exosomes 11 1.4 Key Organelles Involved in Signal Transduction 12 1.4.1 Mitochondria 12 1.4.2 Endoplasmic Reticulum 14 1.4.3 Nucleus 15 References 16 2 Mechanisms of Cellular Signal Transduction 21Richard R. Neubig, Jonathan W. Boyd, Julia A. Mouch, and Nicole Prince 2.1 Posttranslational Modifications and Their Roles in Signal Transduction 22 2.1.1 Phosphorylation 22 2.1.2 Acylation 24 2.1.3 Alkylation 25 2.1.4 Glycosylation 26 2.1.5 Other PTMs 27 2.2 Receptors 27 2.3 Receptor Signaling Mechanisms 29 2.3.1 Basic Principles of Signal Transduction Mechanisms 29 2.3.1.1 Selectivity and Recognition 31 2.3.1.2 Flexible Modularity 31 2.3.1.3 Molecular Switches 34 2.3.1.4 GPCRs and Second Messengers 36 2.3.1.5 Amplification 39 2.3.1.6 Turn‐Off Mechanisms 40 2.3.1.7 Localization 40 2.3.1.8 Biased Signaling/Functional Selectivity 41 2.4 Receptor Tyrosine Kinases 42 2.5 Steroid Receptors 43 2.6 Reactive Oxygen Species (ROS) 43 2.7 Summary 44 References 44 3 From Cellular Mechanisms to Physiological Responses: Functional Signal Integration Across Multiple Biological Levels 49Robert H. Newman 3.1 Introduction 49 3.2 Cellular Information Flow: Mechanisms of Cellular Signal Integration and Regulation 50 3.2.1 The InsR‐aPKC‐NF‐κB Signaling Axis 51 3.2.2 Modes of Regulation in InsR‐PKC‐NF‐κB Signaling Axis 54 3.2.3 Transcriptional Regulation 54 3.2.4 Regulating the Regulators: Phosphatase‐Mediated Regulation of Signaling Molecules 59 3.3 Crosstalk and Functional Signal Integration in Response to Insulin in Hepatocytes 60 3.4 Systemic Signal Integration 65 3.4.1 Pancreatic β‐Cells 65 3.4.2 Skeletal Muscles 66 3.4.3 Adipose Tissue 67 3.5 Dysregulation of Insulin Signaling in the Etiology of Type 2 Diabetes 67 References 69 4 Signal Transduction in Disease: Relating Cell Signaling to Morbidity and Mortality 73Patricia E. Ganey and Sean A. Misek 4.1 Introduction 73 4.2 Fibrosis as an Example of Complex Signaling 75 4.2.1 Development of Liver Fibrosis 75 4.2.2 Animal Models of Hepatic Fibrosis 76 4.2.3 Activation of Hepatic Stellate Cells 77 4.2.4 Epithelial‐to‐Mesenchymal Transition (EMT) 78 4.2.5 Other Cellular Interactions in Fibrosis 78 4.2.6 Intracellular Signaling Pathways Critical to Liver Fibrosis 80 4.2.6.1 TGF‐β1 80 4.2.6.2 Kinase Pathways Involved in Fibrotic Responses 82 4.2.6.3 HIF‐1α 83 4.2.6.4 miRNA 84 4.2.6.5 Toll‐Like Receptors (TLRs) 84 4.3 Cancer Drug Resistance: Complex Cellular and Population Changes 85 4.3.1 Genomic Resistance Mechanisms 85 4.3.2 Non‐genomic Mechanisms 88 4.3.3 Non‐cancer Drug Resistance Paradigms 88 4.3.4 Tumor Heterogeneity as a Driver of Drug Resistance 89 4.3.5 Mutational Drivers of Drug Resistance 90 4.3.6 Drug‐Induced Rewiring of Signaling Networks as a Mechanism of Drug Resistance 91 4.3.7 Parallel Pathways and Combination Treatments 93 4.3.8 Epigenetic Mechanisms of Drug Resistance 95 4.3.9 Summary of Cancer Drug Resistance 97 4.4 Summary 98 References 98 5 Experimental Design in Signal Transduction 113Weimin Gao, Meghan Cromie, Qian Wang, Zhongwei Liu, Song Tang, and Julie Vrana Miller 5.1 Overview of Basic Experimental Design 113 5.1.1 Independent Sample t Test 114 5.1.2 Completely Randomized Analysis of Variance (ANOVA) 114 5.1.3 t Test for Dependent Sample Design 115 5.1.4 Randomized Block Design 115 5.1.5 Completely Randomized Factorial Design 116 5.1.6 Summary 116 5.2 Aseptic Technique 116 5.2.1 Sterile Work Environment and Laminar‐Flow Hood 117 5.2.2 Good Personal Hygiene Practices 117 5.2.3 Sterile Reagents and Materials 118 5.2.4 Sterile Handling 118 5.3 Biological Sample Collection, Processing, and Pretreatment Technology 119 5.3.1 Sample Collection 119 5.3.1.1 Sample Collection In Vivo 119 5.3.1.2 Cell Culture In Vitro 120 5.3.2 Sample Processing 121 5.3.2.1 DNA Isolation 121 5.3.2.2 RNA Extraction 121 5.3.2.3 Protein Extraction 122 5.4 Sample Storage 122 5.5 Common In Vitro Studies in Toxicology/Pharmacology 123 5.5.1 Cytotoxicity Studies 123 5.5.2 Viability Assays 123 5.5.2.1 Trypan Blue 123 5.5.2.2 Erythrosin 124 5.5.2.3 Crystal Violet Staining 124 5.5.2.4 Neutral Red Staining 125 5.5.3 Survival Assays 125 5.5.3.1 Clonogenic or Colony Formation Assay 125 5.5.3.2 Cell Cycle Analysis: Flow Cytometry 126 5.5.4 DNA Damage Assays 126 5.5.4.1 Comet Assay 127 5.5.4.2 Sister Chromatid Exchange Assay 127 5.5.5 Southern Blot and DNA Sequencing 127 5.5.5.1 Southern Blot 127 5.5.5.2 DNA Sequencing 128 5.5.5.3 Transfection and Gene Silencing 128 5.5.6 RNA Quantification and Identification 128 5.5.6.1 Northern Blot 128 5.5.6.2 Promoter Deletion Analysis 129 5.5.6.3 RNase Protection Assay 129 5.5.7 Gene Expression 129 5.5.7.1 Quantitative Real‐Time Polymerase Chain Reaction (qRT‐PCR) 130 5.5.7.2 Microarray 130 5.5.8 Protein‐Related Assays 131 5.5.8.1 Bradford Assay 131 5.5.8.2 Enzyme-Linked Immunosorbent Assay (ELISA) 131 5.5.8.3 Western Blot and 2D Gel Electrophoresis 131 5.5.8.4 Immunolocalization 132 5.5.8.5 Immunoprecipitation Assays 132 5.5.8.6 Chromatin Immunoprecipitation (ChIP) 132 5.5.9 Epigenetics 133 5.5.9.1 Bisulfite Pyrosequencing 133 5.5.9.2 ChIP‐on‐Chip 133 5.5.9.3 Multiplex miRNA Profiling 134 5.6 Common In Vivo Studies in Toxicology 134 5.6.1 Toxicological Endpoints 134 5.6.1.1 Maximum Tolerated Dose (MTD) 134 5.6.1.2 Acute, Subchronic, and Chronic Toxicity 135 5.6.1.3 Reproductive and Developmental Toxicity 135 5.6.1.4 Genotoxicity and Carcinogenicity Studies 136 5.6.2 Routes of Exposure 136 5.6.2.1 Oral, Dermal, and Inhalation 136 5.6.2.2 Exposure via Injection 137 5.6.3 Animal Models 137 5.6.3.1 Rodent Studies 137 5.6.3.2 Other Studies 138 5.7 Basic Advantages and Disadvantages Associated with Sample Types 138 5.8 Human Epidemiology Studies 138 5.8.1 Nonexperimental Studies 139 5.8.2 Experimental Studies 139 5.8.3 Molecular Epidemiology 140 5.9 Examples of Tox‐ and Pharm‐Based Experiments Relevant to Signal Transduction Endpoints 140 5.9.1 Cytotoxicity 141 5.9.1.1 Nicotine‐Derived Nitrosamine Ketone (NNK) 141 5.9.1.2 Doxorubicin (DOX) 142 5.9.1.3 Curcumin 142 5.9.1.4 Combination Effects of Cisplatin and/or Leptomycin B (LMB) 143 5.9.2 DNA Damage 143 5.9.3 Cell Cycle and Apoptosis 145 5.9.4 ROS Induction in A549 Cells After LMB and Epigallocatechin Gallate (EGCG) Treatment 146 5.9.5 Signaling Pathways 146 5.9.5.1 Metabolizing Alterations After Chemical Exposure 146 5.9.5.2 p53 Signaling Pathways 148 5.9.6 Protein Kinase B (Akt/PKB)/Mechanistic Target of Rapamycin (mTOR) Pathway Analysis Using Multiblot 150 5.9.7 Discovery of Unrecognized Pathways/Molecules Using Proteomics 150 5.10 Coupling Experimental Results Within the Larger Literature Framework to Generate Information 152 5.10.1 Cell Proliferation–EGFR Pathway 152 5.10.2 Cell Cycle 154 5.10.3 Signal‐Mediated Cell Death 156 5.10.4 Reactive Oxygen Species (ROS) 161 References 162 6 Techniques for Measuring Cellular Signal Transduction 171Julie Vrana Miller, Weimin Gao, Meghan Cromie, and Zhongwei Liu 6.1 Introduction 171 6.2 High‐Throughput Versus High‐Content Data 172 6.2.1 Ergodic and Nonergodic Systems 173 6.3 Methods to Measure Signal Transduction Data 173 6.3.1 Microscopy 173 6.3.1.1 Widefield Epifluorescence Microscopy 173 6.3.1.2 Confocal Microscopy 174 6.3.1.3 Immunohistochemistry 175 6.3.1.4 FRET 178 6.3.2 Enzyme‐Linked Immunosorbent Assay (ELISA) 179 6.3.2.1 Competitive ELISA 179 6.3.2.2 Sandwich ELISA 180 6.3.2.3 Direct Cellular ELISA 180 6.3.2.4 Multiplex Suspension Array Assays 181 6.3.2.5 Electrochemiluminescence (ECL) Array 182 6.3.3 Gel Electrophoresis 183 6.3.4 Western Blot 183 6.3.5 Protein Nuclear Magnetic Resonance (NMR) 186 6.4 Techniques to Generate Large Datasets for Signal Transduction Network Analysis 187 6.4.1 ’‐omics Using Mass Spectrometry 187 6.4.1.1 Separation Techniques 188 6.4.1.2 Phosphoprotein Enrichment for Phosphoproteomics: IMAC, MOAC, and SMOAC 189 6.4.1.3 Quantitation with Chemical Tags: iTRAQ and TMT 190 6.4.2 RNA Sequencing (RNA‐Seq) 190 6.5 Bioenergetics 191 6.5.1 Oxygen Consumption 191 6.5.2 Reactive Oxygen Species (ROS) Fluorescent Probes 192 6.5.3 ATP Assays 193 6.5.4 Nicotinamide Adenine Dinucleotide (NADH) Assay 193 6.5.5 Mitochondrial Membrane Potential 194 6.6 Relating Signaling to Cellular Outcome Using Relevant Assays 194 6.6.1 MTT/MTS/WST Assays 194 6.6.2 LDH Assay 195 6.6.3 Resazurin Assay (Alamar Blue) 196 6.6.4 Cell Death: Plasma Membrane Degradation Assay 196 6.7 Summary 196 References 197 7 Computational Methods for Signal Transduction: A Network Approach 201Giovanni Scardoni, Gabriele Tosadori, John Morris, Sakshi Pratap, Carlo Laudanna, and Alice Han 7.1 Introduction 201 7.2 Network Construction 203 7.2.1 Introduction to Network Construction 203 7.2.2 Network Construction from a Probe 203 7.2.3 Mapping Methodology 204 7.2.4 Small Networks 208 7.2.5 Large Networks 208 7.3 Facing the Network Analysis 209 7.3.1 Centralities Definition and Description 211 7.3.2 Global Parameters 211 7.3.2.1 Diameter (ΔG) 211 7.3.2.2 Average Distance 212 7.3.3 Local Parameters 213 7.3.3.1 Degree 213 7.3.3.2 Eccentricity 214 7.3.3.3 Closeness 215 7.3.3.4 Radiality 215 7.3.3.5 Centroid Value 217 7.3.3.6 Stress 219 7.3.3.7 S.‐P. Betweenness 219 7.3.3.8 Eigenvector 220 7.3.3.9 Bridging Centrality 221 7.3.3.10 Edge Betweenness 221 7.3.3.11 Normalization and Relative Centralities 222 7.3.4 Clusters 222 7.4 Employing Centrality Analysis to Evaluate Stressed Biological Systems 224 7.5 Interference Notion: How to Perform Virtual Knockout Experiments on Biological Networks 226 7.5.1 Integrating Experimental Dataset into a Topological Analysis 227 7.5.2 Integrating Expression or Activation Levels as Nodes Attributes 228 7.5.3 Edge Attributes as Distance in a Computation 228 7.6 Network Analysis Software 229 7.6.1 Cytoscape and Its Apps 229 7.6.1.1 structureViz/RINalyzer 231 7.6.1.2 CentiScaPe 231 7.6.1.3 PesCa 231 7.6.1.4 Interference 231 7.6.1.5 clusterMaker2 232 7.6.1.6 chemViz 233 7.6.2 Other Tools 233 7.6.2.1 Gephi 233 7.6.2.2 D3.js 234 7.6.2.3 VisANT 234 7.7 Conclusions 236 References 236 8 A Toxicological Application of Signal Transduction: Early Cellular Changes Can Be Indicative of Toxicity 239Julie Vrana Miller, Nicole Prince, Julia A. Mouch, and Jonathan W. Boyd 8.1 Introduction 239 8.2 Classification of Toxic Agent and Exposure Effects: A Toxicological Perspective 240 8.2.1 Dose–Response for Chemical Exposure Toxicity Testing and Risk Assessment 240 8.2.2 Chemical Mixtures 241 8.2.3 Mode of Action Versus Mechanism of Action 242 8.3 Early Cellular Changes Post‐exposure 244 8.3.1 Intracellular Signaling Perturbations Associated with Exposure 245 8.3.2 Bioenergetic Changes Post‐exposure 248 8.3.3 Time Scale of Exposure Effects 249 8.4 Experimentally Testing Early Cellular Changes that May Contribute to Exposure Sensing and Response 250 8.4.1 Paradigm Shift Toward In Vitro Cell Culture 250 8.4.2 Real‐Time In Vitro Assays to Measure Early Cellular Changes 251 8.4.2.1 Using NADH and Oxygen Consumption to Predict ATP Generation 252 8.4.3 Prediction of Posttranslational Phosphorylation Response for Mixtures 253 8.4.3.1 Using Bliss Independence (Response Addition) to Predict Relative Phosphorylation During Critical Signaling Events 253 References 256 Appendix A 262 9 Future Research in Signaling 267Jonathan W. Boyd, Nicole Prince, and Marc Birringer 9.1 Translational Research and a Spatiotemporal Understanding of Signal Transduction 267 9.2 Integrating Second Messengers into Signal Transduction 270 9.3 Understanding Crosstalk in Signal Transduction 272 9.4 Posttranslational Modifications (PTMs) and Target Identification in Signal Transduction 274 9.5 Epigenetic Endpoints in Signal Transduction 276 9.6 The Integration of Nutrition and Signal Transduction 278 9.6.1 Cellular AMPK Signaling 281 9.6.2 Cellular TOR Signaling 282 9.6.3 Gut Microbiota 282 9.6.4 The Integration of Endocrine Gut Signaling 283 References 284 Index 291

Read more less

Book SynopsisPromoting a continued and much-needed renaissance in biopharmaceutical manufacturing, this book covers the different strategies and assembles top-tier technology experts to address the challenges of antibody purification. Updates existing topics and adds new ones that include purification of antibodies produced in novel production systems, novel separation technologies, novel antibody formats and alternative scaffolds, and strategies for ton-scale manufacturing Presents new and updated discussions of different purification technologies, focusing on how they can address the capacity crunch in antibody purification Emphasizes antibodies and innovative chromatography methods for processingTable of ContentsPreface xxiii List of Contributors xxvii 1 Downstream Processing of Monoclonal Antibodies: Current Practices and Future Opportunities 1Brian Kelley 1.1 Introduction 1 1.2 A Brief History of Current Good Manufacturing Process mAb and Intravenous Immunoglobulin Purification 2 1.3 Current Approaches in Purification Process Development: Impact of Platform Processes 4 1.4 Typical Unit Operations and Processing Alternatives 7 1.5 VLS Processes: Ton‐Scale Production and Beyond 10 1.6 Process Validation 12 1.7 Product Life Cycle Management 13 1.8 Future Opportunities 16 1.9 Conclusions 18 Acknowledgments 19 References 19 2 The Development of Antibody Purification Technologies 23John Curling 2.1 Introduction 23 2.2 Purification of Antibodies by Chromatography Before Protein A 25 2.3 Antibody Purification After 1975 28 2.4 Additional Technologies for Antibody Purification 31 2.5 Purification of mAbs Approved in North America and Europe 34 2.6 Current Antibody Process Technology Developments 40 Acknowledgments 45 References 46 3 Harvest and Recovery of Monoclonal Antibodies: Cell Removal and Clarification 55Abhinav A. Shukla and Eric Suda 3.1 Introduction 55 3.2 Centrifugation 59 3.3 Microfiltration 62 3.4 Depth Filtration 67 3.5 Flocculation 70 3.6 Absolute Filtration 71 3.7 Expanded Bed Adsorption Chromatography 73 3.8 Harvesting in Single‐Use Manufacturing 74 3.9 Comparison of Harvest and Clarification Unit Operations 74 References 76 4 Next‐Generation Clarification Technologies for the Downstream Processing of Antibodies 81Nripen Singh and Srinivas Chollangi 4.1 Introduction 81 4.2 Impurity Profiles in Cell Cultures 83 4.3 Precipitation 84 4.4 Affinity Precipitation 89 4.5 Flocculation 90 4.6 Toxicity of Flocculants and Precipitants and Their Residual Clearance 96 4.7 Depth Filtration 97 4.8 Considerations for the Implementation of New Clarification Technologies 102 4.9 Conclusions and Future Perspectives 103 Acknowledgments 104 References 104 5 Protein A‐Based Affinity Chromatography 113Suresh Vunnum, Ganesh Vedantham and Brian Hubbard 5.1 Introduction 113 5.2 Properties of Protein A and Commercially Available Protein A Resins 114 5.3 Protein A Chromatography Step Development 118 5.4 Additional Considerations During Development and Scale‐Up 123 5.5 Virus Removal/Inactivation 127 5.6 Validation and Robustness 128 5.7 Conclusions 129 Acknowledgment 130 References 130 6 Purification of Human Monoclonal Antibodies: Non‐Protein A Strategies 135Alahari Arunakumari and Jue Wang 6.1 Introduction 135 6.2 Integrated Process Design for Human Monoclonal Antibody Production 136 6.3 Purification Process Designs for HuMabs 136 6.4 Conclusions 149 Acknowledgments 151 References 152 7 Hydrophobic Interaction Chromatography for the Purification of Antibodies 155Judith Vajda and Egbert Muller 7.1 Introduction 155 7.2 HIC With mAbs 156 7.3 HIC with Membrane Adsorbers 173 7.4 Future Perspectives 174 References 175 8 Purification of Monoclonal Antibodies by Mixed‐Mode Chromatography 181Pete Gagnon 8.1 Introduction 181 8.2 A Brief History 182 8.3 Prerequisites for Industrial Implementation 183 8.4 Mechanisms, Screening, and Method Development 185 8.5 Capture Applications 192 8.6 Polishing Applications 193 8.7 Sequential Capture/Polishing Applications 193 8.8 Future Prospects 193 Acknowledgments 194 References 194 9 Advances in Technology and Process Development for Industrial‐Scale Monoclonal Antibody Purification 199Nuno Fontes and Robert Van Reis 9.1 Introduction 199 9.2 Affinity Purification Platform 200 9.3 Advances in the Purification of mAbs by CEX Chromatography 201 9.4 High‐Performance Tangential Flow Filtration 209 9.5 A New Nonaffinity Platform 211 References 213 10 Alternatives to Packed‐Bed Chromatography for Antibody Extraction and Purification 215Jorg Thommes, Richard M. Twyman and Uwe Gottschalk 10.1 Introduction 215 10.2 Increasing the Selectivity of Harvest Procedures: Flocculation and Filter Aids 216 10.3 Solutions for Antibody Extraction, Concentration, and Purification 218 10.4 Antibody Purification and Formulation Without Chromatography 220 10.5 Membrane Adsorbers 223 10.6 Conclusions 225 References 226 11 Process‐Scale Precipitation of Impurities in Mammalian Cell Culture Broth 233Judy Glynn 11.1 Introduction 233 11.2 Precipitation of DNA and Protein—Other Applications 235 11.3 A Comprehensive Evaluation of Precipitants for the Removal of Impurities 236 11.4 Industrial‐Scale Precipitation 241 11.5 Cost of Goods Comparison 243 11.6 Summary 244 Acknowledgments 244 References 244 12 Charged Ultrafiltration and Microfiltration Membranes for Antibody Purification 247Mark R. Etzel and Abhiram Arunkumar 12.1 Introduction 247 12.2 Charged UF Membranes 248 12.3 Concentration Polarization and Permeate Flux 248 12.4 Stagnant Film Model 249 12.5 Sieving Coefficient 250 12.6 Mass Transfer Coefficient 251 12.7 Mass Balance Models 251 12.8 Scale‐Up Strategies and the Constant Wall Concentration (Cw) Approach 253 12.9 Membrane Cascades 255 12.10 Protein Fractionation Using Charged UF Membranes 256 12.11 Case Study 257 12.12 Charged MF Membranes 259 12.13 Virus Clearance 260 12.14 Salt Tolerance 261 12.15 Conclusions 264 Acknowledgments 264 References 264 13 Disposable Prepacked‐Bed Chromatography for Downstream Purification: Form, Fit, Function, and Industry Adoption 269Stephen K. Tingley 13.1 Introduction 269 13.2 Development‐Scale Prepacked Column Applications 271 13.3 Process‐Scale Prepacked Column Applications 275 13.4 Basic Technical Datasets 278 13.5 Independent Industry Assessments of “Fit for Purpose” 285 13.6 Case Study 1: Cation‐Exchange Polishing Chromatography 285 13.7 Case Study 2: Prepacked Columns for Pilot‐/Large‐Scale Bioprocessing 287 13.8 Prepacked Columns—Fit 292 13.9 The Economics of Prepacked Column Technologies 295 13.10 The Implementation of Disposable Prepacked Columns 297 13.11 Conclusions 300 References 301 14 Integrated Polishing Steps for Monoclonal Antibody Purification 303Sanchayita Ghose, Mi Jin, Jia Liu, John Hickey and Steven Lee 14.1 Introduction 303 14.2 Polishing Steps for Antibody Purification 304 14.3 Integration of Polishing Steps 316 14.4 Conclusions 320 Acknowledgment 320 References 320 15 Orthogonal Virus Clearance Applications in Monoclonal Antibody Production 325Joe X. Zhou 15.1 Introduction 325 15.2 Model Viruses and Virus Assays 326 15.3 Virus Clearance Strategies at Different Development Stages 328 15.4 Orthogonal Virus Clearance During mAb Production 328 15.5 Conclusions and Future Perspectives 338 Acknowledgments 339 References 339 16 Development of a Platform Process for the Purification of Therapeutic Monoclonal Antibodies 343Yuling Li, Min Zhu, Haibin Luo and Justin R. Weaver 16.1 Introduction 343 16.2 Chromatography Steps in the Platform Process 345 16.3 Virus Inactivation 352 16.4 UF/DF Platform Considerations 352 16.5 Platform Development: Virus Filtration and Bulk Fill 354 16.6 Addressing Future Challenges in Downstream Processing 356 16.7 Representative Platform Processes 356 16.8 Developing a Virus Clearance Database Using a Platform Process 359 16.9 Summary 361 References 361 17 The Evolution of Platform Technologies for the Downstream Processing of Antibodies 365Lee Allen 17.1 Introduction 365 17.2 The Definition of a Platform Purification Process 366 17.3 The Dominant Process Design 367 17.4 The Evolution of Unit Operations 372 17.5 Adapting the Platform Process for Product‐Specific Issues 382 17.6 Future Perspectives—Future Evolutionary Pathways 382 17.7 Concluding Remarks 383 Acknowledgments 384 References 384 18 Countercurrent Chromatography for the Purification of Monoclonal Antibodies, Bispecific Antibodies, and Antibody–Drug Conjugates 391Thomas Muller‐Spath and Massimo Morbidelli 18.1 Introduction 391 18.2 Chromatography to Reduce Product Heterogeneity 392 18.3 Definition of Performance Parameters 394 18.4 Gradient Chromatography for Biomolecules 394 18.5 Continuous and Countercurrent Chromatography 395 18.6 Multicolumn Countercurrent Solvent Gradient Purification 397 18.7 Scalability of Multicolumn Countercurrent Chromatography 403 18.8 Online Process Monitoring for Multicolumn Countercurrent Chromatography 404 18.9 Outlook 405 References 405 19 The Evolution of Continuous Chromatography: From Bulk Chemicals to Biopharma 409Marc Bisschops 19.1 Introduction 409 19.2 Continuous Chromatography in Traditional Process Industries 410 19.3 Continuous Chromatography in the Biopharmaceutical Industry 413 19.4 Advantages of Continuous Chromatography 420 19.5 Implementation Aspects of Continuous Chromatography 422 19.6 Regulatory Aspects 424 19.7 Conclusions 426 References 427 20 Accelerated Seamless Antibody Purification: Simplicity is Key 431Benoit Mothes 20.1 Introduction 431 20.2 Accelerated Seamless Antibody Purification 432 20.3 Advantages of the ASAP Process 437 20.4 Scaling Up the ASAP Process 438 20.5 New Perspectives 440 20.6 Conclusion 442 Acknowledgments 442 Suggested Reading 443 21 Process Economic Drivers in Industrial Monoclonal Antibody Manufacture 445Suzanne S. Farid 21.1 Introduction 445 21.2 Challenges When Striving for the Cost‐Effective Manufacture of mAbs 446 21.3 Cost Definitions and Benchmark Values 448 21.4 Economies of Scale 450 21.5 Overall Process Economic Drivers 453 21.6 DSP Drivers At High Titers 457 21.7 Process Economic Trade‐Offs for Downstream Process Bottlenecks 459 21.8 Summary and Outlook 461 References 462 22 Design and Optimization of Manufacturing 467Andrew Sinclair 22.1 Introduction 467 22.2 Process Design and Optimization 468 22.3 Modeling Approaches 470 22.4 Process Modeling in Practice 481 22.5 Impact of the Process on the Facility 491 Acknowledgments 492 References 492 23 Smart Design for an Efficient Facility With a Validated Disposable System 495Joe X. Zhou, Jason Li, Michael Cui and Haojun Chen 23.1 Design and Optimization of a Manufacturing Facility 495 23.2 Validation of a Disposable System 507 23.3 Conclusion 512 Acknowledgments 512 References 512 24 High‐Throughput Screening and Modeling Technologies for Process Development in Antibody Purification 515Tobias Hahn, Thiemo Huuk and Jurgen Hubbuch 24.1 Introduction 515 24.2 Adsorption Isotherms 516 24.3 Batch Chromatography 519 24.4 Column Chromatography 524 References 532 25 Downstream Processing of Monoclonal Antibody Fragments 537Mariangela Spitali 25.1 Introduction 537 25.2 Production of Antibody Fragments for Therapeutic Use 538 25.3 Downstream Processing 539 25.4 Improving the Pharmacological Characteristics of Antibody Fragments 552 25.5 Conclusions 553 Acknowledgments 555 References 555 26 Downstream Processing of Fc Fusion Proteins, Bispecific Antibodies, and Antibody–Drug Conjugates 559Abhinav A. Shukla and Carnley L. Norman 26.1 Introduction 559 26.2 Biochemical Properties 562 26.3 Purification From Mammalian Expression Systems 576 26.4 Purification From Microbial Production Systems 585 26.5 Future Innovations 587 Acknowledgment 589 References 589 27 Manufacturing Concepts for Antibody–Drug Conjugates 595Thomas Rohrer 27.1 Introduction 595 27.2 Targeting Components 596 27.3 Cytotoxic Drugs 600 27.4 Chemically Labile Linkers 602 27.5 General Process Overview 602 27.6 Facility Design and Supporting Technology 604 27.7 Single‐Use Equipment 607 27.8 Manufacturing ADCs 608 27.9 Analytical Support for ADC Manufacturing 609 27.10 Raw Materials Supply Chain 611 27.11 Conclusion 611 Acknowledgments 613 References 613 28 Purification of IgM and IgA 615Charlotte Cabanne and Xavier Santarelli 28.1 Introduction 615 28.2 Purification of IgM 616 28.3 Purification of IgA 621 28.4 Conclusion 623 Acknowledgments 623 References 623 29 Purification of Monoclonal Antibodies From Plants 631Zivko L. Nikolov, Jeffrey T. Regan, Lynn F. Dickey and Susan L. Woodard 29.1 Introduction 631 29.2 Antibody Production in Plants 632 29.3 Downstream Processing of Antibodies Produced in Plants 636 29.4 Purification of Plant‐Derived Antibodies Using Protein A Resins 641 29.5 Purification of Plant‐Derived Antibodies Using Non‐Protein A Media 642 29.6 Polishing Steps 643 29.7 Conclusions 645 Acknowledgment 645 References 645 30 Very‐Large‐Scale Production of Monoclonal Antibodies in Plants 655Johannes F. Buyel, Richard M. Twyman and Rainer Fischer 30.1 Introduction 655 30.2 Process Schemes for mAb Production in Plants 656 30.3 Scalable Process Models 661 30.4 Process Adaptation for VLS Requirements 663 30.5 Translation into VLS Applications 666 References 667 31 Trends in Formulation and Drug Delivery for Antibodies 673Hanns‐Christian Mahler and Roman Mathas 31.1 Introduction 673 31.2 Degradation Pathways 674 31.3 Physical Instability 674 31.4 Chemical Instability 676 31.5 How to Achieve Product Stability 678 31.6 Developability: Molecule Selection and Elimination of Degradation Hotspots 679 31.7 Stabilizing an Antibody in a Liquid Formulation 679 31.8 Stabilizing an Antibody by Drying 681 31.9 Choice of Adequate Primary Packaging 682 31.10 Minimizing Stress During Drug Product Processing 683 31.11 Implementation of a Formulation Strategy 685 31.12 Hot Topics 685 31.13 Summary 689 References 690 32 Antibody Purification: Drivers of Change 699Narahari Pujar, Duncan Low and Rhona O’Leary 32.1 Introduction 699 32.2 The Changing Regulatory Environment—Pharmaceutical Manufacturing for the 21st Century 701 32.3 Technology Drivers—Advances and Innovations 707 32.4 Economic Drivers 708 32.5 Conclusions 711 Acknowledgment 712 References 713 Index 717

Read more less

Book SynopsisPhotosynthesis and the complex network within plants is becoming more important than ever, because of the earth's changing climate. In addition, the concepts can be used in other areas, and the science itself is useful in practical applications in many branches of science, including medicine, biology, biophysics, and chemistry. This original, groundbreaking work by two highly experienced and well-known scientists introduces a new and different approach to thinking about living organisms, what we can learn from them, and how we can use the concepts within their scientific makeup in practice. This book describes the principles of complex signaling networks enabling spatiotemporally-directed macroscopic processes by the coupling of systems leading to a bottom-up information transfer in photosynthetic organisms. Top-down messengers triggered by macroscopic actuators like sunlight, gravity, environment or stress lead to an activation of the gene regulation on the molecular level. Table of ContentsAbstract ix Foreward 1 xi Foreward 2 xiii Preface xv 1 Multiscale Hierarchical Processes 1 1.1 Coupled Systems, Hierarchy and Emergence 2 1.2 Principles of Synergetics 12 1.3 Axiomatic Motivation of Rate Equations 15 1.4 Rate Equations in Photosynthesis 19 1.5 Top down and Bottom up Signaling 23 2 Photophysics, Photobiology and Photosynthesis 27 2.1 Light Induced State Dynamics 27 2.2 Rate Equations and Excited State Dynamics in Coupled Systems 41 2.3 Light-Harvesting, Energy and Charge Transfer and Primary Processes of Photosynthesis 64 2.4 Antenna Complexes in Photosynthetic Systems 70 2.5 Fluorescence Emission as a Tool for Monitoring PS II Function 91 2.6 Excitation Energy Transfer and Electron Transfer Steps in Cyanobacteria Modeled with Rate Equations 93 2.7 Excitation Energy and Electron Transfer in Higher Plants Modeled with Rate Equations 105 2.8 Nonphotochemical Quenching in Plants and Cyanobacteria 114 2.9 Hierarchical Architecture of Plants 118 3 Formation and Functional Role of Reactive Oxygen Species (ROS) 123 3.1 Generation, Decay and Deleterious Action of ROS 125 3.2 Monitoring of ROS 137 3.3 Signaling Role of ROS 151 4 ROS Signaling in Coupled Nonlinear Systems 157 4.1 Signaling by Superoxide and Hydrogen Peroxide in Cyanobacteria 158 4.2 Signaling by Singlet Oxygen and Hydrogen Peroxide in Eukaryotic Cells and Plants 163 4.3 ROS and Cell Redox Control and Interaction with the Nuclear Gene Expression 167 4.4 ROS as Top down and Bottom up Messengers 174 4.5 Second Messengers and Signaling Molecules in H2O2 Signaling Chains and (Nonlinear) Networking 191 4.6 ROS-Waves and Prey-Predator Models 192 4.7 Open Questions on ROS Coupling in Nonlinear Systems 196 5 Th e Role of ROS in Evolution 199 5.1 Th e Big Bang of the Ecosphere 200 5.2 Complicated Patterns Result from Simple Rules but Only the Useful Patterns are Stable 201 5.3 Genetic Diversity and Selection Pressure as Driving Forces for Evolution 205 6 Outlook: Control and Feedback in Hierarchical Systems in Society, Politics and Economics 209 Bibliography 213 Appendix 249 Index 259

Read more less

Book SynopsisThis book provides the whole spectrum of polysaccharides from basic concepts to commercial market applications. Chapters cover various types of sources, classification, properties, characterization, processing, rheology and fabrication of polysaccharide-based materials and their composites and gels. The applications of polysaccharides include in cosmetics, food science, drug delivery, biomedicine, biofuel production, marine, packaging, chromatography and environmental remediation. It also reviews the fabrication of inorganic and carbon nanomaterials from polysaccharides. The book incorporates industrial applications and will fill the gap between the exploration works in the laboratory and viable applications in related ventures.Table of ContentsPreface xxiii 1 Natural Polysaccharides From Aloe vera L. Gel (Aloe barbadensis Miller): Processing Techniques and Analytical Methods 1Silvana Teresa Lacerda Jales, Raquel de Melo Barbosa, Girliane Regina da Silva, Patricia Severino and Tulio Flávio Accioly de Lima Moura 1.1 Introduction 2 1.1.1 Gel Composition from A. vera 3 1.2 Applications of A. vera Mucilaginous Gel or Fractions 5 1.3 Aloe vera Gel Processing 5 1.3.1 Obtaining Polysaccharide Fraction or Acemannan 8 1.4 Analytical Methods Applied 9 1.4.1 Total Carbohydrates, Oligosaccharides, Acemannan and Free Sugars 9 1.4.2 Analytical Techniques 12 1.4.2.1 Chromatography Analysis 12 1.4.2.2 Infrared Spectroscopy (IR) 13 1.4.2.3 Nuclear Magnetic Resonance Spectroscopy 14 1.4.2.4 Mass Spectrometry 15 1.4.2.5 Ultraviolet–Visible Spectroscopy 16 1.4.2.6 Comprehensive Microarray Polymer Profiling 16 1.5 Conclusion 17 References 17 2 Cell Wall Polysaccharides 23Ata Ullah, Lutufur Rahman, Muhammad Bilal Yazdani, Muhammad Irfan, Waheed S. Khan and Asma Rehman 2.1 Introduction to Cell Wall 23 2.2 Plant Cell Wall Polysaccharides 24 2.2.1 Cellulose 24 2.2.2 Hemicellulose 25 2.2.2.1 Xyloglucan 25 2.2.2.2 Xylans 25 2.2.2.3 Mannans 26 2.2.3 Callose 26 2.2.4 Pectic Polysaccharides 26 2.2.4.1 Homogalacturonan (HG) 27 2.2.4.2 Arabinan 27 2.3 Algal Cell Wall Polysaccharides 28 2.3.1 Alginates 28 2.3.2 Sulfated Galactans 28 2.3.3 Fucoidans 30 2.4 Fungal Cell Wall Polysaccharides 30 2.4.1 Glucan 31 2.4.2 Chitin and Chitosan 31 2.5 Bacterial Cell Wall Polysaccharides 32 2.5.1 Peptidoglycan 32 2.5.2 Lipopolysaccharides 33 References 33 3 Marine Polysaccharides: Properties and Applications 37Tonmoy Ghosh, Rabinder Singh, Asha Arumugam Nesamma and Pannaga Pavan Jutur 3.1 Introduction 37 3.2 Polysaccharide Origins 38 3.3 Properties 38 3.3.1 Cellulose 38 3.3.2 Chitosan 40 3.3.3 Alginate 41 3.3.4 Carrageenan 41 3.3.5 Agar 41 3.3.6 Porphyran 42 3.3.7 Fucoidan 42 3.3.8 Ulvan 42 3.3.9 Exopolysaccharides From Microalgae 43 3.4 Applications of Polysaccharides 44 3.4.1 Biomedical Applications 44 3.4.1.1 Cellulose 44 3.4.1.2 Chitosan 44 3.4.1.3 Alginate 45 3.4.2 Food Applications 45 3.4.2.1 Cellulose 45 3.4.2.2 Chitosan 46 3.4.2.3 Alginates 46 3.4.2.4 Carrageenan 47 3.4.2.5 Agar 47 3.4.3 Pharmaceutical and Nutraceutical Applications 47 3.4.3.1 Cellulose 47 3.4.3.2 Chitosan 47 3.4.3.3 Alginate 48 3.4.3.4 Carrageenan 48 3.4.3.5 Porphyran 49 3.4.3.6 Fucoidan 49 3.4.4 Agriculture 50 3.5 Conclusions 50 References 51 4 Seaweed Polysaccharides: Structure, Extraction and Applications 61Oya Irmak Şahin 4.1 Introduction 61 4.1.1 Agar 62 4.1.2 Carrageenan 63 4.1.3 Alginate (Alginic Acid, Algin) 65 4.1.4 Fucoidan 67 4.1.5 Laminaran 68 4.1.6 Ulvan 69 4.2 Conclusion 70 References 70 5 Agars: Properties and Applications 75Sudhakar Padmesh and Aditi Singh 5.1 History and Origin of Agar 75 5.1.1 Agarophytes Used in Agar Manufacturing 76 5.2 Physical Properties of Agar Producing Seaweeds 76 5.3 Agar Manufacturing 78 5.3.1 Types of Agar Manufacturing 78 5.3.1.1 Freeze–Thaw Method 78 5.3.1.2 Syneresis Method 78 5.4 Structure of Agar 79 5.5 Heterogeneity of Agar 80 5.6 Physico-Chemical Characteristics of Agar 80 5.7 Chemical Characteristics of Agar 82 5.8 Factors Influencing the Characteristics of Agar 83 5.8.1 Techniques to Analyze the Fine Chemical Structure of Agar 85 5.8.2 Synergies and Antagonisms of Agar Gels 86 5.9 Uses of Agar in Various Sectors 87 5.9.1 Applications of Agar in Food Industry 88 5.9.2 Application of Agar in Harvesting Insects and Worms 89 5.9.3 Vegetable Tissue Culture Formulations 90 5.9.4 Culture Media for Microbes 91 5.9.5 Industrial Applications of Agar 91 5.10 Conclusion and Discussion 91 References 92 6 Biopolysaccharides: Properties and Applications 95Sinem Tunçer 6.1 Structure and Classification of Biopolysaccharides 95 6.1.1 Structure 95 6.1.2 Classification 97 6.1.3 Structural Characterization Techniques 98 6.2 Uses and Applications of Biopolysaccharides 99 6.2.1 Functional Fibers 100 6.2.2 Biomedicine 101 6.2.2.1 Tissue Engineering 102 6.2.2.2 Wound Healing 107 6.2.2.3 Drug Loading and Delivery 110 6.2.2.4 Therapeutics 114 6.2.3 Cosmetics 115 6.2.4 Foods and Food Ingredients 116 6.2.5 Biofuels 119 6.2.6 Wastewater Treatment 120 6.2.7 Textiles 121 6.3 Conclusion 122 References 123 7 Chitosan Derivatives: Properties and Applications 135Gincy Marina Mathew, Sarah Bill Ulaeto, Reshmy R., Rajeev Kumar Sukumaran, Parameswaran Binod, Ashok Pandey and Raveendran Sindhu 7.1 Introduction 135 7.2 Properties of Chitosan Derivatives 142 7.2.1 Physiochemical Properties 142 7.2.2 Functional Properties 143 7.2.3 Biological Properties of Chitosan 144 7.3 Applications of Chitosan Derivatives 145 7.3.1 Anticancer Agents 145 7.3.2 Bone Tissue Material Formation 147 7.3.3 Wound Healing, Tissue Regeneration and Antimicrobial Resistance 148 7.3.4 Drug Delivery 149 7.3.5 Chromatographic Separations 150 7.3.6 Waste Management 150 7.3.7 Food Industry 151 7.3.8 In Cosmetics 152 7.3.9 In Paint as Antifouling Coatings 152 7.4 Conclusions 152 Acknowledgement 153 References 153 8 Green Seaweed Polysaccharides Inventory of Nador Lagoon in North East Morocco 163El Asri Ouahid, Ramdani Mohamed and Fadlaoui Soufiane 8.1 Introduction 163 8.2 Nador Lagoon: Situation and Characteristics 164 8.3 Seaweed 165 8.4 Polysaccharides in Seaweed 166 8.5 Algae Polysaccharides in Nador Lagoon’s Seaweed 167 8.5.1 C. prolifera 167 8.5.1.1 Sulfated Galactans 168 8.5.2 U. rigida & E. intestinalis 168 8.5.2.1 Ulvan 169 8.5.3 C. adhaerens, C. bursa, C. tomentosum 170 8.5.3.1 Sulfated Arabinans 170 8.5.3.2 Sulfated Arabinogalactans 170 8.5.3.3 Mannans 171 8.6 Conclusion 172 References 172 9 Salep Glucomannan: Properties and Applications 177Abdullah Kurt 9.1 Introduction 177 9.2 Production 179 9.3 Composition and Physicochemical Structure 181 9.4 Rheological Properties 183 9.5 Purification and Deacetylation 188 9.6 Food Applications 191 9.6.1 Beverage 191 9.6.2 Ice Cream and Emulsion Stabilizing 192 9.6.3 Edible Film/Coating 194 9.6.4 Gelation 195 9.7 Health Benefits 196 9.8 Conclusions and Future Trends 197 References 198 10 Exudate Tree Gums: Properties and Applications 205Aruna Jyothi Kora 10.1 Introduction 205 10.1.1 Gum Arabic 206 10.1.2 Gum Karaya 208 10.1.3 Gum Kondagogu 209 10.1.4 Gum Ghatti 209 10.1.5 Gum Tragacanth 210 10.1.6 Gum Olibanum 211 10.2 Nanobiotechnology Applications 211 10.3 Minor Tree Gums 214 10.4 Conclusions 214 Acknowledgment 217 References 218 11 Cellulose and its Derivatives: Properties and Applications 221Rafael de Avila Delucis, Pedro Henrique Gonzalez de Cademartori, André Ricardo Fajardo and Sandro Campos Amico 11.1 Introduction 221 11.2 Main Raw Materials 222 11.3 Composition and Chemical Structure of Lignocellulosic Materials 224 11.4 Cellulose: Chemical Backbone and Crystalline Formats 225 11.5 Cellulose Extraction 228 11.5.1 Mechanical Methods 228 11.5.2 Chemical Methods 231 11.6 Cellulose Products and its Derivatives 232 11.7 Main Applications 236 11.8 Conclusion 241 References 242 12 Starch and its Derivatives: Properties and Applications 253Bhanita Goswami and Debajyoti Mahanta 12.1 Introduction 253 12.2 Physicochemical and Functional Properties of Starch 254 12.2.1 Size, Morphology and Crystallinity of Starch Granules 255 12.2.2 Physical Properties due to Associated Lipids, Proteins and Phosphorus With Starch Granules 257 12.2.3 Solubility and Swelling Capacity of Starch 257 12.2.4 Gelatinization and Retrogradation of Starch 258 12.2.5 Birefringence and Glass Transition Temperature of Starch 259 12.2.6 Rheological and Thermal Properties of Starch 260 12.2.7 Transmittance and Opacity of Starch 260 12.2.8 Melt Processability of Starch 261 12.3 Modification of Starch 261 12.3.1 Physical Modification of Starch 262 12.3.2 Chemical Modification of Starch 263 12.3.3 Dual Modification of Starch 265 12.3.4 Enzymatic Modification of Starch 265 12.3.5 Genetic Modification of Starch 265 12.4 Application of Starch and its Derivatives 266 12.4.1 In Food Industry 266 12.4.2 In Paper Industry 266 12.4.3 Starch as Binders 267 12.4.4 In Detergent Products 267 12.4.5 As Biodegradable Thermoplastic Materials or Bioplastics 267 12.4.6 In Pharmaceutical and Cosmetic Industries 268 12.4.7 As Industrial Raw Materials 269 12.4.8 As Adsorbents for Environmental Applications 269 12.4.9 As Food Packaging Materials 269 12.4.10 In Drug Delivery 270 12.4.11 As Antimicrobial Films and Coatings 270 12.4.12 In Advanced Functional Materials 271 12.5 Conclusion 273 References 274 13 Crystallization of Polysaccharides 283Mohsen Khodadadi Yazdi, Farzad Seidi, Yongcan Jin, Payam Zarrintaj, Huining Xiao, Amin Esmaeili, Sajjad Habibzadeh and Mohammad Reza Saeb 13.1 Introduction 283 13.2 Principles of Crystallization of Polysaccharides 285 13.3 Techniques for Crystallinity Measurement 287 13.4 Crystallization Behavior of Polysaccharides 287 13.4.1 Cellulose 287 13.4.2 Chitosan and Chitin 290 13.4.3 Starch 291 13.5 Polymer/Polysaccharide Crystalline Nanocomposites 293 13.6 Conclusion 293 References 294 14 Polysaccharides as Novel Materials for Tissue Engineering Applications 301Nandini A. Pattanashetti, Anand I. Torvi, Arun K. Shettar, Pramod B. Gai and Mahadevappa Y. Kariduraganavar 14.1 Introduction 301 14.2 Types of Scaffolds for Tissue Engineering 303 14.3 Biomaterials for Tissue Engineering 304 14.4 Polysaccharide-Based Scaffolds for Tissue Engineering 305 14.4.1 Alginate-Based Scaffolds 306 14.4.2 Chitosan-Based Scaffolds 307 14.4.3 Cellulose-Based Scaffolds 309 14.4.4 Dextran and Pullulan-Based Scaffolds 310 14.4.5 Starch-Based Scaffolds 311 14.4.6 Xanthan-Based Scaffolds 312 14.4.7 Glycosaminoglycans-Based Scaffolds 313 14.5 Current Challenges and Future Perspectives 316 Acknowledgements 317 References 317 15 Structure and Solubility of Polysaccharides 325Vickramjeet Singh, Shikha Indoria, K.J. Jisha and Ramesh L. Gardas 15.1 Introduction 325 15.2 Polysaccharide Structure and Solubility in Water 326 15.3 Solubility and Molecular Weight 329 15.4 Solubility and Branching 330 15.5 Polysaccharide Solutions 332 15.6 Conclusions 334 Acknowledgments 334 References 334 16 Polysaccharides: An Efficient Tool for Fabrication of Carbon Nanomaterials 337Yuliya Dzyazko and Vladimir Ogenko 16.1 Introduction 337 16.2 Aerogels 338 16.2.1 Plant and Bacterial Cellulose 339 16.2.2 Carbon Derived From Nanocrystalline Cellulose of Plant Origin 344 16.2.3 Carbon Aerogels Produced From Bacterial Cellulose 348 16.2.4 Chitosan and Sodium Alginate for Preparation of Carbon Aerogels 350 16.3 Graphene-Like Materials and Nanotubes Produced From Polysaccharides 352 16.4 Biocarbon Quantum Dots 355 16.5 Membranes Containing Carbon Nanoparticles Derived From Cellulose 356 16.6 Conclusions 358 References 358 17 Rheology and Structural Properties of Polysaccharides 367Andreea Irina Barzic 17.1 Introduction 367 17.2 General Structural Features of Polysaccharides 368 17.3 Main Types of Polysaccharides and Their Structural Properties 370 17.4 Rheological Behavior of Polysaccharides 374 17.4.1 Semi-Diluted and Concentrated Solutions of Polysaccharides 374 17.4.2 Gels of Polysaccharides 375 17.4.3 Polysaccharide Liquid Crystals 377 17.5 Conclusions 379 References 379 18 Gums-Based Bionanostructures for Medical Applications 385Hira Munir, Muhammad Bilal, Muhammad Imran Khan and Hafiz M.N. Iqbal 18.1 Plants and Their Bioactive Compounds 386 18.2 Natural Gums—Physicochemical Features 386 18.3 Sources of Natural Gums 387 18.3.1 Exudate Gums 387 18.3.2 Mucilages 387 18.3.3 Seaweed Polysaccharides 388 18.3.4 Microbial Polysaccharides 388 18.3.5 Animal Polysaccharide 388 18.3.6 Other Sources of Polysaccharide Gums 388 18.4 Classification of Gums 388 18.4.1 According to the Charge 388 18.4.2 According to the Source 389 18.4.3 According to Shape 389 18.4.4 According to Monomeric Units in Chemical Structure 389 18.4.5 Semi-Synthetic Gums 390 18.5 Composition of Natural Gums 390 18.6 Extraction and Purification of Natural Gums 390 18.7 Modification and Hydrolysis of Natural Gums 390 18.8 Medical Applications of Gums-Based Bio-Nanostructures 390 18.8.1 Conductive Adhesive Properties and Pharmaceutical Applications 391 18.8.2 Application in Imaging and Cell Studies 393 18.8.3 Application in Sutures 393 18.8.4 Biomaterials for Implantation 394 18.9 Conclusions 395 References 395 19 Alginates: Properties and Applications 399Sapna Raghav, Pallavi Jain and Dinesh Kumar 19.1 Introduction 399 19.2 Properties of Sodium Alginate (Na-Alg) 400 19.2.1 Thickening Property of Alginates 401 19.2.2 Gelling Property of Alginates 401 19.2.3 Film-Forming Property 402 19.2.4 Lipophilicity 402 19.2.5 Solubility 402 19.2.6 pH Sensitivity 402 19.3 Chemical Properties 402 19.4 Applications 403 19.4.1 Bone Tissue Engineering 404 19.4.2 Pharmaceutical Applications 405 19.4.2.1 Small Chemical Drug Delivery 405 19.4.2.2 Protein Delivery 406 19.4.3 Wound Dressing 406 19.4.4 Vaccine Delivery 408 19.4.5 Water Treatment Application 410 19.4.6 Alginate for Anion Removal 410 19.5 Conclusions and Prospects 414 Acknowledgments 414 Abbreviations 414 References 414 20 Marine Polysaccharides: Properties and Applications 423Olugbenga Samuel Michael, Charles Oluwaseun Adetunji, Ayodele Eugene Ayeni, Muhammad Akram, Inamuddin, Juliana Bunmi Adetunji, Mathew Olaniyan and Musa Abidemi Muhibi 20.1 Introduction 424 20.2 Marine Bacteria That Produce Polysaccharides 425 20.3 Marine Fungi That Produce Polysaccharide 431 20.4 Production, Extraction and Purification of Polysaccharides 431 20.4.1 Solid State Fermentation 432 20.4.2 Submerged Fermentation 432 20.4.3 Extraction and Purification of Polysaccharides 432 20.5 Characterization via Molecular, Biochemical and Cultural Characterization of Marine Polysaccharides 433 20.6 Conclusion and Future Recommendation to Knowledge 434 References 434 21 Polysaccharides: Promising Constituent for the Preparation of Nanomaterials 441Rafeeya Shams, Quratul Eain Hyder Rizvi, Aamir Hussain Dar, Ishrat Majid, Shafat Ahmad Khan and Anurag Singh 21.1 Introduction 441 21.1.1 Classification and Types of Nanomaterials 442 21.2 Preparation of Polysaccharide-Dependent Nanomaterials 445 21.2.1 Electrospinning 445 21.2.2 Dip Coating, Film Casting, and Physical Mixing 446 21.2.3 Layer by Layer Assembly 447 21.2.4 Ionotropic Gelation, Colloidal Assembly and Coprecipitation 447 21.2.5 In Situ NP Preparation 447 21.2.6 Ionotropic Gelation 448 21.3 Biocompatibility of Carbon-Based Nanomaterials 451 21.4 Conclusions and Summary 452 References 452 22 Anticancer Potential of Polysaccharides 459Ali Raza, Javed Iqbal, Muhammad Usman Munir, Anila Asif and Arsalan Ahmed 22.1 Introduction 459 22.2 Mode of Action 460 22.2.1 Cell-Cycle Arrest 460 22.2.2 Receptor 460 22.2.3 Immunomodulatory Effect 461 22.2.4 Chemotherapy Enhancement 461 22.2.5 Mitochondrial Membrane Inhibition 461 22.2.6 Free Radicals Capture 462 22.3 Polysaccharides in Cancer Treatment 462 22.3.1 Lung Cancer 463 22.3.2 Blood Cancer 464 22.3.3 Liver Cancer 465 22.3.4 Gastric and Colon Cancer 465 22.3.5 Bladder and Kidney Cancer 466 22.3.6 Breast Cancer 466 22.3.7 Cervical Cancer 467 22.4 Polysaccharides in Conventional Therapies 468 22.4.1 Chemotherapy 468 22.4.2 Radiotherapy 469 22.4.3 Surgery 469 22.4.4 Phototherapy 469 22.4.5 Drug Delivery 469 22.4.6 Bioimaging 470 22.4.7 Food Supplement 470 22.5 Concluding Remarks and Future Trends 471 References 471 23 Polysaccharide-Based Membrane for Packaging Applications 477Saumya Pandey 23.1 Introduction 477 23.2 Polysaccharides as Biomaterials for Biodegradable Packaging 478 23.2.1 Polysaccharides Extracted From Animals 481 23.2.1.1 Chitin and Chitosan 481 23.2.2 Polysaccharides Extracted From Plants 481 23.2.2.1 Cellulose 481 23.2.2.2 Pectin 482 23.2.2.3 Starch 483 23.2.2.4 Galactomannans 484 23.2.3 Polysaccharides Extracted From Algae 484 23.2.3.1 Carrageenan 484 23.2.3.2 Alginate 484 23.2.4 Polysaccharides Synthesized by Microorganisms 485 23.2.4.1 Pullulan 485 23.2.4.2 Gellan Gum 485 23.2.4.3 Xanthan Gum 486 23.2.4.4 FucoPol 486 23.3 Properties of Polysaccharide-Based Packaging Film or Coating 486 23.3.1 Barrier Properties of Film or Coatings 486 23.3.2 Mechanical Properties of the Film 488 23.4 Polysaccharides-Based Nanocomposites Packaging 489 23.5 Polysaccharides-Based Films and Coatings in Food Packaging Applications 490 23.5.1 Food Preservation and Self-Life Extension 490 23.5.2 Antimicrobial Coating 490 23.5.3 Delaying of Post-Harvest Ripening 491 23.5.4 Restoring Color, Aroma and Nutritional Value 491 23.5.5 Antioxidant Properties 491 23.6 Conclusion and Prospects 492 References 493 24 Applications of Polysaccharides in Cancer Treatment 501Nivedita Pujari S., Joy Hoskeri H., Anand I. Torvi and Arun K. Shettar 24.1 Introduction 501 24.2 Types of Polysaccharides Used in Cancer Treatment 502 24.2.1 Animal Polysaccharides 502 24.2.2 Vegetal Polysaccharides 503 24.2.3 Microorganism and Fungi Polysaccharides 503 24.3 Mechanism of Polysaccharides as Anticancer Agent 504 24.3.1 Actions of Polysaccharides as Immunological Functioning 504 24.3.2 Role of Polysaccharides in Cell Signaling 505 24.3.3 Effect of Polysaccharides in Apoptosis and Cell Cycle Arrest 506 24.3.4 Antitumor Effect of Polysaccharides 506 24.4 Usage of Polysaccharides in Preclinical and Clinical Models of Cancer 507 24.4.1 In-Vitro Cell Line Model 507 24.4.2 Polysaccharides as Antitumor/Anticancer in Animal Model Study 508 24.4.3 Clinical Trials of Polysaccharides in Cancer Treatment 508 24.5 Conclusion and Future Perspectives 510 References 510 25 Application of Chitosan-Based Catalysts for Heterocycles Synthesis and Other Reactions 517Yadavalli Venkata Durga Nageswar, Nelson L.C. Domingues, Ramesh Katla and Rakhi Katla 25.1 Introduction 517 25.2 Recent Research Reports 518 25.2.1 Furans 518 25.2.2 Pyrazoles 518 25.2.3 Imidazoles 519 25.2.4 Oxazoles 520 25.2.5 Thiazoles 521 25.2.6 Triazoles 522 25.2.7 Tetrazoles 523 25.2.8 Pyridines 524 25.2.9 Quinolines 524 25.2.10 Pyrazines 525 25.2.11 Pyrimidines 525 25.2.12 Quinazolines 527 25.2.13 Phthalazines 527 25.2.14 Perimidines 527 25.2.15 Pyrans 528 25.2.16 Coumarins 530 25.2.17 Chromenes 530 25.2.18 Other Reactions 531 25.2.18.1 Oxidations 531 25.2.18.2 Reductions 533 25.2.18.3 Coupling/Condensation Reactions 533 25.2.18.4 Isomerization 537 25.2.18.5 Ring Opening 538 25.3 Conclusion 538 References 539 26 Preparation and Applications of Polysaccharide-Based Composites 543Sadaf Ahmad, Bushra Anees Palvasha, Bakar bin Khatab Abbasi, Muhammad Shahid Nazir, Majid Niaz Akhtar, Zaman Tahir and Mohd Azmuddin Abdullah 26.1 Introduction 544 26.2 Types 544 26.2.1 Cellulose 544 26.2.2 Starch 545 26.2.3 Glycogen 545 26.2.4 Chitin 545 26.2.5 Pectin 546 26.3 Importance 546 26.4 Fabrication and Applications of Polysaccharide-Inorganic-Based Composites 547 26.4.1 Cellulose–Inorganic Materials 547 26.4.2 Starch–Inorganic Materials 553 26.4.3 Pectin–Inorganic Materials 557 26.4.4 Chitin and Chitosan–Inorganic Materials 559 26.4.5 Polysaccharides–Metal Organic Frameworks 561 26.5 Recent Applications 564 26.6 Conclusion 565 References 566 27 Polysaccharide-Based Liquid Crystals 573Sumaira Saleem, Gulzar Muhammad, Muhammad Mudassir Iqbal, Muhammad Ajaz Hussain, Muhammad Arshad Raza, Zahid Shafiq and Haseeba Razzaq 27.1 Introduction 573 27.2 Polysaccharides-Based Liquid Crystals 575 27.2.1 Cellulose-Based Liquid Crystals 575 27.2.2 Liquid Crystals From Cellulose Derivatives 578 27.2.3 Amylose-Based Liquid Crystals 579 27.2.4 Dextrin-Based Liquid Crystals 582 27.2.5 Chitin-Based Liquid Crystals 584 27.2.6 Schizophyllan-Based Liquid Crystals 585 27.3 Conclusion 586 References 586 28 Patents on Polysaccharide Applications 591Nadhratun Naiim Mobarak, Sharifah Nabihah Syed Jaafar and Mohamad Azuwa Mohamed 28.1 Introduction 591 28.2 Polysaccharides in Medical Application 595 28.3 Polysaccharides in Cosmetic Application 597 28.4 Polysaccharides in Battery Components 600 28.5 Polysaccharides in Paper Manufacture 601 28.6 Conclusion 601 References 602 29 Applications of Polysaccharides in Controlled Release Drug Delivery System 607Muhammad Harris Shoaib, Muhammad Sikandar, Farrukh Rafiq Ahmed, Fatima Ramzan Ali, Faaiza Qazi, Rabia Ismail Yousuf, Asma Irshad, Sabahat Jabeen and Kamran Ahmed 29.1 Introduction 607 29.2 Polysaccharides From Plant Sources and Their Derivatives 608 29.2.1 Cellulose 608 29.2.2 Cellulose Derivatives 609 29.2.2.1 Cellulose Ethers 609 29.2.2.2 Cellulose Esters 612 29.2.3 Hemicellulose 613 29.2.3.1 Mannans 614 29.2.4 Starch 617 29.2.5 Pectin 618 29.2.6 Lignin 619 29.2.7 Inulin 620 29.3 Gums 620 29.3.1 Exudate Gums 620 29.3.1.1 Gum Arabic (Gum Acacia) 620 29.3.1.2 Gum Tragacanth 621 29.3.1.3 Gum Karaya 621 29.3.2 Mucilage Gums 622 29.3.2.1 Okra Gum 622 29.3.2.2 Khaya Gum 622 29.3.2.3 Hakea Gum 622 29.3.2.4 Cassia tora Gum 623 29.3.2.5 Albizia Gum 623 29.3.2.6 Prunus cerasoides Gum 623 29.3.2.7 Tamarind Gum 623 29.3.2.8 Cissus populnea Gum 624 29.4 Polysaccharides From Algal Sources 624 29.4.1 Alginates 624 29.4.2 Galactans 626 29.4.3 Carrageenan 626 29.4.4 Agar 627 29.4.5 Agarose 628 29.5 Polysaccharides From Fungal Sources 629 29.5.1 Scleroglucan 629 29.5.2 Beta-Glucan 629 29.5.3 Pullulan 630 29.6 Polysaccharides From Animals Sources and Their Derivatives 631 29.6.1 Chitin 631 29.6.2 Chitosan 632 29.6.3 Hyaluronic Acid 633 29.6.4 Glycogen 633 29.6.5 Chondroitin Sulfate 633 29.6.6 Dermatan Sulfate 634 29.6.7 Gelatin 634 29.7 Polysaccharides From Microorganisms 635 29.7.1 Curdlan 635 29.7.2 Xanthan Gum 636 29.7.3 Gellan Gum 637 References 637 30 Applications of Polysaccharides in Nutrition and Medicine 657Nivedita Pujari S., Arun K. Shettar and Joy Hoskeri H. 30.1 Introduction 657 30.2 Sources of Polysaccharides 658 30.2.1 Polysaccharides in Dietary Fibers 658 30.2.2 Polysaccharides in Plants 659 30.2.3 Polysaccharides in Algae and Lichens 659 30.2.4 Polysaccharides in Fungi 660 30.2.5 Polysaccharides From Bacteria 661 30.2.6 Polysaccharides From Other Sources 662 30.3 Role of Polysaccharides in Nutrition 662 30.3.1 Polysaccharides in Food 662 30.3.2 Polysaccharides as Energy Sources 663 30.3.3 Health Impact of Polysaccharides 664 30.3.4 Nutritional Aspect of Polysaccharides 664 30.4 Biomedical Applications of Polysaccharides 665 30.4.1 Polysaccharides as Antimicrobial and Antiviral 665 30.4.2 Polysaccharides as Antitumor/Anticancer 666 30.4.3 Polysaccharides as Anti-Obesity and Anti-Hypercholesterolemic Agents 667 30.4.4 Polysaccharides as Antidiabetic Agents 669 30.4.5 Polysaccharides as Immune Modulator Agent 670 30.4.6 Polysaccharides as Anti-Inflammatory Agent 671 30.4.7 Polysaccharides as Neuro-Protective Agent 672 30.4.8 Polysaccharides as a Source of Antioxidant 672 30.4.9 Polysaccharides in Wound Healing and Wound Dressing 673 30.5 Conclusion 674 References 674 31 Synthetic Polysaccharide-Based Vaccines: Progress and Achievements 683Rafig Gurbanov 31.1 A Brief History of Vaccination 683 31.2 The Leverage of Synthetic Polysaccharide-Based Vaccines Over Natural Polysaccharide-Based Vaccines 684 31.3 The Principles of Synthetic Polysaccharide-Based Vaccines 686 31.3.1 Tumor Vaccines 689 31.3.2 Leishmaniasis Vaccines 690 31.3.3 Human Immunodeficiency Virus Vaccines 690 31.3.4 Bacterial Vaccines 691 31.4 The Opportunities and Prospects of Synthetic Polysaccharide-Based Vaccine Technologies 692 References 694 32 Polysaccharides Derived From Natural Sources: A Panacea to Health and Nutritional Challenges 701Charles Oluwaseun Adetunji, Muhammad Akram, Olugbenga Samuel Michael, Khuram Shahzad, Ayodele Eugene Ayeni, Sidra Hasan, Juliana Bunmi Adetunji, Syed Muhammad Hasan, Inamuddin, Mathew Olaniyan and Musa Abidemi Muhibi 32.1 Introduction 702 32.2 Different Types of Polysaccharides Derived From Different Natural Sources 703 32.2.1 Polysaccharides Derived From Plants and Their Applications 704 32.2.2 Animal Derived Polysaccharides and Their Applications 705 32.2.2.1 Chitosan and Chitin 705 32.2.2.2 Heparin and Heparin Sulfates 706 32.2.2.3 Hyaluronic Acid 707 32.2.3 Microorganisms Derived Polysaccharides and Their Applications 707 32.2.3.1 Alginate 707 32.2.3.2 Dextran 708 32.2.3.3 Fucoidans 708 32.2.3.4 Spirulina 708 32.2.4 Homoglycans 709 32.2.4.1 Starch and Hetastarch 709 32.2.4.2 Cellulose 709 32.2.4.3 Inulin 710 32.2.4.4 Chitin and Chitosan 710 32.2.4.5 Glycogen 712 32.2.4.6 Heteroglycans and Other Polysaccharides 712 32.2.4.7 Glycosaminoglycans Significance 715 32.2.4.8 Chondroitin Sulfates 715 32.2.4.9 Hyaluronic Acid 715 32.2.4.10 Alginic Acid 715 32.2.4.11 Mucopolysaccharidoses 717 32.3 Production, Extraction and Purification of Polysaccharides 718 32.3.1 Solid State Fermentation 719 32.3.2 Submerged Fermentation 719 32.3.3 Extraction and Purification Process of Polysaccharides 720 32.4 Specific Examples of Polysaccharides and Their Various Applications in Nutrition and Medicine 720 32.4.1 Schizophyllan 720 32.4.1.1 Antitumor Activity of Schizophyllan 721 32.4.1.2 Anti-Inflammatory Activity of Schizophyllan 721 32.4.1.3 Immunomodulatory Activity of Schizophyllan 721 32.4.1.4 Prebiotic Potential of Schizophyllan 722 32.4.2 Pleuran and Others Polysaccharides From Pleurotus spp. 722 32.4.2.1 Specific Nutritional and Beneficial Functions of Pleurotus Polysaccharides 722 32.4.3 Scleroglucan 723 32.4.3.1 Applications for Nutritional and Medicinal Purposes Derived From Scleroglucan 723 32.4.4 Curdlan 724 32.4.5 Other Essential Polysaccharides With Medical Significance 725 32.5 Conclusion and Recommendation to Knowledge 725 References 725 Index 739

Read more less

Book SynopsisMicroplastics in Urban Water Management Enables readers to understand the true occurrence and fate of microplastics in drinking water, wastewater and sludge, and receiving water Microplastics in Urban Water Management focuses on the occurrence, fate, effect, and removal of microplastics in the urban water management systems, summarizing relevant methods for enhancing microplastics removal and degradation, providing comprehensive data from source to sink (including occurrence and fate of microplastics in urban water management), and covering practical applications, which are expected to provide some theoretical guidance for controlling or mitigating microplastics pollution and its environmental risks. The work also includes detailed multidisciplinary information on the way in which microplastics behave in urban water management, plus recent advances of nanoplastics, i.e., nano-sized microplastics, in the aquatic environment. In Microplastics in Urban Water Management, readers can expectTable of ContentsNotes of Contributors xiii Preface xvii 1 Techniques for Microplastics Detection in Urban Water Systems 1 Xiaowei Li, Man Li, Lulu Liu, and Xiang Huang 1.1 Introduction 1 1.2 Sample Collection and Separation 1 1.2.1 Freshwater Samples 1 1.2.2 Freshwater Sediments 5 1.2.3 Wastewater Samples 9 1.2.4 Sludge Samples 12 1.2.5 Drinking Water Samples 14 1.3 Sample Purification 16 1.3.1 Wet Peroxidation 16 1.3.2 Enzymatic Degradation 17 1.3.3 Alkaline and Acid Treatment 18 1.3.4 Influence of Chemical Purification on Microplastic Property 20 1.4 Sample Identification 25 1.4.1 Visual Identification 25 1.4.2 Microscopic Identification 26 1.4.3 Spectroscopic Identification 27 1.4.4 Thermal Analysis 29 1.5 Quantitative Analysis 32 1.5.1 LD Method 33 1.5.2 DLS Method 34 1.5.3 NTA Method 34 1.5.4 Challenges in Particle Size Analysis 35 1.6 Quality Control 36 1.6.1 Internal Deviation 36 1.6.2 Judgment Error 37 1.7 Summary and Future Outlooks 37 References 37 2 Occurrence and Removal of Microplastics in Drinking Water Systems 53 Junyeol Kim, Yongli Z. Wager, Carol Miller, and John Norton 2.1 Introduction 53 2.2 What Are Microplastics? 55 2.2.1 Primary and Secondary Microplastics 56 2.3 The Emergence of Microplastic 57 2.3.1 Sources 57 2.3.2 Transformation 59 2.4 Occurrence of Microplastics in Drinking Water Systems 61 2.4.1 Abundance 61 2.4.2 Distribution 64 2.4.2.1 Size Distribution 65 2.4.2.2 Morphological Distribution 66 2.4.3 Composition 67 2.5 Removal of Microplastics in Drinking Water Systems 68 2.5.1 Water Treatment Plant 69 2.5.1.1 Removal of Microplastics by the Overall Process of Water Treatment 69 2.5.1.2 Removal Rate of Microplastics Depending on the Size 70 2.5.1.3 Removal Rate Depending on the Type of Microplastics 73 2.5.1.4 Removal Efficiency Depending on the Composition of Microplastics 74 2.5.1.5 Removal of Microplastics by Coagulation, Flocculation, and Sedimentation 75 2.5.1.6 Removal of Microplastics by Filtration 76 2.5.1.7 Removal of Microplastics by Ozonation 77 2.5.2 Microplastic Removal in Lab-scale Studies 78 2.6 Summary and Prospects 80 References 82 3 Occurrence of Microplastics in Wastewater Treatment Plants 91 Kang Song and Lu li 3.1 Introduction 91 3.2 The Abundance and Removal Performance of Microplastics in WWTPs 92 3.3 The Microplastics Composition in WWTPs 102 3.3.1 Microplastics Size Distribution 102 3.3.2 Microplastic Shapes 103 3.3.3 Microplastic Materials 104 3.3.4 Microplastic Color 105 3.4 Removal of Microplastics in WWTPs and Contribution of Each Process 106 3.4.1 Primary Treatment 106 3.4.2 Secondary Treatment 108 3.4.3 Tertiary Treatment 108 3.5 Summary and Future Outlooks 109 References 110 4 Effects of Microplastics on Wastewater Treatment Processes 119 Yan Laam Cheng, Tsz Ching Tse, Ziying Li, Yuguang Wang, and Yiu Fai Tsang 4.1 Biological Treatment Processes 119 4.1.1 Conventional Unit Operations and Processes 119 4.1.1.1 Suspended-Growth Processes 120 4.1.1.2 Attached-Growth Processes 122 4.1.1.3 Advanced Wastewater Treatment Processes 122 4.2 Interactions Between Sludge and Microplastics 123 4.2.1 Activated Sludge 126 4.2.2 Aerobic Granular Sludge 126 4.2.3 Anaerobic Granular Sludge 127 4.3 Effects of Microplastics on Microorganisms and Key Enzymes 128 4.3.1 Heterotrophic Bacteria 128 4.3.2 Ammonia-Oxidizing Bacteria 129 4.3.3 Nitrite-Oxidizing Bacteria 132 4.3.4 Key Enzymes 132 4.4 Effects on Sludge Stabilization and Dewatering 134 4.4.1 Aerobic Digestion 134 4.4.2 Dewatering 136 4.5 Perspectives 137 4.6 Conclusion 139 Acknowledgments 140 References 140 5 Microplastics in Sewage Sludge of Wastewater Treatment 147 Wei Wei, Xingdong Shi, Yu-Ting Zhang, Chen Wang, Yun Wang, and Bing-Jie Ni 5.1 Introduction 147 5.2 Occurrence 149 5.2.1 Primary Sludge 150 5.2.2 Waste-Activated Sludge 152 5.2.3 Dewatered Sludge 153 5.3 Effects of Microplastics on Sludge Anaerobic Treatment 155 5.3.1 Methane 155 5.3.2 Short-Chain Fatty Acid 156 5.3.3 Hydrogen 158 5.3.4 Enzyme Activity 158 5.3.5 Microbial Community 159 5.4 Transport of Microplastics from Sludge to Soil and Landfills 160 5.4.1 Transport of Microplastics from Sludge to Soil 160 5.4.2 Transport of Microplastics from Sludge to Landfills 162 5.5 Enhanced Removal of Microplastics from Sludge 162 5.5.1 Thickening and Dehydration 162 5.5.2 Anaerobic Digestion 163 5.5.3 High Temperature Composting 163 5.5.4 Incineration 164 5.6 Summary and Outlook 165 References 166 6 Discharge of Microplastics from Wastewater Treatment Plants 175 Hongbo Chen and Yi Wu 6.1 Introduction 175 6.2 Microplastics Concentrations in Effluent of WWTPs 176 6.2.1 Concentration of Microplastics in Effluent 176 6.2.2 Types of Microplastics in Effluent 176 6.3 Important Source of the Receiving Waters 179 6.3.1 River 180 6.3.2 Lake 182 6.3.3 Sea 184 6.3.3.1 Microplastics on Beaches and Coastal Areas 186 6.3.3.2 Microplastics on the Surface of Ocean Water 186 6.3.3.3 Microplastic Pollution in Polar Regions 186 6.3.4 Sediments 188 6.4 Uptake of Microplastics in Aquatic Organisms 193 6.4.1 Freshwater Organisms 193 6.4.2 Marine Life 195 6.4.3 Soil and Crops 197 6.5 Conclusions and Considerations for Future Work 198 6.5.1 Conclusions 198 6.5.2 Considerations for Future Work 199 Acknowledgments 199 References 199 7 Microplastics Removal and Degradation in Urban Water Systems 211 Qiuxiang Xu and Bing-Jie Ni 7.1 Introduction 211 7.2 Use of Separation-based Technology for the Removal of MPs 215 7.2.1 CFS 215 7.2.2 Electrocoagulation 219 7.2.3 Filtration 221 7.2.4 Membrane Separation 222 7.2.5 Adsorption 223 7.3 Photocatalysis Degradation of Microplastics 225 7.3.1 Zinc Oxide-based Photocatalysis 226 7.3.2 Titanium Dioxide-based Photocatalysis 227 7.3.3 Bismuth-based Photocatalysis 229 7.4 Chemical Oxidation Degradation of Microplastics 229 7.5 Future Prospects 231 References 232 8 Microplastics Contamination in Receiving Water Systems 243 Muhammad Junaid and Jun Wang 8.1 Introduction 243 8.2 Occurrence of Microplastics in Freshwater Resources 247 8.2.1 River Surface Waters 247 8.2.2 Lake Surface Waters 248 8.3 Composition of Microplastics in Freshwater 249 8.4 Factors Influencing the Aging of Microplastics 251 8.5 Uptake and Associated Ecological Impacts of Microplastics in Aquatic Organisms 251 8.5.1 Invertebrates 251 8.5.2 Waterbirds 253 8.5.3 Mammals and Megafauna 254 8.6 Interactions among Microplastics and Microbes (Bacteria) 256 8.6.1 Microplastic Biofilms: Formation Mechanisms and Characteristics 256 8.6.2 Factors Affecting Biofilm Formation 257 8.6.3 Role of Microplastic Biofilms in Genetic Material Transfer 258 8.6.4 Microplastics as Pathogen Carriers 260 8.7 Potential Interactions between Microplastics and Humans 260 8.7.1 Dietary Exposure 260 8.7.2 Exposure through Inhalation and Dermal Contact 263 8.7.3 Microplastics’ Toxicity in Humans 264 8.8 Implications and Suggestions 266 Acknowledgments 267 References 268 9 Effects of Microplastics on Algae in Receiving Waters 287 Dongbo Wang, Qizi Fu, Xuemei Li, and Xuran Liu 9.1 Introduction 287 9.2 MPs Induced Effect on the Algae: Growth and Populations 289 9.2.1 Effects of MPs on Algae Growth 289 9.2.2 Effects of MPs on Algae Populations 292 9.3 Factors Affecting Toxicity 293 9.3.1 Dosage 293 9.3.2 Size 295 9.3.3 Materials 295 9.4 Combined Effects of MPs with Contaminants towards Algae 296 9.4.1 Antibiotics 297 9.4.2 Heavy Metals 300 9.4.3 Other Emerging Contaminations 301 9.5 Research Gap and Perspective 302 References 303 10 Effects of Microplastics on Aquatic Organisms in Receiving Waters 315 Gabriela Kalčíková and Ula Rozman 10.1 Introduction 315 10.1.1 Occurrences in Water and Sediment 316 10.1.2 The Concerns about Potential Ecological Risks 318 10.2 Into the Food Chain of Aquatic Animals 319 10.2.1 Accumulation 320 10.2.2 Transfer within the Organizations 321 10.3 Toxicity to Aquatic Organisms 322 10.3.1 Decomposers 322 10.3.2 Producers 323 10.3.3 Consumers 324 10.4 The Sources of Toxicity 326 10.4.1 The Release of Plasticizers and Other Additives 326 10.4.2 The Adsorbed Pollutants 328 10.4.3 Physical Damage 329 10.5 Summary and Outlook 330 References 331 11 Chemicals Associated with Microplastics in Urban Waters 345 Yali Wang 11.1 Introduction 345 11.1.1 Chemicals in Microplastics and Its Fragments 347 11.1.2 Chemical Additives in Plastic Consumer Products 356 11.2 The Release of Chemicals from Microplastics and Environmental Levels 358 11.2.1 Phthalic Acid Esters (PAEs) 359 11.2.2 Bisphenol A 362 References 363 12 Interactions between Microplastics and Contaminants in Urban Waters 373 Tianyi Luo, Xiaohu Dai, and Bing-Jie Ni 12.1 Introduction 374 12.2 Sorption of Contaminants on Microplastics 375 12.2.1 Antibiotics 376 12.2.2 Heavy Metals 376 12.2.3 Organic Pollutants 380 12.3 Enrichment of Antibiotic-Resistant Bacteria and Antibiotic Resistance Genes 383 12.3.1 Single Selection 383 12.3.2 Co-Selection 384 12.4 The Effects of Environmental Conditions 386 12.4.1 pH 386 12.4.2 Temperature 386 12.4.3 Salinity 388 12.4.4 Weathering/Aging Effect 388 12.5 Joint Potential Risks 390 12.5.1 For Contaminants Distribution in Aquatic Environment 390 12.5.2 For ARGs and ARB Distribution in Aquatic Environment 391 12.5.3 For Aquatic Organisms 392 12.5.4 For Human Health 393 12.6 Conclusion and Recommendations 395 References 396 13 Nanoplastics in Urban Waters: Recent Advances in the Knowledge Base 407 Ilaria Corsi, Elisa Bergami, Ian J. Allan, and Julien Gigault 13.1 Introduction 407 13.2 Nanoplastics in the Aquatic Environment 408 13.2.1 Nanoplastics or Polymeric Nanoparticles 408 13.2.2 Formation Pathways of Nanoplastics 410 13.2.3 Source of Nanoplastics 411 13.2.4 The Behavior and Environmental Fate of Nanoplastics 412 13.2.5 Interaction of Nanoplastics with Contaminants 414 13.3 Interactions between Nanoplastics and Aquatic Organisms 418 13.3.1 Effects on Aquatic Organisms: From Microalgae to Fish 419 13.4 Ingestion of Nanoplastics in Aquatic Organisms 427 13.5 Concluding Remarks and Future Recommendation 429 Funding 430 Acknowledgements 430 Competing Interests 431 References 431 Index 445

Read more less

Book SynopsisAn expert resource for chemists using stereochemical analysis methods In Chiral Separations and Stereochemical Elucidation: Fundamentals, Methods, and Applications, a team of distinguished researchers delivers a robust and authoritative discussion of the theoretical fundamentals of chiral separation, the most commonly used chiral selectors, and stereochemical elucidation methods. The book offers expert discussions of a variety of chiral separation methods by gas chromatography (GC), supercritical fluid chromatography (SFC), capillary electrophoresis (CE), and liquid chromatography (LC). The authors also describe several methods for stereochemical elucidation, including X-ray crystallography, nuclear magnetic resonance spectroscopy, and chiroptical methods. The explored material is ideal for practicing chemists seeking a resource to help them guide method development and optimization or to explain quality control-complements during target compound production. RTable of ContentsList of Contributors xv Preface xix Part I Fundamentals of Chiral Separation 1 1 Chiral Separation by LC 3 Juliana Cristina Barreiro and Quezia Bezerra Cass 1.1 Introduction 3 1.2 Workflow for LC Chiral Method Development 7 1.3 New Column Technologies 9 1.4 Selected Examples of Fast Separation 12 1.5 Chiral 2D- LC 14 1.5.1 LC–LC and mLC–LC 14 1.5.2 LC × LC and sLC × LC 17 1.6 Future and Perspectives 19 References 20 2 Chiral Separation by GC 27 Oliver Trapp 2.1 Introduction 27 2.2 Chiral Recognition in Gas Chromatography 29 2.2.1 Chiral Recognition by Hydrogen Bonding 31 2.2.2 Chiral Recognition Using Chiral Metal Complexes 31 2.2.3 Chiral Recognition by Host–Guest Interactions 31 2.3 Preparation of Fused- Silica Capillaries for GC with CSPs 33 2.4 Application of CSPs in Chiral Gas Chromatography 34 2.4.1 CSPs with Diamide Selectors 34 2.4.1.1 Chirasil- Val 34 2.4.2 CSPs with CD Selectors 35 2.4.2.1 Heptakis(2,3,6- tri- O- Methyl)- β- Cyclodextrin (Permethyl- β- Cyclodextrin) 38 2.4.2.2 Heptakis(2,3,6- tri- O- Methyl)- β- Cyclodextrin Immobilized to Hydrido Dimethyl Polysiloxane (Chirasil- β- Dex) 39 2.4.2.3 Heptakis(2,6- di- O- Methyl- 3- O- Pentyl)- β- Cyclodextrin 43 2.4.2.4 Hexakis- (2,3,6-tri- O- Pentyl)- α- Cyclodextrin 47 2.4.2.5 Heptakis(2,3,6- tri- O- Pentyl)- β- Cyclodextrin 48 2.4.2.6 Hexakis- (3- O- Acetyl- 2,6- di- O- Pentyl)- α- Cyclodextrin 51 2.4.2.7 Heptakis(3- O- Acetyl- 2,6- di- O- Pentyl)- β- Cyclodextrin 51 2.4.2.8 Octakis(3- O- Butyryl- 2,6- di- O- Pentyl)- γ- Cyclodextrin 53 2.4.2.9 Hexakis/Heptakis/Octakis(2,6- di- O- Alkyl- 3- O- Trifluoroacetyl)- α/β/γ- Cyclodextrins 57 2.4.2.10 Heptakis(2,3- di- O- Acetyl- 6- O-tert- Butyldimethylsilyl)- β- Cyclodextrin (DIAC- 6- TBDMS- β- CD) 58 2.4.2.11 Heptakis(2,3- di- O- Methyl- 6- O-tert- Butyldimethylsilyl)- β- Cyclodextrin (DIME- 6- TBDMS- β- CD) 58 2.4.3 Cyclofructans 62 2.4.4 CSPs with Metal Complexes 65 2.5 Conclusion 69 References 69 3 Chiral Separation by Supercritical Fluid Chromatography 85 Emmanuelle Lipka 3.1 Introduction 85 3.2 Characteristics and Properties of Supercritical Fluids 87 3.3 Development of a Chiral SFC Method 89 3.3.1 Chiral Stationary Phases 89 3.3.2 Mobile Phases 91 3.3.2.1 Mobile Phase: Type of Co- solvent Used 93 3.3.2.2 Mobile Phase: Percentage of Co- solvent Used 94 3.3.2.3 Mobile Phase: Use of Additives 94 3.4 Operating Parameters 94 3.4.1 Effect of the Flow Rate 95 3.4.2 Effect of the Outlet Pressure (Back- pressure) 95 3.4.2.1 Effect of Pressure When the Mobile Phase is a Gas- Like Fluid 96 3.4.2.2 Effect of Pressure When the Mobile Phase is a Liquid- Like Fluid 97 3.4.3 Effect of Temperature 97 3.4.3.1 Effect of Temperature When the Mobile Phase is a Gas- Like Fluid 98 3.4.3.2 Effect of Temperature When the Mobile Phase is a Liquid- Like Fluid 98 3.5 Detection 99 3.6 Scale- Up to Preparative Separation 99 3.7 Conclusion 100 References 101 4 Chiral Separation by Capillary Electrophoresis and Capillary Electrophoresis–Mass Spectrometry: Fundamentals, Recent Developments, and Applications 103 Charles Clark, Govert W. Somsen, and Isabelle Kohler 4.1 Introduction 103 4.2 Principles of Chiral CE 105 4.2.1 Electrophoretic Mobility 105 4.2.2 CE Separation Efficiency 106 4.2.3 Chiral Resolution in CE 107 4.2.4 Chiral Micellar Electrokinetic Chromatography and Capillary Electrochromatography 109 4.3 Short History of Chiral CE Modes 111 4.3.1 Chiral CE 111 4.3.2 Chiral MEKC and Chiral CEC 111 4.4 State of the Art and Recent Developments 112 4.4.1 Common Chiral Selectors 112 4.4.2 Ionic Liquids as Chiral Selectors 117 4.4.3 Nanoparticles as Chiral Selector Carriers 117 4.4.4 Microfluidic Chiral CE 118 4.5 Applications of Chiral CE 119 4.5.1 Pharmaceutical Analysis 119 4.5.2 Food Analysis 120 4.5.3 Environmental Analysis 121 4.5.4 Bioanalysis 123 4.5.5 Forensic Analysis 126 4.6 Chiral CE- MS: Strategies and Challenges 126 4.6.1 Hyphenation Approaches 129 4.6.1.1 Sheath–Liquid and Sheathless CE- MS Interfacing 129 4.6.1.2 Partial- Filling Techniques 130 4.6.1.3 Counter- Migration Techniques 131 4.6.2 Chiral MEKC- MS 132 4.6.3 Chiral CEC- MS 133 4.7 Conclusions and Perspectives 135 References 135 5 Chiral Separations at Semi and Preparative Scale 143 Larry Miller 5.1 Introduction 143 5.2 Selection of Operating Conditions 145 5.3 Batch HPLC Purification 146 5.3.1 Analytical Method Development for Preparative Separations 146 5.3.2 Batch HPLC Examples 148 5.3.2.1 Batch HPLC Example 1 148 5.3.2.2 Batch HPLC Example 2 149 5.4 Steady- State Recycle Introduction 151 5.4.1 SSR Example 1 153 5.5 Simulated Moving Bed Chromatography – Introduction 154 5.5.1 SMB Examples for R&D and Separation of Compound 2 156 5.5.2 Development of a Manufacturing SMB Process (Compound 1) 158 5.5.3 Cost for SMB Processes 160 5.6 Introduction to Supercritical Fluid Chromatography 161 5.6.1 Analytical Method Development for Scale- up to Preparative SFC 162 5.6.2 Preparative SFC Example 1 163 5.6.3 Preparative SFC Example 2 163 5.7 Options for Increasing Purification Productivity 165 5.7.1 Closed- Loop Recycling 165 5.7.2 Stacked Injections 166 5.7.3 Choosing the Best Synthetic Intermediate for Separation 167 5.7.3.1 Choosing Synthetic Step for Separation – HPLC/SMB Example 168 5.7.3.2 Choosing Synthetic Step for Separation – SFC Example 169 5.7.4 Use of Non- Commercialized CSP 170 5.7.5 Immobilized CSP for Preparative Resolution 173 5.7.5.1 Processing of Low Solubility Racemate 173 5.7.5.2 Preparative Resolution of EMD 53986 174 5.8 Choosing a Technique for Preparative Enantioseparation 176 5.9 Conclusion 178 References 179 Part II Chiral Selectors 187 6 Polysaccharides 189 Weston Umstead, Takafumi Onishi, and Pilar Franco 6.1 Introduction 189 6.2 The Early Years 190 6.3 Polysaccharide Chiral Separation Mechanism 193 6.4 Coated Chiral Stationary Phases 197 6.5 Immobilized Chiral Stationary Phases 201 6.6 Applications of Polysaccharide- Derived CSPs 208 6.6.1 Analytical Applications 210 6.6.1.1 Pharmaceuticals 211 6.6.1.2 Agrochemicals 218 6.6.1.3 Food Analysis 219 6.6.2 Preparative Applications 220 6.7 Summation 224 References 224 7 Macrocyclic Antibiotics and Cyclofructans 247 Saba Aslani, Alain Berthod, and Daniel W. Armstrong 7.1 Introduction 247 7.2 Macrocyclic Glycopeptides Physicochemical Properties 248 7.3 Using the Chiral Macrocyclic Glycopeptides Stationary Phases 253 7.3.1 Mobile Phases and Chromatographic Modes 253 7.3.2 Chromatographic Enantioseparations 254 7.3.2.1 Amino Acids and Peptides 254 7.3.2.2 Chiral Compounds 257 7.3.2.3 Particle Structure 257 7.4 Using and Protecting Macrocyclic Glycopeptide Chiral Columns 260 7.4.1 Operating Conditions 260 7.4.2 Storage 261 7.5 Cyclofructans 261 7.5.1 Cyclofructan Structure and Properties 261 7.5.2 Chiral Separations with Cyclofructan- Based Stationary Phases 264 7.5.3 Cyclofructan Stationary Phases Used in the HILIC Mode 264 7.5.4 Cyclofructan Stationary Phases Used in Supercritical Fluid Chromatography 266 7.6 Conclusions 267 References 268 8 Cyclodextrins 273 Gerhard K. E. Scriba, Mari- Luiza Konjaria, and Sulaiman Krait 8.1 Introduction 273 8.2 Structure and Properties 274 8.3 Cyclodextrin Complexes 279 8.4 Application in Separation Science 288 8.4.1 Gas Chromatography 288 8.4.1.1 Types of Cyclodextrins 289 8.4.1.2 Types of Columns 289 8.4.1.3 Separation Mechanisms 291 8.4.1.4 Applications 293 8.4.2 Thin- Layer Chromatography 294 8.4.3 High- Performance Liquid Chromatography 294 8.4.3.1 Types of Columns 295 8.4.3.2 Types of Cyclodextrins 297 8.4.3.3 Separation Mechanisms 298 8.4.3.4 Applications 300 8.4.4 Supercritical Fluid Chromatography 300 8.4.5 Capillary Electromigration Techniques 301 8.4.5.1 Types of Cyclodextrins 301 8.4.5.2 Separation Mechanisms 302 8.4.5.3 Migration Modes and Enantiomer Migration Order Using CDs as Selectors 304 8.4.5.4 Applications 310 8.4.6 Membrane Technologies 312 8.5 Miscellaneous Applications 314 8.6 Conclusions and Outlook 315 References 315 9 Pirkle Type 325 Maria Elizabeth Tiritan, Madalena Pinto, and Carla Fernandes 9.1 Introduction 325 9.2 CSPs Developed by Pirkle’s Group: Chronological Evolution 327 9.3 Pirkle- Type CSPs Developed by Other Research Groups 334 9.4 Example of Applications in Analytical and Preparative Scales 340 9.4.1 Analytical Applications 341 9.4.2 Preparative Applications 349 9.5 Conclusions and Perspectives 349 References 350 10 Proteins 363 Jun Haginaka 10.1 Introduction 363 10.2 Preparation of Protein- and Glycoprotein- Based Chiral Stationary Phases 364 10.3 Types of Protein- and Glycoprotein- Based Chiral Stationary Phases 368 10.3.1 Proteins 368 10.3.1.1 Bovine Serum Albumin 368 10.3.1.2 Human Serum Albumin 370 10.3.1.3 Trypsin and α- Chymotrypsin 372 10.3.1.4 Lysozyme and Pepsin 372 10.3.1.5 Fatty Acid- Binding Protein 373 10.3.1.6 Penicillin G Acylase 375 10.3.1.7 Streptavidin 375 10.3.1.8 Lipase 376 10.3.2 Glycoproteins 376 10.3.2.1 Human α 1 - Acid Glycoprotein 376 10.3.2.2 Chicken Ovomucoid 377 10.3.2.3 Chicken α 1- Acid Glycoprotein 378 10.3.2.4 Avidin 380 10.3.2.5 Riboflavin- Binding Protein and Ovotransferrin 380 10.3.2.6 Cellobiohydrolase 381 10.3.2.7 Glucoamylase 383 10.3.2.8 Antibody (Immunoglobulin G) 385 10.3.2.9 Nicotinic Acetylcholine Receptor and Human Liver Organic Cation Transporter 387 10.4 Chiral Recognition Mechanisms on Proteinand Glycoprotein- Based Chiral Stationary Phases 387 10.4.1 Human Serum Albumin 387 10.4.2 Penicillin G Acylase 389 10.4.3 Human α 1- Acid Glycoprotein 390 10.4.4 Turkey Ovomucoid 392 10.4.5 Chicken α 1- Acid Glycoprotein 393 10.4.6 Cellobiohydrolase 395 10.4.7 Antibody 396 10.4.8 Nicotinic Acetylcholine Receptor and Human Liver Organic Cation Transporter 400 10.5 Conclusions 401 References 402 11 Chiral Stationary Phases Derived from Cinchona Alkaloids 415 Michael Lämmerhofer and Wolfgang Lindner 11.1 Introduction 415 11.2 Cinchona Alkaloid- Derived Chiral Stationary Phases 416 11.3 Chiral Recognition 420 11.4 Chromatographic Retention Mechanisms 424 11.4.1 Multimodal Applicability 424 11.4.2 Surface Charge of Cinchonan- Based CSPs 424 11.4.3 Retention Mechanisms and Models, and Method Development on Chiral WAX CSPs 427 11.4.4 Retention Mechanisms and Method Development on ZWIX CSPs 430 11.5 Structural Variants of Cinchona Alkaloid CSPs and Immobilization Chemistries 436 11.6 Cinchonan- Based UHPLC Column Technologies 442 11.7 Applications 446 11.7.1 Pharmaceutical and Biotechnological Applications 446 11.7.2 Biomedical Applications 453 11.8 Conclusions 460 References 460 Part III Methods for Stereochemical Elucidation 473 12 X- Ray Crystallography for Stereochemical Elucidation 475 Ademir F. Morel and Robert A. Burrow 12.1 Introduction 475 12.2 Absolute Structure and Absolute Configuration 476 12.3 Best Practices 482 12.4 Structure Validation 486 12.5 The Absolute Configuration of (+)- Lanatine A 486 12.6 The Absolute Configuration of the Diacetylated Form of Acrenol and the Acetylated Form of Humirianthol 488 12.7 The Absolute Configuration of Ester Form of Clemateol 491 12.8 Relative Configurations of Waltherione A, Waltherione B, and Vanessine 492 12.9 The Absolute Configuration of Condaline A 493 12.10 CSD Deposit Numbers 496 12.11 Conclusions and Future Directions 498 References 498 13 NMR for Stereochemical Elucidation 505 Xiaolu Li, Xiaoliang Yang, and Han Sun 13.1 Conventional NMR Methods for Stereochemical Elucidation 505 13.1.1 Determination of the Planar Structure Using 1D 1 H, 13 C NMR (DEPT), 2D HSQC, COSY, TOCSY, HMBC 506 13.1.2 Determination of Relative Configuration Using J- Couplings and NOEs/ROEs 507 13.1.2.1 Scalar Coupling 507 13.1.2.2 NOE/ROE 510 13.1.2.3 Examples of Stereochemical Elucidation Using J- Couplings and NOEs/ROEs 510 13.2 Determination of the Relative Configuration Using Anisotropic NMR- Based Methods 516 13.2.1 Basic Principles of Anisotropic NMR Parameters 517 13.2.2 Alignment Media 518 13.2.2.1 Preparation of Anisotropic Sample with PMMA Gel 520 13.2.2.2 Preparation of Anisotropic Sample with AAKLVFF 521 13.2.3 Acquisition of the Anisotropic NMR Data 522 13.2.4 Computational Approaches for Analyzing Anisotropic NMR Data 525 13.2.5 Successful Examples of Determination of Relative Configuration of Challenging Molecules Using Anisotropic NMR 528 13.3 Determination of the Relative Configuration Using DP 4 Probability and CASE- 3D 529 13.4 Determination of the Absolute Configuration Using a Combination of NMR Spectroscopy and Chiroptical Spectroscopy 533 13.5 Determination of the Absolute Configuration Using NMR Alone 534 13.5.1 Mosher Ester Analysis 535 13.5.2 Other Chiral Derivatizing Agents 536 13.6 Future Perspective 536 References 537 14 Absolute Configuration from Chiroptical Spectroscopy 551 Fernando Martins dos Santos Junior and João Marcos Batista Junior 14.1 Introduction 551 14.2 Chiroptical Methods 554 14.2.1 Optical Rotation and Optical Rotatory Dispersion 554 14.2.1.1 Instrumentation 556 14.2.1.2 Measurements 557 14.2.2 Electronic Circular Dichroism 558 14.2.2.1 Instrumentation 560 14.2.2.2 Measurements 561 14.2.3 Vibrational Circular Dichroism and Raman Optical Activity 561 14.2.3.1 Instrumentation 563 14.2.3.2 Measurements 565 14.2.4 Simulation of Chiroptical Properties 567 14.2.4.1 Common Theoretical Steps 568 14.2.4.2 OR and ORD Simulations 570 14.2.4.3 ECD Simulations 572 14.2.4.4 VCD and ROA Simulations 573 14.2.5 Examples of Application 575 14.2.5.1 OR 575 14.2.5.2 ORD 577 14.2.5.3 ECD 578 14.2.5.4 VCD 579 14.2.5.5 ROA 581 14.2.5.6 Association of Different Chiroptical Methods 582 14.3 Concluding Remarks 585 References 586 Index 593

Read more less

Book SynopsisPERSPECTIVES ON STRUCTURE AND MECHANISM IN ORGANIC CHEMISTRY Beyond the basics physical organic chemistry textbook, written for advanced undergraduates and beginning graduate students Based on the author's first-hand classroom experience, Perspectives on Structure and Mechanism in Organic Chemistry uses complementary conceptual models to give new perspectives on the structures and reactions of organic compounds, with the overarching goal of helping students think beyond the simple models of introductory organic chemistry courses. Through this approach, the text better prepares readers to develop new ideas in the future. In the 3rd Edition, the author thoroughly updates the topics covered and reorders the contents to introduce computational chemistry earlier and to provide a more natural flow of topics, proceeding from substitution, to elimination, to addition. About 20% of the 438 problems have been either replaced or updated, with answers available in the companion solutions manual. To remind students of the human aspect of science, the text uses the names of investigators throughout the text and references material to original (or accessible secondary or tertiary) literature as a guide for students interested in further reading. Sample topics covered in Perspectives on Structure and Mechanism in Organic Chemistry include: Fundamental concepts of organic chemistry, covering atoms and molecules, heats of formation and reaction, bonding models, and double bondsDensity functional theory, quantum theory of atoms in molecules, Marcus Theory, and molecular simulationsAsymmetric induction in nucleophilic additions to carbonyl compounds and dynamic effects on reaction pathwaysReactive intermediates, covering reaction coordinate diagrams, radicals, carbenes, carbocations, and carbanionsMethods of studying organic reactions, including applications of kinetics in studying reaction mechanisms and Arrhenius theory and transition state theory A comprehensive yet accessible reference on the subject, Perspectives on Structure and Mechanism in Organic Chemistry is an excellent learning resource for students of organic chemistry, medicine, and biochemistry. The text is ideal as a primary text for courses entitled Advanced Organic Chemistry at the upper undergraduate and graduate levels.Table of ContentsPreface xi Chapter 1 Fundamental Models of Organic Chemistry 1 1.1 Atoms and Molecules 1 Basic Concepts 1 Molecular Dimensions 5 1.2 Heats of Formation and Reaction 8 Experimental Determination of Heats of Formation 8 Bond Increment Calculation of Heats of Formation 10 Group Increment Calculation of Heats of Formation 11 Heats of Formation and the Concept of Protobranching 13 Homolytic and Heterolytic Bond Dissociation Energies 15 1.3 Bonding Models 18 Electronegativity and Bond Polarity 20 Complementary Theoretical Models of Bonding 23 Pictorial Representations of Bonding Concepts 27 sp3 Hybridization 28 Are There sp3 Hybrid Orbitals in Methane? 30 Hybridization and Molecular Geometry 34 Variable Hybridization 35 1.4 Complementary Models for the Double Bond 41 The σ,π Description of Ethene 41 The Bent Bond Description of Ethene 42 Predictions of Physical Properties with the Two Models 42 1.5 The Role of Complementary Models in Organic Chemistry 46 Problems 47 Chapter 2 Introduction to Computational Chemistry 53 2.1 Hückel Molecular Orbital Theory 53 Correlation of Physical Properties with Results of HMO Calculations 63 Other Parameters Generated Through HMO Theory 67 Properties of Odd Alternant Hydrocarbons 69 The Frost Circle 74 2.2 Aromaticity 75 Benzene 77 Other Aromatic Systems 81 Polycyclic Conjugated Systems 85 Larger Annulenes 90 Dewar Resonance Energy and Absolute Hardness 93 2.3 Contemporary Computational Methods 95 Extended Hückel Theory 95 Semiempirical Methods 96 Ab Initio Theory 97 2.4 Localized Molecular Orbitals 100 Perturbational Molecular Orbital Theory 104 Atoms in Molecules 108 2.5 Density Functional Theory 112 2.6 Another Look at Valence Bond Theory 114 Resonance Structures and Resonance Energies 114 Interpreting Computational Results 117 Problems 119 Chapter 3 Stereochemistry 127 3.1 Representations of Three-Dimensional Structures 127 3.2 Stereoisomerism 130 Isomerism 130 Symmetric, Asymmetric, Dissymmetric, and Nondissymmetric Molecules 133 Fischer Projections 146 Additional Stereochemical Designations 149 3.3 Physical Manifestations of Chirality 159 Optical Activity 159 Configuration and Optical Activity 161 Other Physical Properties of Stereoisomers 166 3.4 Stereotopicity 167 Stereochemical Relationships of Substituents 167 Chirotopicity and Stereogenicity 171 Problems 172 Chapter 4 Molecular Geometry and Steric Energy 183 4.1 Designation of Molecular Conformation 183 4.2 Conformational Analysis 187 Torsional Strain 187 van der Waals Strain 191 Angle Strain and Baeyer Strain Theory 193 Application of Conformational Analysis to Cycloalkanes 194 Conformational Analysis of Substituted Cyclohexanes 198 4.3 Molecular Mechanics 204 4.4 Anomeric Effect 221 4.5 Strain and Molecular Stability 225 Problems 237 Chapter 5 Reactive Intermediates 243 5.1 Reaction Coordinate Diagrams 243 5.2 Radicals 244 Early Evidence for the Existence of Radicals 244 Detection and Characterization of Radicals 246 Structure and Bonding of Radicals 251 Thermochemical Data for Radicals 253 Generation of Radicals 255 Radical Chain Reactions 256 5.3 Carbenes 263 Structure and Geometry of Carbenes 263 Generation of Carbenes 267 Reactions of Carbenes 268 5.4 Carbocations 272 Carbonium Ions and Carbenium Ions 272 Structure and Geometry of Carbocations 274 The 2-Norbornyl Cation 281 Carbocation Rearrangements 283 Radical Cations 285 5.5 Carbanions 290 Generation of Carbanions 294 Stability of Carbanions 296 Reactions of Carbanions 296 5.6 Choosing Models of Reactive Intermediates 298 Problems 299 Chapter 6 Determining Reaction Mechanisms 305 6.1 Reaction Mechanisms 305 6.2 Methods to Determine Reaction Mechanisms 306 Identification of Reaction Products 306 Determination of Intermediates 306 Crossover Experiments 311 Isotopic Labeling 313 Stereochemical Studies 314 Solvent Effects 315 Computational Studies 317 6.3 Applications of Kinetics in Studying Reaction Mechanisms 319 6.4 Arrhenius Theory and Transition State Theory 326 6.5 Reaction Barriers and Potential Energy Surfaces 337 6.6 Kinetic Isotope Effects 348 Primary Kinetic Isotope Effects 349 Secondary Kinetic Isotope Effects 354 Tunneling and Isotope Effects 359 Solvent Isotope Effects 362 6.7 Substituent Effects 363 6.8 Linear Free Energy Relationships 368 Problems 383 Chapter 7 Acid and Base Catalysis of Organic Reactions 393 7.1 Acidity and Basicity of Organic Compounds 393 Acid–Base Measurements in Solution 393 Acid–Base Reactions in the Gas Phase 402 Comparison of Gas Phase and Solution Acidities 408 Acidity Functions 410 7.2 Acid and Base Catalysis of Chemical Reactions 413 Specific Acid Catalysis 413 General Acid Catalysis 414 Brønsted Catalysis Law 417 7.3 Acid and Base Catalysis of Reactions of Carbonyl Compounds and Carboxylic Acid Derivatives 418 Addition to the Carbonyl Group 418 Enolization of Carbonyl Compounds 422 Hydrolysis of Acetals 426 Acid-Catalyzed Hydrolysis of Esters 428 Alkaline Hydrolysis of Esters 431 Hydrolysis of Amides 437 Problems 441 Chapter 8 Substitution Reactions 449 8.1 Introduction 449 8.2 Nucleophilic Aliphatic Substitution 450 8.3 The SN1 Reaction 453 Kinetics 453 Structural Effects in SN1 Reactions 454 Solvent Polarity and Nucleophilicity 455 Solvated Ions and Ion Pairs 459 Anchimeric Assistance in SN1 Reactions 464 Nonclassical Carbocations in SN1 Reactions 469 8.4 The SN2 Reaction 471 Stereochemistry 471 Solvent Effects 473 Substrate Effects 477 8.5 Quantitative Measures of Nucleophilicity 480 Brønsted Correlations 481 Hard–Soft Acid–Base Theory and Nucleophilicity 482 Edwards Equations 483 Swain-Scott Equation 484 Mayr Equations 485 The α-Effect 488 Leaving Group Effects in SN2 Reactions 489 Aliphatic Substitution and Single Electron Transfer 490 8.6 Electrophilic Aromatic Substitution 495 The SEAr Reaction 495 Quantitative Measurement of SEAr Rate Constants: Partial Rate Factors 498 Lewis Structures as Models of Reactivity in SEAr Reactions 500 8.7 Nucleophilic Aromatic and Vinylic Substitution 504 Nucleophilic Aromatic Substitution 504 Nucleophilic Vinylic Substitution 509 8.8 Substitution Involving Benzyne Intermediates 511 8.9 Radical-Nucleophilic Substitution 518 8.10 The Impermanence of Mechanistic Labels 521 Problems 521 Chapter 9 Elimination Reactions 529 9.1 Introduction 529 9.2 Dehydrohalogenation and Related 1,2-Elimination Reactions 534 Potential Energy Surfaces for 1,2-Elimination 534 Competition Between Substitution and Elimination 540 Stereochemistry of 1,2-Elimination Reactions 541 Elimination Reactions to Produce Alkynes 547 Regiochemistry of 1,2-Elimination Reactions 548 9.3 Other 1,2-Elimination Reactions 558 Dehalogenation of Vicinal Dihalides 558 Dehydration of Alcohols 561 Deamination of Amines 568 Pyrolytic Eliminations 572 Problems 578 Chapter 10 Addition Reactions 587 10.1 Introduction 587 10.2 Addition of Halogens to Alkenes 588 Electrophilic Addition of Bromine to Alkenes 588 Role of Charge-Transfer Complexes in Bromine Addition Reactions 592 Kinetics of Bromine Addition Reactions 593 Solvent Effects in Bromine Additions 596 Reversibility of Bromine Addition 598 Intermediates in the Addition of Bromine to Alkyl-Substituted Alkenes 599 Intermediates in the Addition of Bromine to Aryl-Substituted Alkenes 604 Summary of Bromine Addition 608 Addition of Other Halogens to Alkenes 609 10.3 Other Addition Reactions 618 Addition of Hydrogen Halides to Alkenes 618 Hydration of Alkenes 625 Oxymercuration 628 Hydroboration 632 Epoxidation 637 Electrophilic Addition to Alkynes and Cumulenes 639 Nucleophilic Addition to Alkenes and Alkynes 647 Nucleophilic Addition to Carbonyl Compounds 651 Problems 656 Chapter 11 Pericyclic Reactions 661 11.1 Introduction 661 11.2 Electrocyclic Transformations 665 Definitions and Selection Rules 665 MO Correlation Diagrams 670 State Correlation Diagrams 675 11.3 Sigmatropic Reactions 678 Selection Rules for Sigmatropic Reactions 679 Other Examples of Sigmatropic Reactions 687 11.4 Cycloaddition Reactions 691 Introduction 691 Ethene Dimerization 692 The Diels–Alder Reaction 694 Selection Rules for Cycloaddition Reactions 698 11.5 Other Pericyclic Reactions 705 Cheletropic Reactions 705 Double Group Transfer Reactions 707 Ene Reactions 709 11.6 A General Selection Rule for Pericyclic Reactions 711 11.7 Alternative Conceptual Models for Pericyclic Reactions 713 Frontier Molecular Orbital Theory 713 Hückel and Möbius Aromaticity of Transition Structures 719 Synchronous and Nonsynchronous Pericyclic Reactions 725 Potential Energy Surfaces and Ambimodal Reactions 729 11.8 Reaction Dynamics and Potential Energy Surfaces 729 Problems 735 Chapter 12 Organic Photochemistry 745 12.1 Energy and Electronic States 745 12.2 Photophysical Processes 747 Designation of Spectroscopic Transitions 748 Selection Rules for Radiative Transitions 754 Fluorescence and Phosphorescence 756 Energy Transfer and Electron Transfer 759 12.3 Photochemical Kinetics 763 Actinometry and Quantum Yield Determinations 763 Rate Constants for Unimolecular Processes 764 Transient Detection and Monitoring 765 Bimolecular Decay of Excited States: Stern–Volmer Kinetics 768 12.4 Physical Properties of Excited States 770 Acidity and Basicity in Excited States 770 Bond Angles and Dipole Moments of Excited-State Molecules 774 12.5 Representative Photochemical Reactions 777 Photochemical Reactions of Alkenes and Dienes 778 Photochemical Reactions of Carbonyl Compounds 790 Photochemical Reactions of α,ß-Unsaturated Carbonyl Compounds 798 Photochemical Reactions of Aromatic Compounds 800 Photosubstitution Reactions 802 σ Bond Photodissociation Reactions 803 Singlet Oxygen and Organic Photochemistry 808 12.6 Applications of Organic Photochemistry 811 Problems 822 References for Selected Problems 831 Index 837

Read more less

Book SynopsisSOLUTIONS MANUAL FOR PERSPECTIVES ON STRUCTURE AND MECHANISM IN ORGANIC CHEMISTRY Based on the author's first-hand classroom experience, this solutions manual complements the 3rd edition of Perspectives on Structure and Mechanism in Organic Chemistry. The solutions to the 438 textbook problems help students increase their understanding of physical organic chemistry, and more than 550 references stimulate their engagement with the chemical literature.Table of ContentsChapter 1 Fundamental Models of Organic Chemistry 1 Chapter 2 Introduction to Computational Chemistry 11 Chapter 3 Stereochemistry 31 Chapter 4 Molecular Geometry and Steric Energy 49 Chapter 5 Reactive Intermediates 57 Chapter 6 Determining Reaction Mechanisms 65 Chapter 7 Acid and Base Catalysis of Organic Reactions 73 Chapter 8 Substitution Reactions 81 Chapter 9 Elimination Reactions 93 Chapter 10 Addition Reactions 105 Chapter 11 Pericyclic Reactions 117 Chapter 12 Organic Photochemistry 133

Read more less

Book SynopsisPlant Centromere Biology covers plant centromere research. The book covers several topics including the structure of centromeres from several plant species including Arabidopsis thaliana, rice, maize, wheat, and beet.Table of ContentsContributors vii Preface ix Chapter 1 Arabidopsis Centromeres 3 Minoru Murata Chapter 2 Rice Centromeres 15 Jiming Jiang Chapter 3 Maize Centromeres 25 Gernot Presting Chapter 4 A Molecular Cytogenetic Analysis of the Structure, Evolution, and Epigenetic Modifi cations of Major DNA Sequences in Centromeres of Beta Species 39 Falk Zakrzewski, Beatrice Weber, and Thomas Schmidt Chapter 5 Centromere Synteny among Brachypodium, Wheat, and Rice 57 Lili Qi, Bernd Friebe, and Bikram S. Gill Chapter 6 CENH3 for Establishing and Maintaining Centromeres 67 Inna Lermontova and Ingo Schubert Chapter 7 Holokinetic Centromeres 83 Stefan Heckmann and Andreas Houben Chapter 8 Is the Heterochromatin of Meiotic Neocentromeres a Remnant of the Early Evolution of the Primitive Centromere? 95 María J. Puertas and Alfredo Villasante Chapter 9 Misdivision of Centromeres 111 Adam J. Lukaszewski Chapter 10 Female Meiotic Drive in Monkeyfl owers: Insight into the Population Genetics of Selfi sh Centromeres 129 Lila Fishman Chapter 11 Plant Centromere Epigenetics 147 Ryan N. Douglas and James A. Birchler Chapter 12 Centromere Evolution 159 Jiming Jiang Chapter 13 Centromere-Mediated Generation of Haploid Plants 169 Maruthachalam Ravi and Simon W.-L. Chan Chapter 14 Engineered Plant Chromosomes 183 Robert T. Gaeta and James A. Birchler Index 193 Color plate is located between pages 182 and 183

Read more less

Book Synopsis* Comprehensive and accessible introduction to the process of photosynthesis in marine plants and algae * Reader-friendly, accessible style with text boxes to help clarify complex points * Each section contains a summary which sets out the main points * Colour plate section .Table of ContentsAbout the authors ix Preface xi About the companion website xiii Part I Plants and the Oceans 1 Introduction 1 Chapter 1 The evolution of photosynthetic organisms in the oceans 5 Chapter 2 The different groups of marine plants 15 2.1 Cyanobacteria 16 2.2 Eukaryotic microalgae 17 2.3 Photosymbionts 23 2.4 Macroalgae 27 2.5 Seagrasses 34 Chapter 3 Seawater as a medium for photosynthesis and plant growth 39 3.1 Light 40 3.2 Inorganic carbon 45 3.3 Other abiotic factors 52 Summary notes of Part I 55 Part II Mechanisms of Photosynthesis, and Carbon Acquisition in Marine Plants 57 Introduction to Part II 57 Chapter 4 Harvesting of light in marine plants: The photosynthetic pigments 61 4.1 Chlorophylls 61 4.2 Carotenoids 63 4.3 Phycobilins 64 Chapter 5 Light reactions 67 5.1 Photochemistry: excitation, de-excitation, energy transfer and primary electron transfer 67 5.2 Electron transport 74 5.3 ATP formation 76 5.4 Alternative pathways of electron flow 77 Chapter 6 Photosynthetic CO2-fixation and -reduction 81 6.1 The Calvin cycle 81 6.2 CO2-concentrating mechanisms 89 Chapter 7 Acquisition of carbon in marine plants 95 7.1 Cyanobacteria and microalgae 96 7.2 Photosymbionts 101 7.3 Macroalgae 104 7.4 Seagrasses 118 7.5 Calcification and photosynthesis 122 Summary notes of Part II 124 Part III Quantitative Measurements, and Ecological Aspects, of Marine Photosynthesis 127 Introduction to Part III 127 Chapter 8 Quantitative measurements 129 8.1 Gas exchange 131 8.2 How to measure gas exchange 133 8.3 Pulse amplitude modulated (PAM) fluorometry 137 8.4 How to measure PAM fluorescence 142 8.5 What method to use: Strengths and limitations 146 Chapter 9 Photosynthetic responses, acclimations and adaptations to light 157 9.1 Responses of high- and low-light plants to irradiance 157 9.2 Light responses of cyanobacteria and microalgae 163 9.3 Light effects on photosymbionts 164 9.4 Adaptations of carbon acquisition mechanisms to light 169 9.5 Acclimations of seagrasses to high and low irradiances 169 Chapter 10 Photosynthetic acclimations and adaptations to stress in the intertidal 175 10.1 Adaptations of macrophytes to desiccation 175 10.2 Other stresses in the intertidal 181 Chapter 11 How some marine plants modify the environment for other organisms 183 11.1 Epiphytes and other ‘thieves’ 183 11.2 Ulva can generate its own empires 185 11.3 Seagrasses can alter environments for macroalgae and vice versa 187 11.4 Cyanobacteria and eukaryotic microalgae 189 Chapter 12 Future perspectives on marine photosynthesis 191 12.1 ‘Harvesting’ marine plant photosynthesis 191 12.2 Predictions for the future 192 12.3 Scaling of photosynthesis towards community and ecosystem production 194 Summary notes of Part III 197 References 199 Index 203

Read more less

Book SynopsisLABORATORY GUIDE TO ENZYMOLOGY An accessible guide to understanding the foundations of enzymology at its application in drug discovery Enzymes are highly specialized proteins necessary for performing specific biochemical reactions essential for life in all organisms. In disease, the functioning of these enzymes can become altered and, therefore, enzymes represent a large class of key targets for drug discovery. In order to successfully target dysfunctional enzymes pharmaceutically, the unique mechanism of each enzyme must be understood through thorough and in-depth kinetic analysis. The topic of enzymology can appear challenging due its interdisciplinary nature combining concepts from biology, chemistry, and mathematics. Laboratory Guide to Enzymology brings together the theory of enzymology and associated lab-based work to offer a practical, accessible guide encompassing all three scientific disciplines. Beginning with a brief introduction to proteins and enzymes, the book slowly i

Read more less

Book SynopsisMolecules Engineered Against Oncogenic Proteins and Cancer A comprehensive review of the latest molecular advances in cancer treatment Featuring 91 total small molecule kinase/KRAS inhibitors, 80 of which are FDA-approved, Molecules Engineered Against Oncogenic Proteins and Cancer documents the recent scientific advances that have transformed one of medicine's most challenging areascancer treatment. Most of these inhibitors specifically block oncogene-induced carcinogenic proteins with results that have dramatically advanced the treatment of cancer. In addition, the structural formulas of more than 100 kinase/KRAS inhibitors in clinical trials are presented. With a very well-known chemist as an author, Molecules Engineered Against Oncogenic Proteins and Cancer includes information on: Each molecule's structure, function of the kinase target and relevance to cancer, the drug discovery process, and molecular details of drug action MuTable of ContentsPreface vii Chapter 1. Introduction 1 1.1 Types of Protein Kinases 1 1.2 Protein Kinase Domains 1 1.3 ATP-Binding Site 2 1.4 Types of Kinase Inhibitors 3 1.5 Brief History of Smallmolecule Kinase Inhibitors 5 1.6 Peak 12-Month Sales for Leading Kinase Inhibitors 7 1.7 Approved Kinase Inhibitors 7 Chapter 2. BCR-ABL Inhibitors 18 2.1 Imatinib* (1) 19 2.2 Nilotinib* (2) 24 2.3 Dasatinib* (3) 27 2.4 Bosutinib* (4) 30 2.5 Ponatinib* (5) 33 2.6 Olvermbatinib** (6) 37 2.7 Asciminib* (7) 38 Chapter 3. BTK Inhibitors 43 3.1 Ibrutinib* (8) 45 3.2 Acalabrutinib* (9) 51 3.3 Zanubrutinib* (10) 54 3.4 Tirabrutinib** (11) 57 3.5 Orelabrutinib** (12) 58 Chapter 4. EGFR/HER Family Inhibitors 59 4.1 Gefitinib* (13) 61 4.2 Erlotinib * (14) 67 4.3 Icotinib** (15) 72 4.4 Afatinib* (16) 74 4.5 Dacomitinib* (17) 77 4.6 Osimertinib* (18) 80 4.7 Mobocertinib* (19) 86 4.8 Lapatinib* (20) 90 4.9 Tucatinib* (21) 93 4.10 Neratinib* (22) 95 Chapter 5. VEGFR/Multikinase Inhibitors 97 5.1 Sorafenib* (23) 99 5.2 Regorafenib* (24) 104 5.3 Sunitinib* (25) 106 5.4 Pazopanib* (26) 112 5.5 Axitinib* (27) 114 5.6 Nintedanib* (28) 117 5.7 Apatinib** (29) 121 5.8 Lenvatinib* (30) 122 5.9 Tovozanib* (31) 125 Chapter 6. CDK4/6 Inhibitors 127 6.1 Palbociclib* (32) 129 6.2 Ribociclib*(33) 136 6.3 Abemaciclib* (34) 139 6.4 Trilaciclib* (35) 142 Chapter 7. JAK Inhibitors 144 7.1 Tofacitinib* (36) 147 7.2 Baricitinib* (37) 151 7.3 Peficitinib** (38) 153 7.4 Upadacitinib* (39) 158 7.5 Delgocitinib** (40) 161 7.6 Filgotinib** (41) 163 7.7 Abrocitinib* (42) 166 7.8 Ruxolitinib* (43) 170 7.9 Fedratinib* (44) 173 7.10 Pacritinib* (45) 175 7.11 Ritlecitinib # (46) 177 7.12 Brepocitinib # (47) 181 7.13 Ropsacitinib # (48) 184 Chapter 8. Allosteric TYK2 Inhibitors 187 8.1 Deucravacitinib* (49) 189 Chapter 9. ALK/multikinase Inhibitors 195 9.1 Crizotinib* (50) 197 9.2 Ceritinib* (51) 202 9.3 Alectinib* (52) 205 9.4 Brigatinib* (53) 207 9.5 Lorlatinib* (54) 210 Chapter 10. BRAF/Multikinase Inhibitors 214 10.1 Vemurafenib* (55) 216 10.2 Dabrafenib* (56) 222 10.3 Encorafenib* (57) 225 Chapter 11. MEK Inhibitors 227 11.1 Trametinib* (58) 228 11.2 Cobimetinib* (59) 232 11.3 Binimetinib* (60) 235 11.4 Selumetinib* (61) 237 Chapter 12. RET/Multikinase Inhibitors 240 12.1 Vandetanib* (62) 242 12.2 Cabozantinib* (63) 245 12.3 Selpercatinib* (64) 247 12.4 Pralsetinib* (65) 251 Chapter 13. FGFR Inhibitors 253 13.1 Erdafitinib* (66) 255 13.2 Pemigatinib* (67) 260 13.3 Infigratinib* (68) 263 13.4 Futibatinib* (69) 265 Chapter 14. PI3K Inhibitors 267 14.1 Alpelisib* (70) 269 14.2 Idelalisib* (71) 273 14.3 Duvelisib* (72) 277 14.4 Umbralisib* (73) 279 14.5 Copanlisib* (74) 281 Chapter 15. TRK/Multikinase Inhibitors 284 15.1 Larotrectinib* (75) 285 15.2 Entrectinib* (76) 288 15.3 Repotrectinib # (77) 291 Chapter 16. MET Inhibitors 294 16.1 Capmatinib* (78) 295 16.2 Tepotinib* (79) 297 Chapter 17. KIT/PDGFR/Multkinase Inhibitors 299 17.1 Avapritinib* (80) 301 17.2 Ripretinib* (81) 304 Chapter 18. FLT3 Inhibitors 306 18.1 Midostaurin* (82) 308 18.2 Gilteritinib* (83) 313 Chapter 19. mTOR Inhibitors 315 19.1 Sirolimus* and Analogs (84) 317 Chapter 20. Other Kinase Inhibitors 322 20.1 Netarsudil* (85) 324 20.2 Belumosudil* (86) 326 20.3 Fostamatinib* (87) 328 20.4 Pexidartinib* (88) 331 Chapter 21. KRAS Inhibitors 335 21.1 Sotorasib* (89) 337 21.2 Adagrasib* (90) 346 21.3 Jdq443 # (91) 350 Chapter 22. An Overview of the Discovery Process for Medically Useful Inhibitors of Oncogenic Protein Kinases 353 22.1 High-quality Leads 353 22.2 Integrating Substructures from Different High Quality Leads or Established Inhibitors 355 22.3 Variation of Hinge-binding Nucleus 357 22.4 Macrocyclization 359 22.5 Fragment-based Approach 360 22.6 Covalent Inhibitors 361 22.7 Strategic Structural Modification of Prior Drugs 362 22.8 Exploiting a Specific Kinase Pocket to Optimize Selectivity 364 22.9 Solvent-exposed Appendages to Enhance Solubility and PK Properties 367 Chapter 23. Targeted Molecular Anticancer Therapies – Successes and Challenges 368 23.1 The Beginning 368 23.2 Further Developments 368 23.3 Biomarker-driven Drug Development 369 23.4 Mitigation of Drug Resistance 370 23.5 Miscellaneous Approaches 371 23.6 Discovery Chemistry 373 Appendix 1. First FDA Approvals by Year 374 Appendix 2. Kinase/KRAS Inhibitors in Development 375 Appendix 3. Visualization of Differentially Expressed Kinases in Cancer 378 Appendix 4. M & A Transactions Driven by Oncology-focused Kinase and KRAS Inhibitors 379 Appendix 5. Alphabetic List of Oncogenic Protein Inhibitors 380

Read more less

Book SynopsisNew research tools have revealed many surprising aspects of the dynamic nature of lipids and their participation in processes such as recognition, intra- and inter-cellular signalling, deterrence and defence against pathogens, membrane trafficking and protein function. This is in addition to new information on the more established roles of plant lipids as structural components of membranes and as long-term storage products. Plant lipids are also increasingly being seen as sources of a new generation of environmentally friendly, biodegradable and renewable industrial products, including biopolymers and high grade lubricants. This volume provides a broad overview of plant lipid research and its many applications, linking the various disciplines and providing an interesting and wide-ranging perspective on this fast-moving field. Extensive lists of references are provided, totalling well over two thousand non-redundant citations and offering a point of entry to the Trade Review"...this volume provides a review of recent advances of some essential aspects in the biochemistry, molecular biology and biotechnology of plant lipids." (Hartmut Lichtenthaler, Insititute of Botany, University of Karlsruhe, Germany in Journal of Plant Physiology 162 (2005)) "(the book)...guarantees topical reviews, which are needed for the scientific community especially for those newly starting their research in one of the covered fields." (Hartmut Lichtenthaler, Insititute of Botany, University of Karlsruhe, Germany in Journal of Plant Physiology 162 (2005)).Table of Contents1. The study and utilisation of plant lipids: from margarine to lipid rafts. Denis J. Murphy, Biotechnology Unit, School of Applied Sciences, University of Glamorgan, UK. 2. Fatty acid biosynthesis. John L. Harwood, School of Biosciences, University of Cardiff, UK. 3. Fatty acid manipulation. David Hildebrand, Keshun Yu, Charles McCracken and Suryadevara S. Rao, Department of Agronomy, Agricultural Science Center, North Lexington, Kentucky, USA. 4. Non-food lipids. Sevim Z. Erhan, United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, Illinois, USA and Atanu Adhvaryu, Chemical Engineering Department, Pennsylvania State University, Pennsylvania, USA. 5. Membrane lipids. Peter Dörmann, Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Golm, Germany. 6. Storage lipids. Randall J. Weselake, Department of Chemistry and Biochemistry, University of Lethbridge, Alberta, Canada. 7. Lipid-associated proteins. Denis J. Murphy, Biotechnology Unit, School of Applied Sciences, University of Glamorgan, United Kingdom. 8. The plant cuticle: formation and structure of epidermal surfaces. L. Kunst and A.L. Samuels, Department of Botany, University of British Columbia, Vancouver, Canada and R. Jetter, Department of Chemistry and Department of Botany, University of British Columbia, Vancouver, Canada. 9. Inositol-containing lipids - roles in cellular signalling. Bjørn K. Drøbak, Department of Disease and Stress Biology, John Innes Centre, Norwich, UK. 10. Oxylipins. Sabine Rosahl, Department of Stress and Developmental Biology, Institute of Plant Biochemistry, Halle / Saale, Germany and Ivo Feussner, Department for Plant Biochemistry, Albrecht-von-Haller Institute for Plant Sciences, Georg-August-University, Göttingen, Germany. 11. Prenyllipids and their derivatives: Sterols, prenylquinones, carotenoids and terpenoids. Pierre Benveniste, Institut de Biologie Moleculaire des Plantes, Departement Biogenese et Fonctions des Isoprenoides, UPR-CNRS, Strasbourg, France. References. Index

Read more less

Book SynopsisA 'textbook' plant typically comprises about 85% water and 13. 5% carbohydrates. The remaining fraction contains at least 14 mineral elements, without which plants would be unable to complete their life cycles. Understanding plant nutrition and applying this knowledge to practical use is important for several reasons.Trade ReviewThe book is divided into 13 chapters covering three distinct topics: the molecular physiology of individual nutrients, methods for studying plant nutritional genomics, and applications of the knowledge gained. "This is a really good book that should be part of the personal library of all those working in plant nutrition. It should also be consulted by those who want to keep abreast of recent developments or use it as a basis for an initial but integrated introduction to the molecular physiology of nutrient acquisition and assimilation and how this knowledge can potentially be exploited. It will also be useful to those preparing advanced undergraduate or graduate-level lecture courses in plant nutrition." Roger A Leigh - Annals of BotanyTable of Contents1. Nitrogen. Françoise Daniel-Vedele and Sylvain Chaillou, Plant Nitrogen Nutrition Unit, INRA Versailles, Frances. 2. Potassium. Sabine Zimmermann and Isabelle Chérel, INRA - Biochimie et Physiologie Moléculaire des Plantes, Montpellier, France. 3. Calcium. Philip J. White, Horticulture Research International, Wellesbourne, Warwick, UK. 4. Sulphur. Malcolm J. Hawkesford, Agriculture and the Environment Division, Rothamsted Research, Harpenden, UK. 5. Phosphorus. Kashchandra G. Raghothama, Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA. 6. Sodium. Huazhong Shi, Ray A. Bressan, Paul M. Hasegawa and Jian-Kang Zhu, Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, USA. 7. Mapping links between the genome and ionome in plants. Brett Lahner and David E. Salt, Department of Horticulture and Landscape Architechture, Purdue University, West Lafayette, Indiana, USA. 8. Transcriptional profiling of membrane transporters. Frans J.M. Maathuis, Department of Biology, University of York, UK and Anna Amtmann, Laboratory of Plant Physiology and Biophysics, University of Glasgow, UK. 9. Exploring natural genetic variation to improve plant nutrient content. Dick Vreugdenhil , Mark G.M. Aarts and Maarten Koornneef, Laboratory of Genetics, Wageningen University, The Netherlands. 10. Mapping nutritional traits in crop plants. Matthias Wissuwa, International Rice Research Institute, Manila, The Philippines. 11. Sustainable crop nutrition: constraints and opportunities. R. Ford Denison and E. Toby Kiers, Agronomy & Range Science Department, University of California, Davis, USA. 12. Methods to improve the crop-delivery of minerals to humans and livestock. Michael A. Grusak, Baylor College of Medicine, Houston, Texas, USA and Ismail Cakmak, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey. 13. Using plants to manage sites contaminated with heavy metals. Steven N. Whiting, School of Botany, University of Melbourne, Australia, Roger D. Reeves, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand, David Richards, Rio Tinto Plc, London, UK et al.. References. Index

Read more less

Book SynopsisThe largest section of this volume will be devoted to several important areas in human genetics: human genetic disorders which feature premature aging, the effect of human parental aging on the production of genetically abnor­ mal offspring, the genetics of human longevity, and a review of studies on aging human twins.Table of ContentsI. Genome Level.- 1 Molecular Genetics of Aging.- 1. Introduction.- 2. Mechanisms for the Inheritance of the Patterns of Senescence and Longevity.- 2.1. Explicit Inheritance.- 2.2. Implicit Inheritance.- 3. Molecular-Genetic Mechanisms of Senescence.- 3.1. Altered Molecules.- 3.1.1. Somatic Mutations.- 3.1.2. Error Catastrophe.- 3.1.3. Compensation and Repair.- 3.2. Programmed Aging.- 4. Conclusion.- References.- 2 Cytogenetics of Aging.- 1. Introduction.- 2. Alterations in Lymphocyte Chromosome Complement with Human Aging.- 3. Population Studies.- 4. Aneuploidy, Aging, and Organic Brain Disease.- 5. Effect of Genotype on Aneuploidy.- 6. Specific vs. Nonspecific Chromosome Loss.- 7. Polyploidy.- 8. Cross-Sectional vs. Longitudinal Studies.- 9. Chromosomal Alterations with Aging in Tissues Other than Lymphocytes.- 10. Effect of Experimental Conditions on Chromosome Number.- 11. In Vivo Examination of Aneuploidy.- 12. Studies of the Stability of the Chromosome Complement with in Vitro “Aging”.- 13. Chromosomal Alteration, Malignancy, and Aging.- 14. Mechanisms for the Loss of Specific Chromosomes with Aging.- 14.1. Survival of Cells Missing Specific Chromosomes.- 14.2. Selective Loss of Specific Chromosomes.- 14.3. Effect of Aging on Selection.- 15. Future Research on the Cytogenetics of Aging.- 16. Summary.- References.- 3 Aging and DNA-Repair Capability.- 1. Introduction.- 2. DNA-Repair Processes.- 2.1. Strand-Breakage Rejoining.- 2.2. Excision Repair.- 2.3. Postreplication Repair.- 2.4. Photoreactivation.- 2.5. Assay Systems for DNA Repair.- 3. Age-Related Occurrence of Unrepaired DNA Lesions.- 3.1. DNA Strand Breakage.- 3.2. DNA Cross-Linking.- 3.3. Chromosome Aberrations.- 4. DNA-Repair Capability as a Function of Age.- 4.1. In Vitro Investigations.- 4.2. In Vivo Investigations.- 5. Tissue-Specific DNA-Repair Capability.- 6. Acceleration of the Aging Process by Exposure to DNA-Damaging Agents.- 7. Human Genetic Syndromes.- 7.1. Syndromes of DNA-Repair Deficiency.- 7.2. Syndromes of Accelerated Aging.- 7.3. Conclusions.- 8. Longevity and DNA-Repair Processes.- 9. Summary and Conclusion.- References.- 4 Somatic Mutations and Aging.- 1. Introduction.- 2. Terminology of Mutagenesis.- 2.1. Concepts and Definitions.- 2.2. Mutations in Nondividing Cells.- 3. Metabolic Stability of DNA: Contrast to Turnover of Intracellular Macromolecules.- 4. Accumulation of Somatic Mutations with Aging.- 4.1. Chromosome Aberrations.- 4.2. Distinguishing Somatic Mutations from Errors.- 4.3. Base-Substitution Mutations.- 4.4. Germinal vs. Somatic Mutations.- 5. Mutagens, Carcinogens, Cancer, and Aging.- 5.1. Age-Associated Incidence of Cancer in Man and Other Mammals.- 5.2. Mutagenicity of Chemical Carcinogens.- 6. Special Genetic Mechanisms of Aging.- 7. Summary.- References.- II. Organism Level.- 5 Genetics of Aging in Lower Organisms.- 1. Introduction.- 2. Inheritance of Life Span.- 2.1. Effect of Chromosome Number on Longevity.- 2.2. Effect of Genotype on Longevity.- 2.3. Cytoplasmic Inheritance of Aging in Fungi.- 2.4. Effect of Parental Age on Longevity.- 3. Induction of Aging in Immortal Organisms.- 3.1. “Spanning” of Amoeba.- 3.2. Mutants of Neurospora.- 3.3. Autogamy-Deprived Paramecia.- 4. Summary and Conclusions.- References.- 6 Evolution of Longevity and Survival Characteristics in Mammals.- 1. Introduction.- 2. Evolutionary Gerontology: What Evolved, Aging or Longevity?.- 2.1. Allometry of Vertebrate Life Span.- 2.2. “Senescence Gene” Hypothesis of the Evolution of Aging.- 2.3. Evolution of Longevity by Means of Longevity-Assurance Genes.- 3. Evolution of Longevity in Man and the Other Mammals.- 4. Life Tables for Natural Populations.- 5. Evolutionary Change of the Parameters of the Gompertzian Survival Characteristic.- 6. Conclusion.- References.- III. Human Genetics.- 7 Human Genetic Disorders that Feature Premature Onset and Accelerated Progression of Biological Aging.- 1. Introduction.- 2. Specific Criteria of Aging.- 2.1. Physiological Markers.- 3. Premature Aging.- 3.1. General Criteria.- 3.2. A Specific Scoring System for Premature Aging.- 4. Description of Selected Disorders That Feature Premature Aging.- 4.1. Classic Progeroid Syndromes.- 4.2. Numerical Chromosome Anomalies.- 4.3. Miscellaneous Inherited Syndromes.- 5. Comparison of Premature Aging Syndromes with Normal Biological Aging.- 6. Tissue Culture Approaches to Premature Aging.- 6.1. Studies on Cell Growth.- 6.2. Defective Molecules in Prematurely Aging Cells.- 7. Significance of Biochemical Defects in Prematurely Aging Fibroblasts.- 7.1. Defects in Protein Turnover.- 7.2. Defects in RNA Turnover.- 7.3. Defects in DNA Repair.- 7.4. Defects in DNA Replication.- 8. Conclusions and Future Directions.- References.- 8 Parental-Age Effects: Increased Frequencies of Genetically Abnormal Offspring.- 1. Introduction.- 2. Maternal- vs. Paternal-Age Effects.- 3. Maternal-Age-Related Disorders.- 4. Paternal-Age-Related Disorders.- 5. Proposed Etiological Agents.- 5.1. Radiation.- 5.2. Chemicals.- 5.3. Autoimmunity.- 5.4. Infectious Agents.- 5.5. Genetic Predisposition.- 5.6. Preovulatory Overripeness.- 5.7. Postovulatory Aging.- 6. Mechanisms of Nondisjunction.- 6.1. Nucleolar Organization.- 6.2. Univalent Formation.- 6.3. Premature Centromere Division.- 7. Approaches to Studying Parental-Age Effects.- 8. Prevention by Genetic Counseling and Prenatal Diagnosis.- 9. Summary.- References.- 9 Genetics of Longevity in Man.- 1. Introduction.- 2. Evolutionary Implications.- 3. Genetics and Length of Life.- 3.1. Aging May Be Ineluctable.- 3.2. Aging May Be a Programmed Self-Destruction.- 3.3. Aging May Be an Exogenous Process.- 4. Analysis of Empirical Data.- 5. Models of Aging.- 5.1. External Models.- 5.2. Internal Models.- 5.3. Composite Models.- 5.4. Constructive Models.- 6. Studies of the Inheritance of Longevity.- 6.1. Previous Studies.- 6.2. The Baltimore Longevity Study.- 6.3. Our Extension of the Baltimore Study.- 7. Summary and Conclusion.- References.- 10 A Longitudinal Study of Aging Human Twins.- 1. Introduction: History, Methodology, and Purpose.- 2. Genetic Factors and Survival.- 3. Genetic Factors and Mental Functioning.- 3.1. Test-Battery Description and Initial Assessment.- 3.2. Longitudinal Changes in Psychological Test Performance.- 3.3. Psychological Testing and Prediction of Survival.- 3.4. Test Performance, Ability, and Education as Factors in Aging.- 4. Chromosome Change and Survival.- 5. Chromosome Change and Mental Functioning.- 6. Sex Differences and Survival.- 7. Sex Differences and Mental Functioning.- 8. Summary and Conclusions.- References.- IV. Genetic Approaches to Aging Research.- 11 Somatic Cell Genetics in the Analysis of in Vitro Senescence.- 1. Introduction.- 2. Biology of Cultured Mammalian Cells.- 2.1. Historical Background.- 2.2. The Phenomenon of in Vitro Senescence.- 2.3. Relevance of in Vitro Senescence to in Vivo Senescence.- 3. Phenotype of the Senescent Culture.- 3.1. Alterations of Proliferative Behavior with Senescence.- 3.2. Cytogenetic Alterations.- 3.3. Morphology.- 3.4. Implication for Genetic Studies.- 4. Somatic Cell Genetic Studies of in Vitro Cellular Senescence.- 4.1. Theories of the Mechanism of in Vitro Senescence.- 4.2. Scope of Somatic Cell Genetics.- 4.3. Heterokaryon Studies.- 4.4. Enucleation—Fusion Studies.- 4.5. Synkaryon Studies.- 5. Discussion.- References.- 12 Immunogenetics of Aging.- 1. Introduction.- 2. Histocompatibility Systems and Immune Responses.- 3. Immune Functional Changes with Age.- 3.1. T-Dependent Immune Functions.- 3.2. T-Independent Immune Functions.- 3.3. Autoimmunity.- 4. Genetic Influences of Immune Function in Aging.- 4.1. Influence of Sex.- 4.2. Influence of Strain or Race.- 4.3. Studies in Congenic Mice.- 4.4. The Major Histocompatibility (HLA System) in Humans in Relation to Aging.- 5. Immunogenetic Diseases and Aging.- 6. Summary.- References.- 13 Behavior Genetics and Aging.- 1. Introduction.- 2. Life Span.- 2.1. Inbred Mice.- 2.2. Hybrid Mice.- 2.3. Mutant Mice.- 2.4. Body-Weight Increment and Longevity.- 3. Behavior.- 3.1. Exploration and Open-Field Activity.- 3.2. Wheel Activity.- 3.3. Responsiveness to Light Onset.- 3.4. Sucrose Discrimination and Fluid Intake.- 3.5. Alcohol Preference.- 4. Summary.- References.

Read more less

Table of ContentsPART I OVERVIEWS 1 Structural basis of protein-protein interactionsRobert Liddington2 Quantitative analysis of protein-protein interactions Ziad Eletr and Keith Wilkinson3 Protein-protein interaction databases Damian Szklarczyk and Lars Juhl Jensen 4 Computational prediction of protein-protein interactions Tobias Ehrenberger, Lewis C. Cantley, and Michael B. Yaffe5 Structure-based computational approaches for small-molecule modulation of protein-protein interactionsDavid Xu, Bo Wang, and Samy O. Meroueh6 Targeting protein-protein interactions for drug discovery David C. Fry PART II LABEL-FREE BIOSENSORS AND TECHNIQUES 7 Studying protein-protein interactions using surface plasmon resonanceZenata Nikolovska-Coleska8 Resonant waveguide grating for monitoring bimolecular interactions Meng Wu and Min Li 9 Quartz microbalance technology for probing biomolecular interactions Gabriella T. Heller, Alison R. Mercer-Smith, and Malkiat S. Johal10 Label-free kinetic analysis of an antibody-antigen interaction using biolayer interferometry Sriram Kumaraswamy and Renee Tobias11 Characterization of protein-protein interactions by isothermal titration calorimetryAdrian Velazquez-Campoy, Stephanie A. Leavitt, and Ernesto Freiere12 Sedimentation equilibrium studies Ian A. Taylor, John F. Eccleston, and Katrin Rittinger13 Detecting protein-protein interactions by gel filtration chromatographyYan Bai14 Using light scattering to determine the stoichiometry of protein complexes Jeremy Mogridge15 Circular dichroism (CD) analyses of protein-protein interactions Norma Greenfield16 Protein-protein interaction analysis by nuclear magnetic resonance spectroscopy Peter M. Thompson, Moriah R. Beck, and Sharon L. Campbell17 Quantitative protein analysis by mass spectrometry Vishwajeeth Pagala, Anthony High, Xusheng Wang, Haiyan Tan, Kiran Kodali, Ashutosh Mishra, Kanisha Kavdia, Yanji Xu, Zhiping Wu, and Junmin Peng18 Using peptide arrays created by the SPOT method for defining protein-protein interactionsYun Young Yim, Katherine Betke, and Heidi Hamm PART III TAG/AFFINITY-BASED METHODS 19 Fluorescence polarization assay to quantify protein-protein interactions Ronald T. Raines20 Förster resonance energy transfer (FRET) microscopy for monitoring biomolecular interactions Alexa L. Mattheyses and Adam I. Marcus21 Utilizing ELISA to monitor protein-protein interactionsZusen Weng and Qinjian Zhao22 Glutathione-S-transferase (GST)-fusion based assays for studying protein-protein interactions Haris G. Vikis and Kun-Liang Guan23 Hexahistidine (6xHis) fusion-based assays for protein-protein interactions Mary C. Puckett24 Studying protein-protein interactions via blot overlay/Far Western blot Randy A. Hall25 Co-immunoprecipitation from transfected cells Yoshinori Takahashi26 In vivo protein cross-linking Fabrice Agou and Michel Véron PART IV CELL-BASED BIMOLECULAR INTERACTION REPORTER ASSAYS 27 Identification of protein-protein interactions by standard Gal4p-based yeast two-hybrid screeningJeroen Wagemans and Rob Lavigne28 Reverse two-hybrid techniques in the yeast Saccharomyces cerevisiae Matthew A. Bennett, Jack F. Shern, and Richard A. Kahn 29 MAPPIT, a mammalian two-hybrid method for in-cell detection of protein-protein interactionsIrma Lemmens, Sam Lievens, and Jan Tavernier30 Bioluminescence resonance energy transfer to detect protein-protein interactions in live cells Nicole E. Brown, Joe B. Blumer, and John R. Hepler31 Mapping biochemical networks with protein fragment complementation assays Ingrid Remy and Stephen W. Michnick32 Detection of protein-protein interaction using bimolecular fluorescence complementation assayCau D. Pham33 Split-luciferase complementation assay to detect channel-protein interactions in live cells Alexander S. Shavkunov, Syed R. Ali, Neli I. Panova-Elektronova, and Fernanda Laezza34 Confocal microscopy for intracellular co-localization of proteins Toshiyuki Miyashita PART V HIGH THROUGHPUT SCREENING ASSAYS FOR PROTEIN- PROTEIN INTERACTIONS - CASE STUDIES 35 Fluorescence polarization assay to quantify protein-protein interactions in an HTS formatYuhong Du36 Estrogen receptor alpha/co-activator interaction assay - TR-FRET Terry W. Moore, Jillian R. Gunther, and John A. Katzenellenbogen37 High content screening biosensor assay to identify disruptors of p53-hDM2 protein-protein interactionsYun Hua, Christopher J. Strock. and Paul A. Johnston38 Discovery of inhibitors of the MDM2-p53 protein-protein interactionLiu Liu, Denzil Bernard, and Shaomeng Wang39 Biophysical methods for identifying fragment-based inhibitors of protein-protein interactionsSamuel J. Pfaff, Michael S. Chimenti, Mark J. S. Kelly, and Michelle R. Arkin

Read more less

Book Synopsis

Read more less

Book Synopsis

Read more less

Book SynopsisImmunology has rapidly evolved as a field, in particular, by moving beyond merely understanding the basic mechanisms of the immune system to developing diagnostic and clinical applications. As part of this globally broadening effort, the Fifth Congress of the Federation of Immunological Societies of Asia-Oceania (FIMSA) was held in New Delhi March 14–17 2012. The presentations centered on the theme: “Translational Immunology in Health and Diseases.” Extending this theme, this volume comprises the topics covered in ten Master Lectures and five award-winning poster presentations, including work on genetic control of immunity, autoimmunity, and the immune response in relation to specific conditions. NOTE: Annals volumes are available for sale as individual books or as a journal. For information on institutional journal subscriptions, please visit http://ordering.onlinelibrary.wiley.com/subs.asp?ref=1749-6632&doi=10.1111/(ISSN)1749-6632. ACADEMY MEMBERS: Please contact the New York Academy of Sciences directly to place your order (www.nyas.org). Members of the New York Academy of Science receive full-text access to Annals online and discounts on print volumes. Please visit http://www.nyas.org/MemberCenter/Join.aspx for more information about becoming a member.Table of ContentsA brief history of the Federation of Immunological Societies of Asia-Oceania (FIMSA) v Narinder K. Mehra Immunology and world health: key contributions from the global community 1 G. J. V. Nossal The life of regulatory T cells 8 Iris K. Gratz, Michael D. Rosenblum, and Abul K. Abbas Cross-reactive humoral responses to influenza and their implications for a universal vaccine 13 Christopher Chiu, Jens Wrammert, Gui-Mei Li, Megan McCausland, Patrick C. Wilson, and Rafi Ahmed The dual role of biomarkers for understanding basic principles and devising novel intervention strategies in tuberculosis 22 January Weiner 3rd, Jeroen Maertzdorf, and Stefan H. E. Kaufmann Clinical relevance of antibody development in renal transplantation 30 Narinder Mehra, Jamshaid Siddiqui, Ajay Baranwal, Sanjeev Goswami, and Gurvinder Kaur Th2-type innate immune responses mediated by natural helper cells 43 Shigeo Koyasu and Kazuyo Moro A unique vaccine for control of fertility and therapy of advanced-stage terminal cancers ectopically expressing human chorionic gonadotropin 50 G. P. Talwar Immunology of neuromyelitis optica: a T cell-B cell collaboration 57 Meike Mitsdoerffer, Vijay Kuchroo, and Thomas Korn Regulation of Toll-like receptor signaling pathways in innate immune responses 67 Cheng Quian and Xuetao Cao Best Oral Presentation Winners TAP expression level in tumor cells defines the nature and processing of MHC class I peptides for recognition by tumor-specific cytotoxic T lymphocytes 75 Faten El Hage, Aurélie Durgeau, and Fathia Mami-Chouaib Proinflammatory cytokines contribute to development and function of regulatory T cells in type 1 diabetes 81 Helen E. Thomas, Kate L. Graham, Jonathan Chee, Ranjeny Thomas, Thomas W. Kay, and Balasubramanian Krishnamurthy Development of novel genetic cancer vaccines based on membrane-attached β2 microglobulin 87 Gal Cafri, Alon Margalit, Esther Tzehoval, Lea Eisenbach, and Gideon Gross Genomic evaluation of HLA-DR3+ haplotypes associated with type 1 diabetes 91 Neeraj Kumar, Gurvinder Kaur, Nikhil Tandon, Uma Kanga, and Narinder Mehra PPE2 protein of Mycobacterium tuberculosis may inhibit nitric oxide in activated macrophages 97 Khalid Hussain Bhat, Arghya Das, Aparna Srikantam, and Sangita Mukhopadhyay 102 Corrigendum for Ann. N.Y. Acad. Sci. 2012.1274: 86-91 103 Erratum for Ann. N.Y. Acad. Sci. 2012. 1275: 54-62

Read more less

Book SynopsisBiophysical chemistry is a multidisciplinary field that uses models of chemistry and physics to comprehend organic systems by interpreting the quantitative, energetics, structural, functional and interactional context of the physical nature. In this introductory volume, the authors provide insight into the significance of biophysics chemistry as a developing area of science and the wide variety of strategies that have been applied to explain the related phenomena. The book discusses a few specific methods for reviewing biological molecules and how they function. A few of these procedures use environmental and semi-environmental factors as that for organic particles in the natural environment. The book focuses on different methods that up to date are utilized in biophysical chemistry. Every method comes with a brief definition and is cited with proper reference for future research.Table of Contents Chapter 1 Principles of Physical Chemistry (Basic Rules and Constants) Chapter 2 Thermodynamics Chapter 3 Chemical Equilibria Chapter 4 Chemical Kinetics with Enzymology Chapter 5 Membranes and Surfaces in Biological Systems Chapter 6 Protein Conformation Chapter 7 Mass Spectrometry Chapter 8 Nanopore-Based Measurements Chapter 9 Fluorimetry and its Applications Chapter 10 The Future of Biophysical Chemistry

Read more less

Book SynopsisAmino acids play a role in the defence mechanisms and stress responses of plants, as well as in food quality and safety for humans and animals. Recent advances in the field make a comprehensive overview of the information a necessity; this book collates chapters on plant enzymes and metabolism, modulation, molecular aspects and secondary products. Also including information on ecology, the environment and mammalian nutrition and toxicology, it provides an authoritative resource.Table of Contents1: Enzymes and Metabolism 1: Glutamate Dehydrogenase 2: Alanine Aminotransferase: Amino Acid Metabolism in Higher Plants 3: Aspartate Aminotransferase 4: Tyrosine Aminotransferase 5: An Insight Into the Role and Regulation of Glutamine Synthetase in Plants 6: Asparagine Synthetase 7: Glutamate Decarboxylase 8: l-Arginine-Dependent Nitric Oxide Synthase Activity 9: Ornithine: At the Crossroads of Multiple Paths to Amino Acids and Polyamines 10: Polyamines in Plants: Biosynthesis From Arginine, and Metabolic, Physiological and Stress-response Roles 11: Serine Acetyltransferase 12: Cysteine Homeostasis 13: Lysine Metabolism 14: Histidine 15: Amino Acid Synthesis Under Abiotic Stress 16: The Central Role of Glutamate and Aspartate in the Post-translational Control of Respiration and Nitrogen Assimilation in Plant Cells 2: Dynamics 17: Amino Acid Export in Plants 18: Uptake, Transport and Redistribution of Amino Nitrogen in Woody Plants 3: Chemical Ecology 19: Auxin Biosynthesis 20: Involvement of Tryptophan-pathway-derived Secondary Metabolism in the Defence Responses of Grasses 21: Melatonin: Synthesis From Tryptophan and its Role in Higher Plants 22: Glucosinolate Biosynthesis From Amino Acids 23: Natural Toxins that Affect Plant Amino Acid Metabolism 24: Glyphosate: The Fate and Toxicology of a Herbicidal Amino Acid Derivative 4: Plant Products: Quality and Safety 25: Amino Acid Analysis of Plant Products 26: Metabolic Amino Acid Availability in Foods of Plant Origin: Implications for Human and Livestock Nutrition 27: Toxicology of Non-protein Amino Acids 5: Conclusions 28: Delivering Innovative Solutions and Paradigms for a Changing Environment

Read more less

Book SynopsisPlants are important source of lead molecules for drug discovery. These lead molecules serve as starting materials for laboratory synthesis of drug as well a model for production of biologically active compounds. Phytochemical processing of raw plant materials is essentially required to optimize the concentration of known constituents and also to maintain their activities. Extraction techniques and analytical techniques have played critical roles in phytochemical processing of raw materials. Extraction technologies from conventional extraction to green extraction as well as analytical techniques from single technique to hyphenated/coupled techniques most frequently used in phytochemistry laboratories are covered in the book.Table of Contents1: Analytical Techniques in Natural Product Research 2: Phytochemical Processing: Extraction Methods 3: Supercritical Fluid Extraction 4: Chromatographic Techniques I: High-Performance Thin-Layer. Chromatography and High-Speed Countercurrent Chromatography 5: Chromatography Techniques II: High-Performance Liquid Chromatography and Ultra-Performance Liquid Chromatography 6: Tandem Techniques 7: Non-Destructive Techniques 8: Antioxidant Assay

Read more less

Book SynopsisThis book collates and reviews recent advances in the microbial metabolism of amino acids, emphasizing diversity - in terms of the range of organisms under investigation and their natural ecology - and the unique features of amino acid metabolism in bacteria, yeasts, fungi, protozoa and nematodes. As well as studying the individual amino acids, including arginine, sulfur amino acids, branched-chain amino acids and aromatic amino acids, a number of themes are explored throughout the work. These include: - Comparative issues between the metabolism of microbes and those of higher organisms, including plants and mammals - Potential for drug targets in pathways of both biosynthesis and degradation of amino acids - Relationship between amino acids or associated enzymes and virulence in parasitic pathogens - Practical implications for food microbiology and pathogen characterization - Future priorities relating to fundamental biochemistry of microrganisms, food quality and safety, human and animal health, plant pathology, drug design and ecology As the volume of research into the metabolism of amino acids grows, this comprehensive study of the subject is a vital tool for researchers in the fields of biological, medical and veterinary sciences, including microbiology, biochemistry, genetics and pathology. This book is also essential for corporate organizations with active research and development programmes, such as those in the pharmaceutical industry.Table of Contents-: Preface PART I: GLUTAMATE 1: Structural and Functional Properties of Glutamate Dehydrogenases 2: Glutamate Decarboxylase in Bacteria 3: The Yeast GABA Shunt PART II: LYSINE, ARGININE AND HYDROXYPROLINE 4: Lysine Biosynthesis in Microorganisms 5: Arginine Deiminase in Microorganisms 6: Arginase and Microbial Pathogenesis in the Lungs 7: Arginine and Methionine as Precursors of Polyamines in Trypanosomatids 8: Ornithine and Lysine Decarboxylation in Bacteria 9: The Role of Nitric Oxide Signalling in Yeast Stress Response and Cell Death 10: Hydroxyproline Metabolism in Microorganisms PART III: SERINE AND THREONINE 11: Cellular Responses to Serine in Yeast 12: Threonine Degradation in Hyperthermophilic Organisms PART IV: SULFUR AMINO ACIDS 13: Methionine Synthesis in Microbes 14: Regulation of Sulfur Amino Acid Metabolism in Fungi 15: Insight on O-Acetylserine Sulfhydrylase Structure, Function and Biopharmaceutical Applications PART V: BRANCHED-CHAIN AMINO ACIDS 16: Metabolic Engineering of Corynebacterium glutamicum for L-Valine Production 17: Flavour Formation From Leucine by Lactic Acid Bacteria PART VI: AROMATIC AMINO ACIDS AND HISTIDINE 18: Microbial Degradation of Phenolic Amino Acids 19: The Biosynthesis of Tryptophan 20: Tryptophan Biosynthesis in Bacteria: Drug Targets and Immunology 21: The Kynurenine Pathway of Tryptophan Metabolism in Microorganisms 22: Histidine Degradation in Bacteria 23: Histidine Phosphatase Superfamily in Pathogenic Bacteria PART VII: D-AMINO ACIDS 24: Functions and Metabolism of D-Amino Acids in Microorganisms 25: Pathways of Utilization of D-Amino Acids in Higher Organisms PART VIII: ECOLOGY 26: Rhizobial Amino Acid Metabolism: Polyamine Biosynthesis and Functions 27: Working Together: Amino Acid Biosynthesis in Endosymbiont-Harbouring Trypanosomatidae 28: Amino Acid Metabolism in Helminths 29: Microbial Degradation of Amino Acids in Anoxic Environments 30: Utilization of N-Methylated Amino Acids by Bacteria 31: Biofilm Formation: Amino Acid Biomarkers in Candida albicans 32: Recent Advances Underpinning Innovative Strategies for the Future

Read more less

Book SynopsisEnzyme dysfunction, an essential catalyst for the smooth running of biochemical reactions and the maintenance of vital processes, is at the root of many pathologies that have paved the way for the development of numerous drugs. Aimed at pharmacists, biologists, biochemists, doctors, veterinarians, medicinal chemists and students from a wide range of disciplines, Enzymes and Drugs brings together, for the first time, extensive documentation highlighting the relationships between a large number of drugs and enzymes. The book also highlights new prospects for therapeutic discoveries offered by enzyme targeting. Numerous applications have been developed thanks to strategies for studying enzyme inhibition or activation, as well as the development of allosteric effectors, presented with their advantages and disadvantages. Various rare diseases, known as orphan diseases, have resulted from enzyme deficiency or absence. For their treatment, the introduction of substitute enzymes has led to major therapeutic advances.

Read more less

Book SynopsisAntimicrobial peptides (AMPs) have attracted extensive research attention worldwide. Harnessing and creating AMPs synthetically has the potential to help overcome increasing antibiotic resistance in many pathogens. This new edition lays the foundations for studying AMPs, including a discovery timeline, terminology, nomenclature and classifications. It covers current advances in AMP research and examines state-of-the-art technologies such as bioinformatics, combinatorial libraries, high-throughput screening, database-guided identification, genomics and proteomics-based prediction, and structure-based design of AMPs. Thoroughly updated and revised, this second edition contains new content covering: defensins; cathelicidins; anti-MRSA, antifungal, antiviral, anticancer and antibiofilm strategies; combined treatments; adjuvants in vaccines; advances in AMP technologies that cover surface coating to prevent biofilm formation; nanofiber encapsulation technologies for delivery and sustained release; and understanding innate immunity and the basis for immune boosting to overcome obstacles in developing AMPs into therapeutic agents. Written and reviewed by a group of established investigators in the field, Antimicrobial Peptides is a valuable resource for postgraduate students, researchers, educators, and medical and industrial personnel.Table of ContentsPART I: OVERVIEW OF ANTIMICROBIAL PEPTIDES 1: Discovery, Classification and Functional Diversity of Antimicrobial Peptides PART II: NATURAL TEMPLATES FOR PEPTIDE ENGINEERING 2: Structural and Functional Diversity of Cathelicidins 3: Disulfide-linked Defensins and Their Therapeutic Potential 4: Lantibiotics: Bioengineering and Applications PART III: EXPANDING PEPTIDE SPACE: COMBINATORIAL LIBRARY, GENOME-BASED PREDICTION AND DE NOVO DESIGN 5: Discovery of Novel Antimicrobial Peptides Using Combinatorial Chemistry and High-throughput Screening 6: Prediction and Design of Antimicrobial Peptides: Methods and Applications to Genomes and Proteomes PART IV: MECHANISMS OF ACTION: BIOPHYSICS AND STRUCTURAL BIOLOGY 7: Antimicrobial Peptides: Multiple Mechanisms Against a Variety of Targets 8: Microbial Membranes and the Action of Antimicrobial Peptides 9: Non-membranolytic Mechanisms of Action of Antimicrobial Peptides – Novel Therapeutic Opportunities? 10: Structural Insight into the Mechanisms of Action of Antimicrobial Peptides and Structure-based Design PART V: NOVEL THERAPEUTIC STRATEGIES: SYNERGY, IMMUNE MODULATION, SURFACE COATING, AND DELIVERY 11: Synergy of Antimicrobial Peptides 12: Surface Immobilization of Antimicrobial Peptides to Prevent Biofilm Formation 13: Sustained Delivery of Cathelicidin Antimicrobial Peptide-Inducing Compounds to Minimize Infection and Enhance Wound Healing 14: Immunomodulatory Activities of Cationic Host Defence Peptides and Novel Therapeutic Strategies

Read more less

Book SynopsisThis book provides comprehensive and up-to-date knowledge relating to the morphological, structural, and functional characteristics of tuber starches, particularly in relation to their applications in food and industry. In recent years there has been significant progress and extensive research conducted on tropical root starches and especially on some of the lesser known tuber crop starches. There has also been a shift towards using biomaterials in place of synthetic materials in various applications. As researchers investigate the availability of natural products with similar properties, starch has been identified as a reliable alternative to these synthetic materials. Reflecting the growing body of research, Tropical Tuber Starches: - Explores the structure, properties and applications of tropical root and tuber starches (cassava, sweet potato, aroids, yams and other minor tuber crops) - Includes a chapter on the methodology for starch characterisation - Covers patents on starch-based products and the commercial potential of tropical root starches A valuable resource for researchers and students, plant breeders, and commercial producers working with, or considering working with, tropical tuber starches.Table of Contents1: Introduction - Tropical Tuber Crops and Their Importance 2: Starch - General Considerations 3: Cassava 4: Sweet Potato 5: Aroids 6: Yams 7: Other Starches 8: Starch Modifications 9: Applications of Tuber Starches 10: Characterization and Analysis of Starches 11: Conclusions and Future Prospects

Read more less

Book SynopsisSpices are high value, export-oriented crops used extensively in food and beverage flavourings, medicines, cosmetics and perfumes. Interest is growing however in the theoretical and practical aspects of the biosynthetic mechanisms of active components in spices as well as the relationship between the biological activity and chemical structure of these secondary metabolites. A wide variety of phenolic substances and amides derived from spices have been found to possess potent chemopreventive, anti-mutagenic, anti-oxidant and anti-carcinogenic properties. Representing the first discussion of the chemical properties of a wide cross section of important spices, this book covers extensively the three broad categories of plant-derived natural products: the terpenoids, the alkaloids and the phenyl propanoids and allied phenolic compounds. Spice crops such as black pepper, ginger, turmeric and coriander are covered with information on botany, composition, uses, chemistry, international specifications and the properties of a broad range of common and uncommon spices.Table of Contents1: Spices covered include: 1.1: Black pepper 1.2: Cardamom 1.3: Ginger 1.4: Turmeric 1.5: Cinnamon 1.6: Vanilla 1.7: Coriander 1.8: Cumin 1.9: Fennel 1.10: Fenugreek 1.11: Celery 1.12: Ajowan 1.13: Star Anise 1.14: Aniseed 1.15: Parsley 1.16: Paprika 1.17: Clove 1.18: Nutmeg and Mace 1.19: Garcinia 1.20: Tamarind

Read more less

Book SynopsisFruits and vegetables are one of the richest sources of ascorbic acid, other antioxidants and produce-specific bioactive compounds. A general consensus from health experts has confirmed that an increased dietary intake of specific bioactive compounds found in some fresh produce types may protect against oxidative damage and reduce the incidence of certain cancers and chronic diseases. This book collectively discusses and reviews empirical data on health-promoting properties of major fresh produce types. It provides detailed information on identity, nature, bioavailablity, chemopreventative effects and postharvest stability of specific chemical classes with known bioactive properties. In addition, chapters discuss the various methodologies for extraction, isolation, characterisation and quantification of bioactive compounds and the in vitro and in vivo anticancer assays. This book is an essential resource for researchers and students in food science, nutrition and fruit and vegetable production.Table of Contents1: Introduction 2: Alliums 3: Avocado 4: Blueberry and Cranberry 5: Brassicas 6: Citrus 7: Cucurbits 8: Exotics 9: Grape 10: Leafy Vegetables and Salads 11: Pome Fruit 12: Potato and Other Root Crops 13: Prunus 14: Ribes and Rubus 15: Strawberry 16: Tomato and Other Solanaceous Fruits 17: Tropical Fruit 18: Methodologies for Extraction, Isolation, Characterization and Quantification of Bioactive Compounds 19: Methodologies for Evaluating In Vitro and In Vivo Activities of Bioactive Compounds

Read more less

Book SynopsisThe ability of pathogenic bacteria to adapt to various chemical, biochemical and physical conditions within the human host and their ability to respond to stresses generated in these environments is a central feature of infectious diseases and the outcome of bacterial infection. This book covers the key aspects of this rapidly developing field, including the generation of stresses by the host immune system, bacterial response to reactive chemicals, and adaptation to environmental conditions of anatomical niches such as the gut, mouth and urogenital tract. It also addresses the increasing importance of different metal ions in the pathogenesis and survival of specific bacteria. With chapters by active research experts in the field, the book provides a comprehensive outline of the current understanding of this field, the latest developments and where future research is likely to be directed.Table of ContentsPart 1: Oxidative and Nitrosative Stress 1: Oxidative and Nitrosative Stress Defence Systems in Escherichia coli and Pseudomonas aeruginosa 2: Coordinated Regulation of Stress and Virulence Adaptations in Stages of Haemophilus Pathogenesis 3: Nitric Oxide Stress in E. coli and Salmonella 4: Nitric Oxide and Gram-positive Pathogens Part 2: Novel Gene Regulation in Response to Host Defences 5: Novel Regulation in Response to Host-generated Stresses 6: Stress Responses in the Pathogenic Neisseria Part 3: Acid Stress: pH Control and Survival in the Human Host 7: Acid Survival Mechanisms of Bacterial Pathogens of the Digestive Tract 8: Urease and the Bacterial Acid Stress Response Part 4: Nutrient Stress 9: Secretion Systems and Metabolism in the Pathogenic Yersiniae 10: Response of Neisseria gonorrhoeae to Oxygen Limitation and Excess Part 5: Metal Ions and Pathogenic Bacteria 11: Copper and Zinc Stress in Bacteria 12: Metal Ion Sensing in Mycobacterium tuberculosis 13: Salmonella and the Host in the Battle for Iron

Read more less

Book SynopsisHuman health issues relating to amino acids are extremely broad and include metabolic disorders of amino acid metabolism as well as their presence in food and use as supplements. This book covers the biochemistry of amino acid metabolism in the context of health and disease. It discusses their use as food supplements, in clinical therapy and nutritional support and focuses on major recent developments, highlighting new areas of research that will be needed to sustain further interest in the field.Table of ContentsPART I: ENZYMES AND METABOLISM 1: Glutamate Dehydrogenase 2: Aminotransferases 3: Arginase 4: Bypassing the Endothelial L-Arginine-Nitric-Oxide Pathway: Effects of Dietary Nitrite and Nitrate on Cardiovascular Function 5: Histidine Decarboxylase 6: Glutamate Decarboxylase 7: Glutaminase 8: D-Serine and Serine Racemase in Retina 9: Tryptophan Hydroxylase 10: Methionine Metabolism PART II: DYNAMICS 11: Amino Acid Transport Across Each Side of the Blood-Brain Barrier 12: Inter-Organ Fluxes of Amino Acids 13: Cellular Adaptation to Amino Acid Availability: Mechanisms Involved in the Regulation of Gene Expression PART III: NUTRITION 14: Endogenous Amino Acids at the Terminal Ileum of the Adult Human 15: Metabolic Availability of Amino Acids in Food Proteins: New Methodology 16: Amino Acid Requirements: Quantitative Estimates 17: Amino Acid Supplements and Muscular Performance 18: Amino Acids in Clinical and Nutritional Support: Glutamine in Duchenne Muscular Dystrophy 19: Adverse Effects 20: The Umami Taste of Glutamate PART IV: HEALTH 21: Homocysteine Status: Factors Affecting and Health Risks 22: Modified Amino Acid-Based Molecules: Accumulation and Health Implications 23: Phenylketonuria: Newborn Identification Through to Adulthood 24: Principles of Rapid Tryptophan Depletion and its use in Research on Neuropsychiatric Disorders 25: Excitatory Amino Acids in Neurological and Neurodegenerative Disorders 26: Efficacy of L-DOPA Therapy in Parkinson's Disease 27: Amino Acid Profiles for Diagnostic Applications PART V: CONCLUSIONS 28: Emergence of a New Momentum

Read more less

Book SynopsisThis comprehensive collection of up-to-the-minute research in the field of poisonous plants investigates the effects of toxins on animals and humans. It covers the effects of poisonous plants on the liver, the reproductive system, and the nervous system, as well as exploring the field of herbal medicine. In a specialised section devoted to control measures, the book highlights techniques such as vaccination and taste aversion, providing the reader with important information on safeguarding against disaster. This volume is an essential reference for veterinarians, researchers, toxicologists and chemists.Table of Contents1: Sections: 2: Overview 3: The Liver 4: Reproductive System 5: Nervous System 6: Toxic Plants Affecting Other Systems 7: Mycotoxins and Other Toxins 8: Toxic Compounds and Chemical Methods 9: Control Measures 10: Herbals

Read more less

Book SynopsisBacteriophages are viruses that infect bacteria. As such, they have many potential uses for promoting health and combating disease. This book covers the many facets of phage-bacterial-human interaction in three sections: the role and impact of phages on natural bacterial communities, the potential to develop phage-based therapeutics and other aspects in which phages can be used to combat disease, including bacterial detection, bacterial epidemiology, the tracing of fecal contamination of water and decontamination of foods.Table of Contents1: Phages Section I: Phages, Bacterial Disease, and Normal Flora 2: Bacteriophages as Part of the Human Microbiome 3: Diseases Caused by Phages 4: Prophage-Induced Changes in Cellular Cytochemistry and Virulence 5: The Lion and the Mouse: How Bacteriophages Create, Liberate, and Decimate Bacterial Pathogens 6: Phages and Bacterial Epidemiology Section II: Phage-Based Biomedical Technology 7: Phages as Therapeutic Delivery Vehicles 8: Clinical Applications of Phage Display 9: Phages and Their Hosts: A Web of Interactions - Applications to Drug Design 10: Bacteriophage-Based Methods of Bacterial Detection and Identification 11: Phage Detection as Indication of Fecal Contamination Section III: Phage-Based Antibacterial Strategies 12: Phage Translocation, Safety, and Immunomodulation 13: Phage Therapy of Wounds and Related Purulent Infections 14: Phage Therapy of Non-Wound Infections 15: Phage-Based Enzybiotics 16: Role of Phages in Control of Bacterial Pathogens in Food 17: Phage Therapy Best Practices

Read more less

Book SynopsisThis book is part of a set of books which offers advanced students successive characterization tool phases, the study of all types of phase (liquid, gas and solid, pure or multi-component), process engineering, chemical and electrochemical equilibria, and the properties of surfaces and phases of small sizes. Macroscopic and microscopic models are in turn covered with a constant correlation between the two scales. Particular attention has been given to the rigor of mathematical developments. This fifth volume is devoted to the study of transformations and equilibria between phases. First- and second-order pure phase transformations are presented in detail, just as with the macroscopic and microscopic approaches of phase equilibria. In the presentation of binary systems, the thermodynamics of azeotropy and demixing are discussed in detail and applied to strictly-regular solutions. Eutectic and peritectic points are examined, as well as the reactions that go with them. The study of ternary systems then introduces the concepts of ternary azeotropes and eutectics. For each type of solid-liquid system, the interventions of definite compounds with or without congruent melting are taken into account. The particular properties of the different notable points of a diagram are also demonstrated.Table of ContentsPreface xi Notations and Symbols xv Chapter 1. Phase Transformations of Pure Substances 1 1.1. Standard state: standard conditions of a transformation 1 1.2. Classification and general properties of phase transformations 2 1.2.1. First-order transformations and the Clapeyron relation 4 1.2.2. Second-order transformations 7 1.3. Liquid–vapor transformations and equilibrium states 16 1.3.1. Method of two equations of state, using the Clapeyron equation 16 1.3.2. Gibbs energy and fugacity method 18 1.3.3. Unique equation of state method 19 1.3.4. The region of the critical point and spinodal decomposition 21 1.3.5. Microscopic modeling 22 1.3.6. Liquid–vapor equilibrium in the presence of an inert gas 26 1.4. Solid–vapor transformations and equilibriums 28 1.4.1. Macroscopic treatment 28 1.4.2. Microscopic treatment 29 1.5. Transformations and solid–liquid equilibria 30 1.5.1. Macroscopic treatment 31 1.5.2. Microscopic treatment 31 1.6. Diagram for the pure substance and properties of the triple point 32 1.7. Allotropic and polymorphic varieties of a solid 35 1.7.1. Enantiotropy 36 1.7.2. Monotropy 39 1.7.3. Transition from enantiotropy to monotropy and vice versa 39 1.8. Mesomorphic states 40 Chapter 2. Properties of Equilibria Between Binary Phases 43 2.1. Classification of equilibria between the phases of binary systems 43 2.2. General properties of two-phase binary systems 45 2.2.1. Equilibrium conditions for two-phase binary systems 45 2.2.2. Conditions of evolution of a two-phase binary system 46 2.3. Graphical representation of two-phase binary systems 47 2.3.1. Gibbs energy graphs 47 2.3.2. Phase diagram in the mono- and bi-phase zones 53 2.3.3. Isobaric cooling curves 63 2.4. Isobaric representation of three-phase binary systems 66 2.4.1. Gibbs energy curve 66 2.4.2. Isobaric phase diagram in tri-phase regions 68 2.4.3. Isobaric cooling curves with tri-phase zones 70 2.5. Isothermal phase diagrams 72 2.6. Composition/composition curves 73 2.7. Activity of the components and consequences of Raoult’s and Henry’s laws 73 Chapter 3. Equilibria Between Binary Condensed Phases 75 3.1. Equilibria between phases of the same nature: liquid–liquid or solid–solid 76 3.1.1. Thermodynamics of demixing 76 3.1.2. Demixing in the case of low reciprocal solubilities 79 3.1.3. Demixing of strictly-regular solutions 81 3.2. Liquid–solid systems 84 3.2.1. Thermodynamics of the equilibria between a liquid phase and a solid phase 86 3.2.2. Isobaric phase diagrams of equilibria between a solid and a liquid 90 3.2.3. Solidus and liquidus in the vicinity of the pure substance 97 3.3. Equilibria between two solids with two polymorphic varieties of the solid 100 3.4. Applications of solid–liquid equilibria 102 3.4.1. Solubility of a solid in a liquid: Schröder–Le Châtelier law 102 3.4.2. Determination of molar mass by cryometry 104 3.5. Membrane equilibria – osmotic pressure 106 3.5.1. Thermodynamics of osmotic pressure 107 3.5.2. Osmotic pressure of infinitely-dilute solutions: the Van ‘t the Hoff law 109 3.5.3. Application of osmotic pressure to the determination of the molar mass of polymers 110 3.5.4. Osmotic pressure of strictly-regular solutions 111 3.5.5. Osmotic pressure and the osmotic coefficient 112 Chapter 4. Equilibria Between Binary Fluid Phases 113 4.1. Thermodynamics of liquid–vapor equilibrium in a binary system 113 4.2. Liquid–vapor equilibrium in perfect solutions far from the critical conditions 117 4.2.1. Partial pressures and total pressure of a perfect solution 118 4.2.2. Isothermal diagram of a perfect solution 119 4.2.3. Isobaric diagram of a perfect solution 120 4.2.4. Phase composition curve 121 4.3. Liquid–gas equilibria in ideal dilute solutions 122 4.4. Diagrams of the liquid–vapor equilibria in real solutions 125 4.4.1. Total miscibility in the liquid phase 125 4.4.2. Partial miscibility in the liquid phase, heteroazeotropes 128 4.5. Thermodynamics of liquid–vapor azeotropy 129 4.5.1. Relation between the pressure of the azeotrope and the activity coefficients of the liquid phase at the azeotropic composition 129 4.5.2. Relation between the activity coefficient and the temperature of the azeotrope 130 4.6. Liquid–vapor equilibria and models of solutions 132 4.6.1. Liquid–vapor equilibria in strictly-regular solutions 132 4.6.2. Liquid–vapor equilibrium in associated solutions 137 4.7. Liquid–vapor equilibria in the critical region 140 4.8. Applications of liquid–vapor equilibria 143 4.8.1. Solubility of a gas in a liquid 143 4.8.2. Determination of molar masses by tonometry 145 4.8.3. Determination of molar masses by ebulliometry 146 4.8.4. Continuous rectification or fractional distillation 149 Chapter 5. Equilibria Between Ternary Fluid Phases 163 5.1. Representation of the composition of ternary systems 163 5.1.1. Symmetrical representation of the Gibbs triangle 163 5.1.2. Dissymmetrical representation of the right triangle 168 5.2. Representation of phase equilibria 169 5.2.1. Isothermal projections 169 5.2.2. Conjugate points and conodes 170 5.2.3. Isopleth sections 171 5.3. Equilibria in liquid phases with miscibility gaps 171 5.3.1. Representation of the miscibility gap 171 5.3.2. Sharing in liquid–liquid systems 173 5.3.3. Application of sharing between two liquids to solvent extraction 177 5.4. Liquid–vapor systems 182 5.4.1. Isothermal and isopleth sections (boiling and dew) 182 5.4.2. Distillation trajectories 184 5.4.3. Systems with two distillation fields 186 5.4.4. Systems with three distillation fields 187 5.5. Examples of applications of ternary diagrams between fluid phases 187 5.5.1. Treatment of argentiferous lead 187 5.5.2. Purity of oil products: aniline point 188 5.5.3. Obtaining concentrated ethyl alcohol 189 Chapter 6. Equilibria Between Condensed Ternary Fluid Phases 191 6.1. Solidification of a ternary system with total miscibility in the liquid state and in the solid state 192 6.2. Solidification of a ternary system with no miscibility and with a ternary eutectic 192 6.2.1. Invariant transformations of a liquid–solid ternary system 193 6.2.2. Representations of the ternary system with no miscibility in the solid state 194 6.2.3. Lowering of the melting point of a binary system by the addition of a component 199 6.2.4. Slope at the ternary eutectic 202 6.3. Ternary systems with partial miscibilities in the solid state and ternary eutectic 204 6.4. Solidification of ternary systems with definite compounds 208 6.4.1. Ternary system with a binary definite compound binary with congruent melting 208 6.4.2. Generalization to the case of a ternary compound and of multiple definite compounds 211 6.4.3. Definite compound with incongruent melting: quasi-peritectic transformation 213 6.5. A peritectic transformation in one binary system and total miscibility in the other two 215 6.6. The ternary peritectic transformation 217 Bibliography 219 Index 221

Read more less

Book SynopsisThe book features comparative perspectives on the field of chemical ecology, present and future, offered by scientists from a wide variety of disciplines. The scientists contributing to this book –biologists, ecologists, biochemists, chemists, biostatisticians – are interested in marine, freshwater and terrestrial ecosystems and work on life forms ranging from micro-organisms to mammals, including humans, living in areas from the tropics to polar regions. Here, they cross their analyses of the present state of chemical ecology and its perspectives for the future. Those presented here include complex, multispecies communities and cover a wide range both of organisms and of the types of molecules that mediate the interactions between them. Up to now, no book has presented a solid scientific treatment of a wide range of examples. This book illustrates a diverse panel of the most advanced aspects of this rapidly expanding field.Table of ContentsForeword xiStéphanie THIÉBAULT and Françoise GAILL Introduction xiiiAnne-Geneviève BAGNÈRES and Martine HOSSAERT-MCKEY Chapter 1. Biodiversity and Chemical Mediation 1Bertrand SCHATZ, Doyle MCKEY and Thierry PÉREZ 1.1. Systematic and integrative taxonomy from chemical ecology 2 1.2. Scent communication between sexual partners 4 1.3. Scent communication between species 6 1.4. Chemical mimicry, to enhance reproduction 8 1.5. A dialog that sometimes evolves into an interaction network 10 1.6. Conclusions 18 1.7. Bibliography 18 Chapter 2. Chemical Ecology: An Integrative and Experimental Science 23Anne-Marie CORTESERO, Magali PROFFIT, Christophe DUPLAIS and Frédérique VIARD 2.1. Semiochemicals 23 2.2. Chemical ecology in multitrophic networks and co-evolution between species 28 2.3. Contribution of chemical ecology to the study of tropical plant diversification 32 2.4. When chemical ecology sheds light on the process of biological invasion – an example demonstratingintegration between chemistry and ecology 36 2.5. Protection is in the air: how plants defend themselves against phytophagous insects through VOC emissions 40 2.6. Conclusions 43 2.7. Bibliography 43 Chapter 3. Scents in the Social Life of Non-Human and Human Primates 47Marie CHARPENTIER, Guillaume ODONNE and Benoist SCHAAL 3.1. Primate societies and their complex systems of communication 47 3.2. The role of odors in human communication 53 3.2.1. Human odors convey a large panel of cues 53 3.2.2. Body odors reflect internal states 55 3.2.3. What are the functions of social smells in human daily life? 56 3.2.4. Human pheromones, fact or fiction? 59 3.3. The senses of smell and taste in the search for food and remedies 61 3.3.1. Interactions between senses and food in primates 61 3.3.2. Senses and self-medication in animals 62 3.3.3. Senses in human therapies 63 3.3.4. An evolutionary conception of the link between senses and health 65 3.4. Conclusions – the adaptive functions of the sense of smell in “microsmatic” species 66 3.5. Bibliography 68 Chapter 4. Microbiota and Chemical Ecology 71Soizic PRADO, Catherine LEBLANC and Sylvie REBUFFAT 4.1. The protagonist microorganisms of chemical ecology 71 4.2. Strategies for the study of microbiota 72 4.2.1. How should the microbiota be characterized? 72 4.2.2. What tools are available to help understand the roles of the microbiota? 73 4.3. The molecular dialog of microorganisms 75 4.3.1. Language and social life of microorganisms 75 4.3.2. The AMPs, main actors in the equilibrium of bacterial communities 78 4.3.3. Fungi and bacteria communicate to better help each other 79 4.3.4. When helping each other degenerates into chemical warfare between bacteria and fungi 80 4.3.5. The Trichoderma fungi: heavy artillery against pathogenic fungi 80 4.4. Chemical communication between microorganisms and their hosts 81 4.4.1. Plant–bacteria relationships: essential interactions with different partners 81 4.4.2. Plants also establish intimate relations with fungi 83 4.4.3. Mutualist actinobacteria provide care to insects 85 4.4.4. Chemical communication between microorganisms and their host in the marine environment 87 4.5. Regulations and evolution of the interactions in changing ecosystems and environments 89 4.5.1. Contribution of chemical ecology to the understanding of biosynthesis mechanisms of chemical mediators 90 4.5.2. Metabolic networks: new tools for studying the evolution of host/microbiota interactions 91 4.6. Conclusions – from chemical ecology to future applications: impacts of the study of the microbiota 91 4.7. Bibliography 92 Chapter 5. From Chemical Ecology to Ecogeochemistry 95Catherine FERNANDEZ, Virginie BALDY and Nadine LE BRIS 5.1. Balance between primary and secondary metabolism 96 5.2. Role of secondary metabolites in biotic interactions and community structure 99 5.3. Secondary metabolites and ecosystem functioning: plant soil relation – brown food chain 103 5.4. Integration of biotic and abiotic dynamics: benthic marine microhabitats 109 5.5. Conclusions 114 5.6. Bibliography 114 Chapter 6. Omics in Chemical Ecology 117Sylvie BAUDINO, Christophe LUCAS and Carole SMADJA 6.1. Introduction: the different “omic” technologies 118 6.2. From “omics” to signals: identifying new active molecules 120 6.3. From “omics” to the ecology of communities: identifying chemical interactions of organisms in their environment 121 6.4. From “omics” to molecular bases: revealing the genetic and molecular bases of chemical interactions 122 6.5. From “omics” to physiology: characterizing the modes of production and the modes of reception of active molecules 127 6.6. From “omics” to the role of environment: understanding the impact of biotic and abiotic factors on interactions 128 6.7. From “omics” to evolution: understanding and predicting the adaptive value of chemical interactions 131 6.8. Conclusions and perspectives 133 6.9. Bibliography 134 Chapter 7. Metabolomic Contributions to Chemical Ecology 139Philippe POTIN, Florence NICOLÈ and Olivier P. THOMAS 7.1. Definition of metabolomics 139 7.2. Different strategies of the metabolomic approaches 140 7.3. The different steps for conducting a metabolomic study 141 7.3.1. Experimental design and sampling 142 7.3.2. Analytical approaches 144 7.3.3. Data processing 144 7.4. Applications of metabolomics 151 7.4.1. Chemical biodiversity and chemotaxonomy 151 7.4.2. Study of the regulation and evolution of metabolic/ biosynthesis pathways 152 7.4.3. Contributions to functional ecology 155 7.4.4. Application of metabolomics to the study of environmental disturbances 157 7.5. Conclusions 157 7.6. Bibliography 158 Chapter 8. Chemical, Biological and Computational Tools in Chemical Ecology 161Nicolas BARTHÈS, Jean-Claude CAISSARD, Jérémy JUST and Xavier FERNANDEZ 8.1. Chemical tools 161 8.1.1. Analytical tools of chromatography 161 8.1.2. Analytical approach by nuclear magnetic resonance 168 8.1.3. Secondary metabolite imagery techniques 170 8.2. Sequencing tools 173 8.2.1. Principles, strengths and limitations of NGS 174 8.2.2. Major domains of NGS applications 175 8.3. Databases: biodiversity in silico 179 8.3.1. Databases of chemical compounds and general ecology 180 8.3.2. Databases for the omics that can be used in chemical ecology 181 8.4. Conclusions 183 8.5. Bibliography 183 Chapter 9. Academic and Economic Values of Understanding Chemical Communication 185Bernard BANAIGS, Ali AL MOURABIT, Guillaume CLAVE and Claude GRISON 9.1. Nature as a model 185 9.2. Nature as a model for development of new molecules of interest 187 9.2.1. From chemical mediators to new bioactive structural archetypes 188 9.2.2. Biosynthesis and biomimetic synthesis 192 9.2.3. Chemical mediators and ligand/receptor interactions: to the discovery of new cellular receptors and biochemical tools 195 9.3. Chemical ecology and sustainable development 196 9.3.1. Bio-control 198 9.3.2. Bio-inspired chemistry and remedial phytotechnologies 200 9.4. Conclusions 205 9.5. Bibliography 205 Conclusion 207Martine HOSSAERT-MCKEY and Anne-Geneviève BAGNÈRES Glossary 213 List of Authors 217 Index 221

Read more less

Book SynopsisThis third volume in the Handbook of Food Science and Technology Set explains the processing of raw materials into traditional food (bread, wine, cheese, etc.). The agri-food industry has evolved in order to meet new market expectations of its products; with the use of separation and assembly technologies, food technologists and engineers now increasingly understand and control the preparation of a large diversity of ingredients using additional properties to move from the raw materials into new food products. Taking into account the fundamental basis and technological specificities of the main food sectors, throughout the three parts of this book, the authors investigate the biological and biochemical conversions and physicochemical treatment of food from animal sources, plant sources and food ingredients.Table of ContentsIntroduction xi Gérard Brulé Part 1 Food from Animal Sources 1 Chapter 1 From Milk to Dairy Products 3 Thomas Croguennec, Romain Jeantet and Pierre Schuck 1.1 The biochemistry and physical chemistry of milk 3 1.1.1 Milk fat 4 1.1.2 Carbohydrates 8 1.1.3 Proteins 10 1.1.4 Milk minerals 15 1.2 Biological and physicochemical aspects of milk processing 17 1.2.1 The stability of fat globules 17 1.2.2 Protein stability 19 1.3 Dairy product technology 25 1.3.1 Liquid milk 25 1.3.2 Fermented milk products 29 1.3.3 Milk powder 32 1.3.4 Cheese 39 1.3.5 Cream and butter 58 Chapter 2 From Muscle to Meat and Meat Products 65 Catherine Guérin 2.1 The biochemistry of muscle (land animals and fish) 65 2.1.1 The structure and composition of meat and fish muscle 66 2.1.2 Muscle structure 73 2.1.3 Proteins 78 2.1.4 Carbohydrates 88 2.1.5 Vitamins and minerals 88 2.2 Biological and physicochemical changes in muscle 89 2.2.1 Muscle contraction 89 2.2.2 Changes in muscle after death 91 2.3 Meat and fish processing technology 102 2.3.1 Meat processing technology 102 2.3.2 Fish processing technology 109 Chapter 3 From Eggs to Egg Products 115 Marc Anton, Valérie Lechevalier and Françoise Nau 3.1 Chicken egg – raw material in the egg industry 117 3.1.1 Structure and composition 117 3.1.2 Biochemical and physicochemical properties of the protein and lipid fractions of egg 120 3.2 Physicochemical properties of the different egg fractions 125 3.2.1 Interfacial properties 125 3.2.2 Gelling properties 131 3.3 The egg industry: technology and products 136 3.3.1 Decontamination of shells 138 3.3.2 Breaking and separation of the egg white and yolk 138 3.3.3 Primary processing of egg products – decontamination and stabilization 139 3.3.4 Secondary processing of egg products 142 3.3.5 Egg extracts 143 Part 2 Food from Plant Sources 145 Chapter 4 From Wheat to Bread and Pasta 147 Hubert Chiron and Philippe Roussel 4.1 Biochemistry and physical chemistry of wheat 150 4.1.1 Overall composition 150 4.1.2 Structure and properties of the constituents 154 4.2 Biological and physicochemical factors of wheat processing 163 4.2.1 Development of texture 164 4.2.2 Development of color and flavor 170 4.3 The technology of milling, bread making and pasta making 172 4.3.1 Processing of wheat into flour and semolina 172 4.3.2 Bread making 180 4.3.3 Pasta making 195 Chapter 5 From Barley to Beer 205 Romain Jeantet and Ludivine Perrocheau 5.1 Biochemistry and structure of barley and malt 205 5.1.1 Morphology of barley grain 206 5.1.2 Biochemical composition of barley 207 5.1.3 Composition and structure of starch and protein 208 5.1.4 Effect of malting 209 5.2 Biological and physicochemical factors of processing 213 5.2.1 Enzymatic degradation of starch and protein 214 5.2.2 Fermentability of the wort 220 5.3 Brewing technology 221 5.3.1 Stages of malting 221 5.3.2 Stages of beer production 224 Chapter 6 From Fruit to Fruit Juice and Fermented Products 231 Alain Baron, Mohammad Turk and Jean-Michel Le Quéré 6.1 Fruit development 231 6.1.1 Stages of development 231 6.1.2 Fruit ripening 233 6.2 Biochemistry of fruit juice 237 6.2.1 Pectins 238 6.2.2 Pectinolytic enzymes 241 6.2.3 Bitter and astringent compounds 245 6.3 Fruit juice processing 249 6.3.1 Preparation of fruit 249 6.3.2 Pre-treatment 250 6.3.3 Pressing 250 6.3.4 Treatment of fruit juice 253 6.3.5 Pasteurization, high-pressure treatment, pulsed electric fields and concentration 262 6.4 Cider 264 6.4.1 French cider 264 6.4.2 Fermentation process 265 6.4.3 Action of microorganisms 267 6.4.4 Fermentation and post-fermentation 271 Chapter 7 From Grape to Wine 275 Thomas Croguennec 7.1 Raw materials 276 7.1.1 Grape variety 276 7.1.2 Composition of grapes 276 7.2 Winemaking techniques 280 7.2.1 State of the harvest and adjustments 281 7.2.2 Physicochemical processes involved in winemaking 282 7.2.3 Biological processes involved in winemaking: fermentation 285 7.3 Stabilization and maturation of wine 289 7.3.1 Biological stabilization 289 7.3.2 Physicochemical stabilization 290 7.3.3 Maturation of wine 291 7.4 Specific technology 292 7.4.1 Sparkling wines (traditional method) 292 7.4.2 Sweet wines 293 Chapter 8 From Fruit and Vegetables to Fresh-Cut Products 297 Florence Charles and Patrick Varoquaux 8.1 Respiratory activity of plants 298 8.1.1 Measurement and modeling of respiratory activity 299 8.1.2 Control of respiratory activity 301 8.2 Enzymatic browning 302 8.2.1 Mechanism and evaluation 302 8.2.2 Prevention of enzymatic browning 303 8.3 Unit operations in the production of fresh-cut products: main scientific and technical challenges 304 8.3.1 Raw materials: selection of varieties and cultivation methods 306 8.3.2 Raw material quality control: grading 307 8.3.3 Trimming and mixing 307 8.3.4 Cutting 308 8.3.5 Washing and disinfection 309 8.3.6 Draining and drying 312 8.3.7 Weighing 313 8.3.8 Bagging 313 8.4 Modified atmosphere packaging 314 8.4.1 Diffusion of gases through packaging 315 8.4.2 Change in gas content in modified atmosphere packaging 317 8.5 Conclusion 319 Part 3 Food Ingredients 321 Chapter 9 Functional Properties of Ingredients 323 Gérard Brulé and Thomas Croguennec 9.1 Interactions with water: hydration and thickening properties 324 9.1.1 Types of interaction 324 9.1.2 Influence of hydrophilic components on water availability and mobility 325 9.1.3 Influence of hydration on the solubilization, structure and mobility of compounds 325 9.1.4 Effect of the hydration of components on rheological properties 326 9.2 Intermolecular interactions: texture properties 326 9.2.1 Aggregation/gelation by destabilization of macromolecules or particles 326 9.2.2 Aggregation/gelation by covalent cross-linking 327 9.2.3 Sol–gel transitions 329 9.2.4 Influence of denaturation kinetics and molecular interactions 329 9.3 Interfacial properties: foaming and emulsification 330 9.3.1 Interfacial tension 330 9.3.2 Surfactants 332 9.3.3 Emulsification and foaming 332 Chapter 10 Separation Techniques 335 Thomas Croguennec and Valérie Lechevalier 10.1 Proteins and peptides 335 10.1.1 Milk proteins and peptides 335 10.1.2 Extraction of lysozyme from egg white 346 10.1.3 Extraction of gelatin 348 10.1.4 Plant proteins 349 10.2 Carbohydrates 351 10.2.1 Sucrose 351 10.2.2 Lactose 364 10.2.3 Polysaccharides 369 10.3 Lipids 378 10.3.1 Production of vegetable oils 379 10.3.2 Lipid modification 383 10.4 Pigments and flavorings 391 10.4.1 Types of pigments and flavorings 391 10.4.2 Extraction/concentration of colorings and flavors 397 10.4.3 Formulation 400 Bibliography 403 List of Authors 417 Index 419

Read more less

Book SynopsisThis volume provides an authoritative account of the use of a wide range of spectroscopic methods in the analysis of lipids, with an emphasis on topics that are attracting special current attention. Some essential background theory is included within chapters.Trade Review"Fills [an] information gap, as it now combines all aspects of lipid structural analysis by various techniques in one single volume" - Lipid Technology NewsletterTable of ContentsIntroduction. Atomic spectroscopy for heavy metal determination in edible oils and fats. Lipid chemiluminescence. NMR in conjunction with GC-MS and UV methods: a case study in marine lipids. Pulse-NMR in the food science laboratory. Mass spectrometric techniques in the analysis of triacylglycerols. Gas chromatography - mass spectrometry of lipids. Infrared spectroscopy of lipids: principles and applications. Electron spin resonance studies of lipids. UV / visible light spectroscopy of lipids. X-ray diffraction of lipids. Use of colorimetry. References. Index.

Read more less

Book SynopsisThis volume has been designed to offer a balanced account of the laboratory synthesis, industrial manufacture and biosynthesis of lipids. Authors describe the synthesis of all the major lipid classes, including new and revised procedures, and there are chapters devoted to the synthesis and manufacture of vitamin E, other natural antioxidants, sugar esters and ethers, and food surfactants. This authoritative work of reference has something for all lipid scientists and technologists. It is directed at chemists and technologists working in oils and fats processing, the food industry, the oleochemicals industry and the pharmaceutical industry; at analytical chemists and quality assurance personnel; and at lipid chemists in academic research laboratories.Trade Review"An important compilation, as comprehensive as possible and therefore 'a must' for any chemist synthesising lipids" - Fett / Lipid "An essential reference text for scientists interested in the synthesis or isolation of lipids" - Food Chemistry "There is sufficient and basic up-to-date material that it will be good for handy reference for a long time" - Food Research InternationalTable of ContentsPolyene acids; The availability of polyunsaturated fatty acids (appendix to chapter 1); Isotopically labelled fatty acids; Synthesis of long-chain compounds with conjugated unsaturation; Eicosanoids: oxygenated derivatives of polyunsaturated fatty acids containing twenty carbon atoms; Synthesis of triacylglycerols; Chemical synthesis of glycerophospholipids and their analogs; Sphingolipids; Synthesis and production of vitamin E; The production of natural antioxidants (other than vitamin E); Enzymic processes; The preparation of derivatives for lipid analysis; Alkyl and acyl sugars; Synthesis and commercial preparation of surfactants for the food industry; Novel chemistry of delta-5 fatty acids; Lipid biosynthesis; References; Index.

Read more less