Biochemistry Books
Cambridge University Press Photosynthesis
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£69.34
Cambridge University Press Nanometer Technology Designs High Quality Delay Tests Frontiers in Electronic Testing 38
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£112.10
Cambridge University Press Molecular Chaperones and Cell Signalling
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£75.05
Cambridge University Press Van der Waals Forces
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£104.50
Cambridge University Press Chemical Biophysics
Book SynopsisChemical Biophysics provides an engineering-based approach to biochemical system-analysis for graduate level courses on systems biology, computational bioengineering and molecular biophysics. It was the first textbook to apply rigorous physical chemistry principles to mathematical and computational modelling of biochemical systems for an interdisciplinary audience.Trade ReviewReview of the hardback: 'There are a growing number of physicists, engineers, mathematicians and chemists who are interested in joining the post-genomics party and addressing cutting-edge problems in molecular and cell biology. The barrier to entry can be high and prohibitive. This marvelous new book opens the door for the quantitively inclined. Beard and Qian, in an accessible and clear style, present fundamental methods that can be used to model and analyze an array of biomolecular systems and processes, ranging from enzyme kinetics to gene regulatory networks to cellular transport. This book will appeal to autodidacts as well as professors looking for course texts.' J. J. Collins, Professor of Biomedical Engineering and MacArthur Fellow, Boston UniversityReview of the hardback: 'This is one of the most useful and readable accounts of biochemical thermodynamics that I have seen for a long time, if indeed ever. It is very definitely a book that I shall want to have on my shelves and to refer others to, because it contains a considerable amount of information not easy to find elsewhere.' Athel Cornish-Bowden, Directeur de Recherche, CNRS, MarseillesReview of the hardback: 'Dan Beard's and Hong Qian's Chemical Biophysics is a masterful portrayal of a critically important new area of science. The success of genomics now makes it imperative to understand the relationships between proteomics, biochemical systems behavior and the physiology of the intact animal or human. This book provides the path. Its clarity of description, making the complexities seem simple by adhering to fundamental principles, avoiding cluttering detail while painting the broad picture to great depth, makes it a pleasure to read and a treasure to study. It's a must for scientists and scholars working to understand integrative biology.' James B. Bassingthwaighte, Professor of Bioengineering, Biomathematics and Radiology at the University of Washington, SeattleReview of the hardback: 'This wonderful book will be indispensable to specialists in the fields of systems biology, biochemical kinetics, cell signaling, genetic circuits and quantitative aspects of biology, and also to undergraduate and graduate students. It presents a systematic approach to analyzing biochemical systems. The complex subjects are described in a clear style, with carefully crafted definitions and derivations. This unique book is an important step in the development and dissemination of systems biology approaches.' Aleksander S. Popel, Professor of Biomedical Engineering, Johns Hopkins UniversityReview of the hardback: 'Chemical Biophysics: Quantitative Analysis of Cellular Systems by Daniel Beard and Hong Qian fills a significant niche. The text is a concise yet clear exposition of the fundamentals of chemical thermodynamics and kinetics, aimed specifically at practitioners of the new science of systems biology. It is marvellously illustrated with biochemical examples that will aid those who aim to analyze and model the workings of biological cells.' David Eisenberg, Director UCLA-DOE Institute for Genomics & Proteomics, University of California, Los Angeles, Investigator, Howard Hughes Medical InstituteReview of the hardback: 'As computational biology moves into a more integrative and multi-scale phase, to provide the quantitative framework for linking the mass of experimental data generated by molecular techniques at the subcellular level to tissue and organ scale physiology, it is vitally important that models are based on quantitative approaches that incorporate, wherever possible, thermodynamically constrained biophysical mechanisms. This new book on the Chemical Biophysics of Cellular Processes by Dan Beard and Hong Qian does a wonderful job of formulating models for metabolic pathways, gene regulatory networks and protein interaction networks on the well-established principles of physical chemistry. Topics include enzyme catalyzed reactions, reaction-diffusion modelling, membrane transport, the chemical master equation and much more. This book will be of lasting value to computational biologists and bioengineers.' Professor Peter J Hunter, Auckland Bioengineering Institute at the University of AucklandReview of the hardback: 'It is recommended for institutional or personal purchase as it comprises a substantial reference textbook.' Microbiology TodayTable of ContentsPreface; Introduction; Part I. Background Material: 1. Concepts from physical chemistry; 2. Conventions and calculations for biochemical systems; 3. Chemical kinetics and transport processes; Part II. Analysis and Modeling of Biochemical Systems: 4. Enzyme-catalyzed reactions; 5. Biochemical signaling modules; 6. Biochemical reaction networks; 7. Coupled biochemical systems and membrane transport; Part III. Special Topics: 8. Spatially distributed systems and reaction-diffusion modeling; 9. Constraint-based analysis of biochemical systems; 10. Biomacromolecular structure and molecular association; 11. Stochastic biochemical systems and the chemical master equation; 12. Appendix: the statistical basis of thermodynamics; Bibliography; Index.
£69.34
Cambridge University Press Protein Interaction Networks Computational Analysis
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£67.44
Cambridge University Press Chemistry and the Environment
Book SynopsisThis textbook presents the chemistry of the environment using the full strength of physical, inorganic and organic chemistry, in addition to the necessary mathematics and physics. It provides a broad yet thorough description of the environment and the environmental impact of human activity using scientific principles. It gives an accessible account while paying attention to the fundamental basis of the science, showing derivations of formulas and giving primary references and historical insight. The authors make consistent use of professionally accepted nomenclature (IUPAC and SI), allowing transparent access to the material by students and scientists from other fields. This textbook has been developed through many years of feedback from students and colleagues. It includes more than 400 online student exercises that have been class tested and refined. The book will be invaluable in environmental chemistry courses for advanced undergraduate and graduate students and professionals in chTrade Review'… [a] thorough, well-written, advanced work … A thorough understanding of this material could occupy a full academic year and would provide a valuable graduate education in environmental chemistry … Highly recommended. Graduate students, researchers/faculty, professionals.' D. H. Stedman, ChoiceTable of Contents1. The Earth; 2. Environmental dynamics; 3. The spheres; 4. Chemistry of the atmosphere; 5. Chemistry of the hydrosphere; 6. Chemistry of the pedosphere; 7. Global cycles of the elements; 8. The chemicals industry; 9. Environmental impact of selected chemicals; 10. The chemistry of climate change.
£46.54
McGraw-Hill Education - Europe Lab Manual for General Organic Biochemistry
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£130.33
Hachette Go Drink
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£16.14
Random House USA Inc The Demon in the Freezer
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£9.49
Taylor & Francis Molecular Exercise Physiology An Introduction
Book SynopsisMolecular Exercise Physiology: An Introduction is the first student-friendly textbook to be published on this key topic in contemporary sport and exercise science. It introduces sport and exercise genetics and the molecular mechanisms by which exercise causes adaptation. The text is linked to real life sport and exercise science situations such as âwhat makes people good at distance running?â, âwhat DNA sequence variations code for a high muscle mass?â or âby what mechanisms does exercise improve type2 diabetes?âThe book includes a full range of useful features, such as summaries, definitions of key terms, guides to further reading, review questions, personal comments by molecular exercise pioneers (Booth, Bouchard) and leading research in the field, as well as descriptions of research methods. A companion website offers interactive and downloadable resources for both student and lecturers. Structured around central themes in sport and exercise science, such a
£52.99
John Wiley & Sons Inc ABC Transporters and Multidrug Resistance
Book SynopsisThis book gathers present knowledge on the involvement of ABC transporters in drug transport and resistance. Bringing together updated information from an otherwise-scattered field of scientific literature, this resource helps researchers in pharmaceutical science in discovering drugs able to counteract multidrug resistance in diseases like cancer.Trade Review"The book is both interesting for both novice and experienced researches in the field." (ChemMedChem, July 2010) Table of ContentsPREFACE ix CONTRIBUTORS xi INTRODUCTION: WHAT IS MULTIDRUG RESISTANCE? 1Jonathan A. Sheps and Victor Ling PART I ABC PROTEINS: AN OVERVIEW AND DESCRIPTION OF THE STRUCTURE, GENOME, NORMAL TISSUE EXPRESSION, PHYSIOLOGICAL ASPECT, AND MECHANISM OF ACTION 15 1 The P-glycoprotein 170: Just a multidrug resistance protein or a protean molecule? 17Fabienne Grandjean-Forestier, Christophe Stenger, Jacques Robert, Mireille Verdier, and Marie-Hélène Ratinaud 2 Multidrug resistance-associated protein (MRP/ABCC proteins) 47Mylène Honorat, Charles Dumontet, and Lea Payen 3 ABCG2: A new challenge in cancer drug resistance 83Orsolya Polgar, Robert W. Robey, Kin Wah To, John Deeken, Patricia A. Fetsch, and Susan E. Bates PART II ABC PROTEINS AND ONCOLOGY: EXPRESSION, DETECTION, AND IMPLICATION OF ABC PROTEINS IN HEMATOLOGICAL MALIGNANCIES AND SOLID TUMORS 119 4 Expression, detection, and implication of ABC proteins in acute myeloblastic leukemia 121Ollivier Legrand, Ruo-Ping Tang, and Jean-Pierre Marie 5 ABC proteins and oncology: Expression, detection, and implication of ABC proteins in solid tumors 143Jean François Bernaudin, Anne Fajac, Jocelyne Fleury-Feith, Khaldoun Kerrou, and Roger Lacave PART III ABC PROTEINS AND PATHOGENIC MICROORGANISMS 177 6 ABC transporters and resistance to antibiotics 179Serge Michalet and Marie-Geneviève Dijoux-Franca 7 ABC proteins involved in protozoan parasite resistance 195Bruno Pradines PART IV MULTIDRUG RESISTANCE (MDR) MODULATION THROUGH INHIBITION OF ABC TRANSPORTERS: DESIGN OF INHIBITORS AND MECHANISM OF ACTION 239 8 Reversal agents for P-glycoprotein-mediated multidrug resistance 241Hamid Morjani and Claudie Madoulet 9 Reversal agents of multidrug resistance mediated by multidrug resistance-associated proteins (MRPs) 261Ahcène Boumendjel, Anne Florin, and Jean Boutonnat 10 Reversal agents for breast cancer resistance protein (BCRP)-mediated multidrug resistance 289Jean Boutonnat, Anne Florin, and Ahcène Boumendjel 11 Strategies to overcome drug resistance in acute and chronic leukemias 315Eric Solary, Vincent Ribrag, and Stéphane de Botton 12 Multidrug resistance reversal in solid tumors 349Tatiana Bogush and Jacques Robert PART V BIOLOGICAL AND CLINICAL ASPECTS OF MULTIDRUG RESISTANCE: THE ROLE OF THE TRANSPORTERS AT THE MAIN PROTECTION BARRIERS (ABCB1, ABCC1, ABCC2, ABCG2) ON THE BIOAVAILABILITY OF MANY TYPES OF DRUGS AND MEDICATIONS 363 13 ABC superfamily transporters at the human blood–brain barrier 365Jean-Michel Scherrmann 14 The role of ABC transporters at the intestinal barrier 385Roos L. Oostendorp, Jos H. Beijnen, and Jan H.M. Schellens 15 Genetic polymorphisms in ABC transporters 411Leslie W. Chinn and Deanna L. Kroetz PERSPECTIVES 437 INDEX 441
£132.95
John Wiley & Sons Inc Flexible Viruses
Book SynopsisThis book provides up-to-date information on experimental and computational characterization of the structural and functional properties of viral proteins, which are widely involved in regulatory and signaling processes. With chapters by leading research groups, it features current information on the structural and functional roles of intrinsic disorders in viral proteomes. It systematically addresses the measles, HIV, influenza, potato virus, forest virus, bovine virus, hepatitis, and rotavirus as well as viral genomics. After analyzing the unique features of each class of viral proteins, future directions for research and disease management are presented.Table of ContentsPreface. 1. Do viral proteins possess unique features? (Vladimir Uversky). 2. Functional role of structural disorder in capsid proteins (Lars Liljas). 3. Structural disorder within the nucleoproteins and phosphoproteins of measles, Nipah and Hendra viruses (Johnny Habchi and Sonia Longhi). 4. Structural disorder within the Sendai virus nucleoprotein and phosphoprotein (Rob Ruigrok and Martin Blackledge). 5. Structural disorder in Rhabdoviridae phosphoproteins (Marc Jamin). 6. Structural disorder in matrix proteins from HiV-related viruses (Vladimir Uversky and Keith Dunker). 7. Structural disorder in proteins from influenza virus (Vladmir Uversky and Keith Dunker). 8. Structural disorder in the HIV-1 Vif protein and oilgomerization-dependent gain of structure (Assaf Friedler). 9. Order from Disorder: Structure, Function and Dynamics of the HIV-1 Transactivator of Transcription (Joe D. O’Neil). 10. Intrinsically disordered protein domains of the non structural proteins of Sesbania mosaic virus and their functional role (Handanahal S. Savithri). 11. Intrinsic disorder in genome-linked viral proteins VPgs of potyviruses (Jadwiga Chroboczek, Eugénie Hébrard, Kristiina Mäkinen, Thierry Michon and Kimmo Rantalainen). 12. Intrinsic disorder in HPV 16 E7 protein (Gonzalo de Prat-Gay). 13. The Semiliki forest virus serine protease is disordered and yet displays catalytic activity (Manuel Morillas). 14. Intrinsic disorder in the core proteins of Flaviviridae (Jean-Luc Darlix). 15. Domains 2 and 3 of non-structural protein 5A (NS5A) of hepatitis C virus is natively unfolded (Ho Sup Yoon). 16. Intrinsic disorder within phage λ N protein and interaction with the E. coli NusA protein (Kristian Schweimer). 17. The N-terminal extension region of Hordeivirus movement TGB1 protein consists of two domains with different content of disordered structure (V.V. Makarov, M.E. Tailansky, E.N. Dobrov, N.O. Kalinina).
£141.50
John Wiley & Sons Inc Chemistry and Biochemistry of Oxygen Therapeutics
Book SynopsisHuman blood performs many important functions including defence against disease and transport of biomolecules, but perhaps the most important is to carry oxygen the fundamental biochemical fuel - and other blood gases around the cardiovascular system. Traditional therapies for the impairment of this function, or the rapid replacement of lost blood, have centred around blood transfusions. However scientists are developing chemicals (oxygen therapeutics, or blood substitutes) which have the same oxygen-carrying capability as blood and can be used as replacements for blood transfusion or to treat diseases where oxygen transport is impaired. Chemistry and Biochemistry of Oxygen Therapeutics: From Transfusion to Artificial Blood links the underlying biochemical principles of the field with chemical and biotechnological innovations and pre-clinical development. The first part of the book deals with the chemistry, biochemistry, physiology and toxicity of oxygen, including cTable of ContentsList of Contributors xvii Preface xxiii 1. Introduction 1 Richard B. Weiskopf References 5 Part I. Oxygen: Chemistry, Biochemistry, Physiology and Toxicity 9 2. Hemoglobin Reactivity and Regulation 11 Stefano Bettati and Andrea Mozzarelli 2.1 Introduction 11 2.2 Oxygen Loading and Transport 11 2.3 NO Reactivity with Hb 15 2.4 Hb Oxidation 16 2.5 Nitrite Reactivity with Hb 16 2.6 Amino-acid Determinants of Hb Reactivity: Natural and Engineered Hbs 17 2.6.1 Modulation of Oxygen Affinity and Cooperativity 17 2.6.2 NO Reactivity and Oxidation 18 2.7 Conclusion 18 Acknowledgments 19 References 19 3. The Major Physiological Control Mechanisms of Blood Flow and Oxygen Delivery 23 Raymond C. Koehler 3.1 Introduction 23 3.2 Autoregulation of Blood Flow to Changes in Perfusion Pressure 23 3.3 Metabolic Regulation of Blood Flow 26 3.4 O2 Transport 27 3.5 O2 Delivery 27 3.6 Endothelial Control of Vasomotor Tone 29 3.7 Effect of Cell-free Hb on Endothelial Function 31 3.8 Hypoxic Hypoxia 33 3.9 Carbon Monoxide Hypoxia 36 3.10 Anemia 36 3.11 Conclusion 39 References 39 4. The Main Players: Hemoglobin and Myoglobin; Nitric Oxide and Oxygen 47 Tim J. McMahon and Joseph Bonaventura 4.1 Introduction 47 4.2 Role of Mammalian Mb in O2 Homeostasis 47 4.3 What’s Missing in the Mb Knockout Mouse 48 4.4 Evolutionary Origins of Mb and the Nitrogen Cycle 49 4.5 Human Hb: Evolved Sensor of pO2 and Redox 49 4.6 Broad Reactivity and Influence of NO: Lessons from the Microcosm Hb 49 4.7 Some Fish Demonstrate a Fundamental “Need” for Hb-dependent NO Cycling, as in Humans 50 4.8 Reactions of NO with Hb that Preserve NO Bioactivity 52 4.9 Mammalian RBC/Hb–NO Interactions 52 4.10 A Mutant Mouse Challenges the SNO-Hb Hypothesis, but does not Overthrow it 54 4.11 Signaling by Hb-derived SNO: A Metabolically Responsive, Regulated Pathway 54 4.12 Signaling by Hb-derived SNO: Pathway Complexity Revealed by Multiple Defects in Disease States 55 4.13 Therapeutic Implications of the Hb–NO Signaling System 56 4.14 HBOCs, NO, and SNO 56 4.15 Other Gaseous Hb Ligands of Potential Therapeutic Significance 57 4.16 NO-related Enzymatic Activities of Hb: Reconciling Nitrite Reductase and SNO Synthase Functions 57 4.17 Measuring Biologically Relevant Hb–NO Adducts 58 4.18 Conclusion 58 Acknowledgments 58 References 59 5. The Role of Reactive Oxygen and Nitrogen Species in Ischemia/Reperfusion Injury 63 Ester Spagnolli and Warren M. Zapol 5.1 Introduction 63 5.2 Redox System and Free Radicals in Biological Systems 64 5.3 Pathophysiology of Ischemia/Reperfusion Injury 65 5.3.1 Cell Death 65 5.3.2 The Inflammatory Response 67 5.4 Protection Against I/R Injury 67 5.4.1 Ischemic Pre- and Post-conditioning 67 5.4.2 Pharmacological Conditioning 68 5.4.2.1 The Protective Role of ROS and Antioxidants 68 5.4.2.2 The Protective Role of NO 69 5.4.2.3 NO-based Therapies for I/R Injury 70 5.5 Conclusion 72 Acknowledgments 72 References 72 Part II. Medical Needs for Oxygen Supply 79 6. Acute Traumatic Hemorrhage and Anemia 81 Lena M. Napolitano 6.1 Introduction 81 6.2 Blood Transfusion in Trauma 83 6.2.1 Massive Transfusion 83 6.2.2 Massive Transfusion and Coagulopathy 83 6.2.3 Hypotensive or Delayed Resuscitation 84 6.2.4 Hemostatic Resuscitation 84 6.2.5 Massive Transfusion Protocols 86 6.2.6 Transfusion after Hemorrhage Control 86 6.2.7 Efficacy of RBC Transfusion in Trauma and Associated Risks 86 6.3 Oxygen Therapeutics in Trauma 88 6.3.1 Diaspirin Crosslinked Hb 90 6.3.2 Hemopure 90 6.3.3 PolyHeme 91 6.3.4 MP4OX 93 6.3.5 Recombinant Human Hb 95 6.3.6 Adverse Effects of HBOCs 95 6.3.7 HBOCs in Trauma: A Way Forward? 96 6.4 Conclusion 97 References 97 7. Diagnosis and Treatment of Haemorrhages in ‘Nonsurgical’ Patients 107 Umberto Rossi and Rosa Chianese 7.1 Introduction 107 7.1.1 Aetiopathogenetic Classification 107 7.1.2 Multifactorial Pathogenesis 108 7.1.3 Haemorrhagic Syndromes from Antithrombotic Treatment or Prophylaxis 108 7.2 Clinical Assessment 111 7.2.1 Medical History 111 7.2.2 Physical Examination 112 7.3 Laboratory Tests 113 7.3.1 Screening Tests 113 7.3.2 Second-level Laboratory Tests 113 7.3.3 Other Tests 114 7.4 Haemorrhagic Syndromes Clinically Indicative of Systemic Defects with Normal Screening Tests 117 7.5 Blood and Blood Components in the Treatment of Haemorrhagic Syndromes 118 Further Reading 118 8. Management of Perioperative Bleeding 121 Sibylle A. Kozek-Langenecker 8.1 Introduction 121 8.2 Pathomechanisms of Coagulopathy in Massive Bleeding 121 8.3 Perioperative Coagulation Monitoring 122 8.4 Limitations of Routine Coagulation Tests in the Perioperative Setting 123 8.5 Thromboelastography (TEG) and Rotational Thromboelastometry (ROTEM) 124 8.6 Procoagulant Interventions 124 8.7 Algorithm for Coagulation Management 126 References 127 9. Oxygenation in the Preterm Neonate 131 Vidheya Venkatesh, Priya Muthukumar, Anna Curley and Simon Stanworth 9.1 Introduction 131 9.2 Physiology of Oxygen Transport in Fetal and Postnatal Life 132 9.2.1 Oxygenation of the Fetus 132 9.2.2 Measuring Oxygenation in the Neonate 133 9.3 Oxygen Therapy in the Postnatal Period 133 9.3.1 Oxidative Stresses in the Newborn Period 134 9.3.2 Clinical Sequelae of Hyperoxia 134 9.3.2.1 Retinopathy of Prematurity 134 9.3.2.2 Oxygen and Chronic Lung Disease 135 9.3.2.3 Oxygen and Periventricular Leukomalacia 136 9.4 Oxygen and Resuscitation of the Newborn Infant 136 9.5 Transfusion in the Newborn 137 9.6 ROP and Transfusions 137 9.7 Conclusion 137 References 138 10. Ischemia 145 Hooman Mirzakhani and Ala Nozari 10.1 Introduction 145 10.2 Pathophysiology 145 10.2.1 Energy Failure 145 10.2.2 Cell Membrane Damage 146 10.2.3 Increased Cytosolic Calcium 146 10.2.4 Inflammation 148 10.2.5 The No-reflow Phenomenon 149 10.2.6 Free Radicals and Reactive Oxygen Species 149 10.2.7 Excitotoxicity 150 10.3 Therapeutic Potentials 150 10.3.1 Preconditioning 150 10.3.2 Antioxidants 151 10.3.3 Anti-inflammation Therapy 151 10.3.4 Therapeutic Hypothermia 151 10.3.5 Hydrogen Sulfide 152 10.3.6 Hyperoxia and Hyperbaric Oxygen 152 10.3.7 Hemoglobin-based Oxygen Carriers 152 10.4 Conclusion 153 References 153 11. Normobaric and Hyperbaric Oxygen Therapy for Ischemic Stroke and Other Neurological Conditions 159 Ari Moskowitz, Yu-Feng Yvonne Chan and Aneesh B. Singhal 11.1 Introduction 159 11.2 Rationale of Oxygen Therapy in AIS 160 11.3 Hyperbaric Oxygen Therapy 162 11.4 Normobaric Oxygen Therapy 164 11.5 The Status of Supplemental Oxygen Delivery 165 11.6 Comparison of HBO and NBO in AIS 165 11.7 Safety Concerns 168 11.8 HBO and NBO in Other Conditions 169 11.9 Conclusion 169 References 170 12. Transfusion Therapy in β Thalassemia and Sickle Cell Disease 179 Carlo Brugnara and Lucia De Franceschi 12.1 Introduction 179 12.2 β Thalassemia and Transfusion 179 12.3 Sickle Cell Disease and Transfusion 182 12.4 Iron Chelation Tools 185 12.5 Conclusion 186 References 186 Part III. “Old” and New Strategies for Oxygen Supply 193 13. Transfusion: Political, Administrative and Logistic Issues 195 John R. Hess and Giuliano Grazzini Disclaimer 195 13.1 Introduction 195 13.2 Blood Safety 196 13.3 Blood Availability 198 13.4 Cost and Fairness 200 13.5 Transfusion Medicine 201 References 202 14. Conscientious Objection in Patient Blood Management 205 Kenneth E. Nollet and Hitoshi Ohto 14.1 Introduction 205 14.2 Conscientious Objection 205 14.3 Patient Blood Management 206 14.4 Jehovah’s Witnesses 207 14.5 Will the Real Objection Please Stand Up? 208 14.6 Conscientious Objection in Relation to Oxygen Therapeutics and Other Innovations 208 Acknowledgements 209 References 210 15. Red-cell Transfusion in Clinical Practice 213 Harvey G. Klein 15.1 Introduction 213 15.2 Red-cell Use 214 15.3 The Red-cell-transfusion Trigger 215 15.4 Risks of Red-cell Transfusion 216 15.5 Conclusion 218 Disclaimer 218 References 218 16. Causes and Consequences of Red Cell Incompatibility 221 Chisa Yamada and Robertson Davenport 16.1 Introduction 221 16.2 Red Cell Antigens 221 16.2.1 ABO and the H System 221 16.2.2 The Lewis System and Structurally Related Antigens 222 16.2.3 The Rh System 222 16.2.4 Other Blood Group Systems 222 16.3 Red Cell Antibodies 223 16.3.1 Naturally Occurring Antibodies and Immune Antibodies 223 16.3.2 Autoantibodies 224 16.3.3 Drug Induced Antibodies 224 16.4 Compatibility Testing 224 16.4.1 ABO and Rh D Typing 224 16.4.2 Antibody Screening and Identification 224 16.4.3 Selection of Appropriate Blood 225 16.4.4 Crossmatch Testing 225 16.5 Hemolytic Transfusion Reactions 225 16.5.1 Pathophysiology 226 16.5.2 Prevention 228 References 228 17. Biochemistry of Storage of Red Blood Cells 231 Ryan Stapley, Dario A. Vitturi and Rakesh P. Patel 17.1 Introduction 231 17.2 Pathologic Consequences of Transfusion with Aged RBCs 232 17.3 Changes in Oxygen Affinity During RBC Storage 232 17.4 Role of Oxidative Damage During RBC Storage 233 17.5 Changes in the Physical Properties of RBCs During Storage 234 17.6 RBCs as Modulators of Vascular Flow 234 17.6.1 ATP Release Hypothesis 234 17.6.2 SNO-hemoglobin Hypothesis 235 17.6.3 Nitrite Reductase/Anhydrase Hypothesis 236 17.7 RBC-dependent Modulation of Inflammation 237 17.8 Conclusion 237 Acknowledgements 238 References 238 18. Proteomic Investigations of Stored Red Blood Cells 243 Lello Zolla and Angelo D’Alessandro 18.1 Introduction 243 18.2 RBC Ageing and Metabolism in vivo 244 18.3 RBC Storage Lesions Through Proteomics 248 18.4 Conclusion 252 References 252 19. Red Blood Cells from Stem Cells 257 Anna Rita Migliaccio, Carolyn Whitsett and Giovanni Migliaccio 19.1 Introduction 257 19.2 Stem-cell Sources for ex vivo Generation of Erythroid Cells as a Transfusion Product 258 19.3 Conditions that Favor ex vivo Erythroid Cell Expansion 260 19.4 A Clinical-grade Production Process for ex vivo Generation of Red-cell Transfusion Products 261 19.4.1 The Nature of the Production Process 261 19.4.2 Cellular Composition of the Product 263 19.4.3 Functional Status of Product 264 19.4.4 Safety Considerations 265 19.5 Time Line of the Clinical Application of ex vivo-generated Erythroid Cells 266 19.5.1 Drug Discovery 266 19.5.2 Drug Delivery 267 19.5.3 Ex vivo-expanded EBs for Alloimmunized Patients 268 References 268 20. The Universal Red Blood Cell 273 Luca Ronda and Serena Faggiano 20.1 Introduction 273 20.1.1 ABO Antigens 274 20.1.2 The Rh System 274 20.2 Enzymatic Removal of A and B Antigens 275 20.2.1 Conversion of B RBCs to Group O 275 20.2.2 Conversion of A RBCs to Group O 277 20.3 RBC Camouflage Through PEGylation 277 20.3.1 Functionalized Methoxy PEG 278 20.3.2 Cyanuric Chloride PEG 279 20.3.3 Extension Arm-facilitated RBC PEGylation 279 20.3.4 Increasing the Degree of RBC PEGylation 280 20.4 Conclusion 280 References 280 21. Allosteric Effectors of Hemoglobin: Past, Present and Future 285 Martin K. Safo and Stefano Bruno 21.1 Introduction 285 21.2 Natural and Synthetic Allosteric Effectors 288 21.2.1 Organic Phosphates 288 21.2.2 Synthetic Aromatic Propionate Right-shifters 289 21.2.3 Aromatic Aldehyde Left-shifters 290 21.3 Molecular Mechanism of Action of Allosteric Effectors 293 21.3.1 Oxygen Binding Curve and Hb Structural Changes 293 21.3.2 How Allosteric Effectors can Bind to the Same Site and Have Opposite Allosteric Properties 294 21.3.3 Decreasing Subunit Mobility and Changes in Allosteric Properties: Molecular Ratchets 294 21.4 The First Visualization of an Important Pharmacological Theory via Hb Allosteric Effector Binding 295 21.5 The Clinical Importance of Hemoglobin Allosteric Effectors 295 References 296 22. Hemoglobin-based Oxygen Carriers: History, Limits, Brief Summary of the State of the Art, Including Clinical Trials 301 Jonathan S. Jahr, Arezou Sadighi, Linzy Doherty, Alvin Li and Hae Won Kim 22.1 Introduction 301 22.2 American Society of Anesthesiologists Guidelines and Risks of Blood Transfusion 302 22.3 Limitations of Blood Transfusion 302 22.4 History 302 22.5 Development 303 22.6 Definitive Clinical Trials 304 22.6.1 Diaspirin Crosslinked Hemoglobin (DCLHb, HemeAssist, Baxter Laboratories, Deerfield, IL) 304 22.6.2 Hemoglobin Raffimer (HR, Hemolink, Hemosol Inc., Ontario, Canada) 306 22.6.3 Human Polymerized Hemoglobin (PolyHeme, Northfield Laboratories, Evanston, IL) 307 22.6.4 Hemoglobin Glutamer-250 (Bovine) (HBOC-201, Hemopure, Biopure Corp., Cambridge, MA) 308 22.6.5 Maleimide-polyethylene Glycol-modified Hemoglobin (MP4, Hemospan, Sangart Inc., San Diego, CA) 309 22.7 Current Status and Future Directions of HBOCs 311 References 314 23. Oxygen Delivery by Natural and Artificial Oxygen Carriers 317 Enrico Bucci 23.1 Introduction 317 23.2 The Role of Oxygen Carriers 317 23.3 The Role of Natural Cell-bound Oxygen Carriers 318 23.4 Matching the Rate of Oxygen Delivery with the Rate of Oxygen Consumption 320 23.4.1 The Imbalance 320 23.4.2 The Rate of Oxygen Release from the Red Cells 320 23.4.3 Matching the Delivery/Consumption Rates 321 23.4.4 The Hematocrit is a Critical Parameter 321 23.5 The Role of Artificial Cell-free Oxygen Carriers 321 23.5.1 Facilitated Diffusion 321 23.5.2 Toxicity 322 23.6 Other Parameters 322 23.7 Clinical Use? 323 Acknowledgments 324 References 324 24. Crosslinked and Polymerized Hemoglobins as Potential Blood Substitutes 327 Kenneth W. Olsen and Eugene Tarasov 24.1 Introduction 327 24.2 Crosslinking the Hb Tetramer 328 24.3 Hb Polymers 332 24.4 Conclusion 337 References 338 25. Engineering the Molecular Shape of PEG-Hemoglobin Adducts for Supraperfusion 345 Seetharama A. Acharya, Marcos Intaglietta, Amy G. Tsai, Kulal Ananda and Fantao Meng 25.1 Introduction 345 25.2 Enzon DecaPEGylated Bovine Hb is Nonhypertensive 346 25.3 EAF HexaPEGylated Hb (EAF P5K6-Hb) is Nonhypertensive 347 25.4 Molecular and Solution Properties of EAF HexaPEGylated Human Hb (EAF-P5K6-Hb) 347 25.5 High O2 Affinity of EAF HexaPEGylated Hb and Tissue Oxygenation in Extreme Hemodilution 349 25.6 Influence of Total PEG Mass Conjugated to Hb on O2 Affinity and Tissue Oxygenation by PEG-Hbs 350 25.7 Influence of PEGylation Chemistry on Structural, Functional, and Solution Properties of HexaPEGylated Hb 351 25.8 Reductive PEGylation-induced Weakening of Interdimeric Interactions of Tetrameric Hbs 352 25.9 PEGylation-promoted Dissociation of Hb Tetramer is Attenuated by the Extension Arms of EAF PEGylated Hbs 353 25.10 Does Urethane-linkage-mediated PEGylation of Hb Promote its Dissociation? 354 25.11 Hemospan: Prototype of EAF HexaPEGylated Hb Designed at Einstein 354 25.12 EAF HexaPEGylated Hb Compared to other Blood Substitutes of Earlier Designs 355 25.13 Reversible Protection of Cys-93(β) during EAF PEGylation of Hb and Crosslinked Hbs: A Structural Requirement to Generate Medium- and Low-O2-affinity PEG-Hbs 355 25.14 Engineering Extension Arms between the Protein Core and PEG Shell Attenuates PEGylation-promoted Tetramer Dissociation 356 25.15 Attenuation of Direct HexaPEGylation-promoted Dissociation of Hb Tetramers by Increasing the Tetramer Stability Through Chemical Modification 359 25.16 Influence of the Extension Arm on the HexaPEGylation-enhanced Thermal Stability of Hb 359 25.17 PEGylation of Hb Induces a Hydrostatic Molecular Drag to the PEG-Hb Conjugate 360 25.18 EAF HexaPEGylated Hb is a Superperfusion Agent 360 25.19 EAF PEG-Hb-induced Vasodilation 361 25.20 In vivo Vasodilation by EAF PEG-Hb through its Enhanced Nitrite Reductase Activity 361 25.21 EAF PEG-Hbs as Mechanotransducers of e-NOS Activity 363 25.22 The Pattern of PEGylation of Intramolecularly Crosslinked Hbs Influences the Viscosity of the PEG-Hb Solution 364 25.23 Conclusion 364 Acknowledgments 366 References 367 26. Hb Octamers by Introduction of Surface Cysteines 371 V´eronique Baudin-Creuza, Chien Ho and Michael C. Marden 26.1 Introduction 371 26.2 Genetic Engineering of Proteins with Cysteines 373 26.2.1 Protein Expression 373 26.2.2 Oligomer Size 374 26.2.3 Disulfide Bond Formation 375 26.2.4 Functional Properties of the Octamers 376 26.2.5 Octamer Properties 378 26.2.6 Octamer Constraint 378 26.3 Conclusion 378 References 378 27. Hemoglobin Vesicles as a Cellular-type Hemoglobin-based Oxygen Carrier 381 Hiromi Sakai, Hirohisa Horinouchi, Eishun Tsuchida and Koichi Kobayashi 27.1 Introduction 381 27.2 The Concept of Hb Encapsulation in Liposomes 382 27.3 Hb Encapsulation Retards Gas Reactions 383 27.4 HBOCs as a Carrier of not only O2 but also CO 385 27.5 Conclusion 387 Acknowledgments 387 References 387 28. Animal Models and Oxidative Biomarkers to Evaluate Preclinical Safety of Extracellular Hemoglobins 391 Paul W. Buehler and Felice D’Agnillo Disclaimer 391 28.1 Introduction 391 28.2 HBOC Safety and Efficacy 392 28.2.1 Proposed Mechanisms of Toxicity 392 28.2.1.1 Hypertension 392 28.2.1.2 Oxidative Stress 392 28.2.2 Safety Pharmacology and Toxicology Studies 393 28.2.3 In vivo Models of Efficacy “Proof of Concept” 395 28.2.3.1 Tissue Blood Flow and Oxygenation 395 28.2.3.2 Traumatic Hemorrhage 396 28.2.3.3 Local Ischemia 397 28.2.3.4 Sickle Cell Disease 397 28.2.4 Experimental Approaches to Assessing Preclinical Safety of HBOCs 398 28.2.4.1 Species Antioxidant Status (Natural Evolution) 398 28.2.4.2 Chemically Induced Antioxidant Depletion 398 28.2.4.3 Endothelial Dysfunction 399 28.2.4.4 Sepsis and Endotoxemia 400 28.3 Experimental Oxidative Biomarkers and Extracellular Hb Exposure 400 28.3.1 Heme Iron Oxidation 400 28.3.2 Amino-acid Oxidation 401 28.3.3 Heme Catabolism and Iron Sequestration 401 28.4 Markers of in vivo Oxidative Stress and Tissue Damage 403 28.4.1 4-hydroxy-2-nonenal (4-HNE) Protein Adducts 403 28.4.2 8-hydroxy-2-deoxyguanosine (8-OHdG) 403 28.5 Conclusion 404 References 405 29. Academia–Industry Collaboration in Blood Substitute Development: Issues, Case Histories and a Proposal 413 Hae Won Kim, Andrea Mozzarelli, Hiromi Sakai and Jonathan S. Jahr 29.1 Introduction 413 29.2 Generic Issues in Academia–Industry Collaboration 414 29.3 Academia–Industry Collaboration in HBOC Development 415 29.4 Proposal for a New Academia–Industry Collaboration Model in HBOC Development: an HBOC Research Consortium (a Conceptual Model) 417 29.4.1 Mission 417 29.4.2 Guiding Principles 417 29.4.3 Key Objectives 417 29.4.4 Structure 418 29.4.5 Operation 419 29.5 Discussion 420 29.6 Conclusions 421 Appendix: Successful Academia–Industry Collaboration Cases in HBOC Development 422 Case A: Waseda–Keio–Industry Research Collaboration 422 Case B: EuroBloodSubstitutes Consortium 424 References 426 Index 429
£131.05
John Wiley & Sons Inc Proteins in Solution and at Interfaces
Book SynopsisProteins in solution and at interfaces are increasingly used in exciting new applications, from biomimetic materials to nanoparticle patterning.Table of ContentsPREFACE ix CONTRIBUTORS xiii PART I 1 X-Ray Crystallography of Biological Macromolecules: Fundamentals and Applications 3 Antonio L. Llamas-Saiz and Mark J. van Raaij 2 Nuclear Magnetic Resonance Methods for Studying Soluble, Fibrous, and Membrane-Embedded Proteins 23 Victoria A. Higman 3 Small-Angle X-Ray Scattering Applied to Proteins in Solution 49 Leandro Ramos Souza Barbosa, Francesco Spinozzi, Paolo Mariani, and Rosangela Itri 4 Analyzing the Solution State of Protein Structure, Interactions, and Ligands by Spectroscopic Methods 73 Veronica I. Dodero and Paula V. Messina 5 Resolving Membrane-Bound Protein Orientation and Conformation by Neutron Reflectivity 99 Hirsh Nanda 6 Investigating Protein Interactions at Solid Surfaces—In Situ, Nonlabeling Techniques 113 Olof Svensson, Javier Sotres, and Alejandro Barrantes 7 Calorimetric Methods to Characterize the Forces Driving Macromolecular Association and Folding Processes 139 Conceic¸ ˜ao A.S.A. Minetti, Peter L. Privalov, and David P. Remeta 8 Virtual Ligand Screening Against Comparative Models of Proteins 179 Hao Fan 9 Atomistic and Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins 193 Thomas J. Piggot, Peter J. Bond, and Syma Khalid PART II 10 Preparation of Nanomaterials Based on Peptides and Proteins 209 Yujing Sun and Zhuang Li 11 Natural Fibrous Proteins: Structural Analysis, Assembly, and Applications 219 Mark J. van Raaij and Anna Mitraki 12 Amyloid-Like Fibrils: Origin, Structure, Properties, and Potential Technological Applications 233 Pablo Taboada, Silvia Barbosa, Josue Juarez, Manuel-Alatorre Meda, and Výctor Mosquera 13 Proteins and Peptides in Biomimetic Polymeric Membranes 283 Alfredo Gonzalez-Perez 14 Study of Proteins and Peptides at Interfaces By Molecular Dynamics Simulation Techniques 291 David Poger and Alan E. Mark 15 A Single-Molecule Approach to Explore the Role of the Solvent Environment in Protein Folding 315 Katarzyna Tych and Lorna Dougan 16 Enhanced Functionality of Peroxidases By Its Immobilization at The Solid–Liquid Interface of Mesoporous Materials and Nanoparticles 335 Jose Campos-Teran, Iker Inarritu, Jorge Aburto, and Eduardo Torres 17 Superactivity of Enzymes in Supramolecular Hydrogels 353 Ye Zhang and Bing Xu 18 Surfactant Proteins and Natural Biofoams 365 Malcolm W. Kennedy and Alan Cooper 19 Promiscuous Enzymes 379 Luis F. Olguin 20 Thermodynamics and Kinetics of Mixed Protein/Surfactant Adsorption Layers at Liquid Interfaces 389 Reinhard Miller, E.V. Aksenenko, V.S. Alahverdjieva, V.B. Fainerman, C.S. Kotsmar, J. Kragel, M.E. Leser, J. Maldonado-Valderrama, V. Pradines, C. Stefaniu, A. Stocco, and R. Wustneck 21 Application of Force Spectroscopy Methods to the Study of Biomaterials 429 Chuan Xu and Erika F. Merschrod S. 22 Protein Gel Rheology 437 Katie Weigandt and Danilo Pozzo 23 Exploring Biomolecular Thermodynamics in Aqueous and Nonaqueous Environments using Time-Resolved Photothermal Methods 449 Randy W. Larsen, Carissa M. Vetromile, William A. Maza, Khoa Pham, Jaroslava Miksovska INDEX 473
£175.70
John Wiley & Sons Inc Molecular Descriptors in QSARQSPR CDROM
Book SynopsisThis work provides a comprehensive and critical overview of all the main classes of theoretical molecular descriptors. It reviews computational methods that can be employed in the development of QSAR and QSPR equations.Trade Review"This text for academic and industrial chemists covers empirical and molecular descriptors, and methods for QSAR/QSPR development." (SciTech Book News, Vol. 24, No. 4, December 2000)Table of ContentsEmpirical Molecular Descriptors. Theoretical Molecular Descriptors. Methods for the Development of QSAR/QSPR. Appendix. Index.
£322.95
John Wiley & Sons Inc Buprenorphine
Book SynopsisBuprenorphine: Combatting Drug Abuse with a Unique Opioid Editors: Alan Cowan and John W. Lewis Scientists involved in the study of opioid pharmacology and drug abuse have long included among their goals the development of effective analgesics with reduced potential for abuse and dependence, and the development of effective pharmacological agents for the treatment of opioid abuse and dependence. Buprenorphine appears to have made an important scientific and clinical contribution on both of these fronts. In this timely volume, international experts describe the unusual chemical and biological characteristics which make this agent unique, from the opiate receptor, through animal pharmacology, to clinical uses, culminating in a discussion of the use of buprenorphine as a medication in the treatment of opioid abuse. Buprenorphine holds great promise as a significant addition to the therapeutic menu available to drug abuse therapists. Buprenorphine: CombaTable of ContentsPartial table of contents: CHEMISTRY. Buprenorphine-Medicinal Chemistry (J. Lewis). PRECLINICAL PHARMACOLOGY. Update on the General Pharmacology of Buprenorphine (A. Cowan). ASSAY, METABOLISM, AND PHARMACOKINETICS. Analysis (R. Moore). CLINICAL PHARMACOLOGY AND EVALUATION. Buprenorphine in Psychiatric Disorders (D. Nutt, et al.). STUDIES RELATING TO TREATMENT OF SUBSTANCE ABUSE. Detoxification and Induction Onto Naltrexone (M. Rosen & T. Kosten). PERSPECTIVE. Buprenorphine: What Interests the National Institute on Drug Abuse? (D. Segal & C. Schuster). Index.
£229.85
John Wiley and Sons Ltd A Field Guide to Common Animal Poisons
Book SynopsisThis field guide should be useful for veterinary practitioners and veterinary students. Murphy covers all aspects of common animal poisons and provides references for more in-depth research. As a text, the book is designed for teaching applied aspects of veterinary toxicology.Table of ContentsPreface. Acknowledgements. Abbreviations.. I. Prevalence of Animal Exposures to Toxins. II. Treatment regimens. III. Toxin Summaries. Adverse Drug Reactions. Neurological System. Neurological System. Gastrointestinal System. Renal System. Hepatic System. Dermal System. Respiratory System. Respiratory System. Cardiovascular System. Hematopoietic System. Hematopoietic System. Musculoskeletal System. Reproductive System.. IV. Selected Bibliographies. V. Additional Sources of Information. VI. Indices to Toxins by:. Clinical Sign. Diagnostic test result. Toxin name, system, and LD. Response form.
£55.05
John Wiley & Sons Inc Comprehensive Chiroptical Spectroscopy Volume 2
Book SynopsisThis book provides an introduction to the important methods of chiroptical spectroscopy in general, and circular dichroism (CD) in particular, which are increasingly important in all areas of chemistry, biochemistry, and structural biology.The book can be used as a text for undergraduate and graduate students and as areference for researchers in academia and industry.Experimental methods and instrumentation are described with topics ranging from the most widely used methods (electronic and vibrational CD) to frontier areas such as nonlinear spectroscopy and photoelectron CD, as well as the theory of chiroptical methods and techniques for simulating chiroptical properties.Applications of chiroptical spectroscopy to problems in organic stereochemistry, inorganic stereochemistry, and biochemistry and structural biologyare alsodiscussed, and each chapter is written by one or more leading authorities with extensive experience in the field. Table of ContentsComprehensive Chiroptical Spectroscopy, Volume 2 PREFACE xi CONTRIBUTORS xiii PART I A HISTORICAL OVERVIEW 1 1 THE FIRST DECADES AFTER THE DISCOVERY OF CD AND ORD BY AIME COTTON IN 1895 3 Peter Laur PART II ORGANIC STEREOCHEMISTRY 37 2 SOME INHERENTLY CHIRAL CHROMOPHORES—EMPIRICAL RULES AND QUANTUM CHEMICAL CALCULATIONS 39 Marcin Kwit, Pawel Skowronek, Jacek Gawronski, Jadwiga Frelek, Magdalena Woznica, and Aleksandra Butkiewicz 3 ELECTRONIC CD OF BENZENE AND OTHER AROMATIC CHROMOPHORES FOR DETERMINATION OF ABSOLUTE CONFIGURATION 73 Tibor Kurtan, Sandor Antus, and Gennaro Pescitelli 4 ELECTRONIC CD EXCITON CHIRALITY METHOD: PRINCIPLES AND APPLICATIONS 115 Nobuyuki Harada, Koji Nakanishi, and Nina Berova 5 CD SPECTRA OF CHIRAL EXTENDED p-ELECTRON COMPOUNDS: THEORETICAL DETERMINATION OF THE ABSOLUTE STEREOCHEMISTRY AND EXPERIMENTAL VERIFICATION 167 Nobuyuki Harada and Shunsuke Kuwahara 6 ASSIGNMENT OF THE ABSOLUTE CONFIGURATIONS OF NATURAL PRODUCTS BY MEANS OF SOLID-STATE ELECTRONIC CIRCULAR DICHROISM AND QUANTUM MECHANICAL CALCULATIONS 217 Gennaro Pescitelli, Tibor Kurtan, and Karsten Krohn 7 DYNAMIC STEREOCHEMISTRY AND CHIROPTICAL SPECTROSCOPY OF METALLO-ORGANIC COMPOUNDS 251 James W. Canary and Zhaohua Dai 8 CIRCULAR DICHROISM OF DYNAMIC SYSTEMS: SWITCHING MOLECULAR AND SUPRAMOLECULAR CHIRALITY 289 Angela Mammana, Gregory T. Carroll, and Ben L. Feringa 9 ELECTRONIC CIRCULAR DICHROISM OF SUPRAMOLECULAR SYSTEMS 317 Cheng Yang and Yoshihisa Inoue 10 THE ONLINE STEREOCHEMICAL ANALYSIS OF CHIRAL COMPOUNDS BY HPLC-ECD COUPLING IN COMBINATION WITH QUANTUM-CHEMICAL CALCULATIONS 355 Gerhard Bringmann, Daniel Gotz, and Torsten Bruhn 11 DETERMINATION OF THE STRUCTURES OF CHIRAL NATURAL PRODUCTS USING VIBRATIONAL CIRCULAR DICHROISM 387 Prasad L. Polavarapu 12 DETERMINATION OF MOLECULAR ABSOLUTE CONFIGURATION: GUIDELINES FOR SELECTING A SUITABLE CHIROPTICAL APPROACH 421 Stefano Superchi, Carlo Rosini, Giuseppe Mazzeo, and Egidio Giorgio PART III INORGANIC STEREOCHEMISTRY 449 13 APPLICATIONS OF ELECTRONIC CIRCULAR DICHROISM TO INORGANIC STEREOCHEMISTRY 451 Sumio Kaizaki PART IV BIOMOLECULES 473 14 ELECTRONIC CIRCULAR DICHROISM OF PROTEINS 475 Robert W. Woody 15 ELECTRONIC CIRCULAR DICHROISM OF PEPTIDES 499 Claudio Toniolo, Fernando Formaggio, and Robert W. Woody 16 ELECTRONIC CIRCULAR DICHROISM OF PEPTIDOMIMETICS 545 Claudio Toniolo and Fernando Formaggio 17 CIRCULAR DICHROISM SPECTROSCOPY OF NUCLEIC ACIDS 575 Jaroslav Kypr, Iva Kejnovska, Klara Bednarova, and Michaela Vorlickova 18 ELECTRONIC CIRCULAR DICHROISM OF PEPTIDE NUCLEIC ACIDS AND THEIR ANALOGUES 587 Roberto Corradini, Tullia Tedeschi, Stefano Sforza, and Rosangela Marchelli 19 CIRCULAR DICHROISM OF PROTEIN–NUCLEIC ACID INTERACTIONS 615 Donald M. Gray 20 DRUG AND NATURAL PRODUCT BINDING TO NUCLEIC ACIDS ANALYZED BY ELECTRONIC CIRCULAR DICHROISM 635 George A. Ellestad 21 PROBING HSA AND AGP DRUG-BINDING SITES BY ELECTRONIC CIRCULAR DICHROISM 665 Miklos Simonyi 22 CONFORMATIONAL STUDIES OF BIOPOLYMERS, PEPTIDES, PROTEINS, AND NUCLEIC ACIDS. A ROLE FOR VIBRATIONAL CIRCULAR DICHROISM 707 Timothy A. Keiderling and Ahmed Lakhani 23 STRUCTURE AND BEHAVIOR OF BIOMOLECULES FROM RAMAN OPTICAL ACTIVITY 759 Laurence D. Barron and Lutz Hecht 24 OPTICAL ROTATION, ELECTRONIC CIRCULAR DICHROISM, AND VIBRATIONAL CIRCULAR DICHROISM OF CARBOHYDRATES AND GLYCOCONJUGATES 795 Tohru Taniguchi and Kenji Monde 25 ELECTRONIC CIRCULAR DICHROISM IN DRUG DISCOVERY 819 Carlo Bertucci and Marco Pistolozzi INDEX 843
£204.20
John Wiley & Sons Inc Introduction to General Organic and Biochemistry
Book Synopsis
£133.16
John Wiley & Sons Inc Fundamentals of Biochemistry Life at the
Book Synopsis
£128.66
John Wiley and Sons Ltd Fungal Biomolecules
Book SynopsisFungi have an integral role to play in the development of the biotechnology and biomedical sectors. The fields of chemical engineering, Agri-food,Biochemical, pharmaceuticals, diagnostics and medical device development allemploy fungal products, with fungal biomolecules currently used in a wide range of applications, ranging from drug development to food technology and agricultural biotechnology. Understanding the biology of different fungi in diverse ecosystems, as well as their biotropic interactions with other microorganisms, animals and plants, is essential to underpin effective and innovative technological developments.Fungal Biomolecules is a keystone reference, integrating branches of fungal product research into a comprehensive volume of interdisciplinary research. As such, it:reflects state-of-the-art research and current emerging issues in fungal biology and biotechnology reviews the methods and experimental work used to invTable of ContentsContributors ix Foreword xiii Preface xvii Section 1 Fungi as cell factories 1 Chapter 1 Fungal biofilms: An overview 3 Virginia Medeiros de Siqueira Chapter 2 Fungal biomolecules for the food industry 11 Quang D. Nguyen, Erika Bujna, Gabriella Styevko, Judit M. Rezessy-Szabo and Agoston Hoschke Chapter 3 Fungal biocatalysts in the textile industry: Whole?]cell systems in real textile wastewater treatment 39 Federica Spina, Valeria Tigini, Valeria Prigione and Giovanna Cristina Varese Chapter 4 Discovery of fungal enzymes and pathways 51 Aleksandra Mitrovic and Anton Glieder Chapter 5 Fungal laccase in the textile industry 63 Susana Rodriguez?]Couto Section 2 Production of recombinant peptides 73 Chapter 6 Lignocellulose?]degrading enzymes: An overview of the global market 75 Paula M. D. Jaramillo, Helder A. R. Gomes, Antonielle V. Monclaro, Caio O. G. Silva and Edivaldo X. F. Filho Chapter 7 Recent advancements in the role of volatile organic compounds from fungi 87 Lourdes Macias?]Rodriguez, Hexon Angel Contreras?]Cornejo, Jesus Salvador Lopez?]Bucio and Jose Lopez?]Bucio Chapter 8 Peptaibiotics and peptaibols from fungi 101 Susanne Zeilinger Section 3 Fungal secondary metabolites and synthesis 115 Chapter 9 Biosynthesis of silver nanoparticles by fungi 117 Ana Olivia de Souza and Alexandre Gomes Rodrigues Chapter 10 Fungal biomolecules as modulators of growth and pathogenesis 137 Rajesh N. Patkar and Naweed I. Naqvi Chapter 11 Fungi as a source of antitumour agents 145 Shin Yee Fung and Nget Hong Tan Chapter 12 Fungal mycotoxins: an overview 153 Svetlana V. Malysheva, Jose Diana Di Mavungu and Sarah De Saeger Chapter 13 Fungal pigments: An overview 173 Marcela C. Pagano and Partha P. Dhar Chapter 14 An overview regarding bioherbicide and their production methods by fermentation 183 Rodrigo Klaic, Raquel C. Kuhn, Edson L. Foletto, Valeria Dal Pra, Rodrigo J. S. Jacques, Jerson V. C. Guedes, Helen Treichel, Altemir J. Mossi, Debora Oliveira, J. Vladimir Oliveira, Sergio L. Jahn and Marcio A. Mazutti Section 4 Regulation of fungal secondary metabolism 201 Chapter 15 The role of nutrients in fungal development and pathogenesis 203 YiZhen Deng, Fan Yang and Naweed I. Naqvi Chapter 16 Role of nitrogen sources in regulation of fungal secondary metabolism 213 Bidisha Sharma and Dhruva Kumar Jha Chapter 17 Regulatory genes in fungal secondary metabolism 225 Jaswinder Kaur and Catherine Collins Chapter 18 Fungal metabolic diversity 239 Andrei Stecca Steindorff, Gabriela F. Persinoti, Valdirene Neves Monteiro and Roberto Nascimento Silva Chapter 19 Secreted biomolecules in fungal plant pathogenesis 263 Neil Andrew Brown and Kim E. Hammond?]Kosack Section 5 Developments and advancements 311 Chapter 20 Fungal molecular taxonomy: an overview 313 Marcela C. Pagano and Luiz H. Rosa Chapter 21 Fungal biomolecules in wines and beer industries 323 Carlos Roberto Felix and Eliane Ferreira Noronha Chapter 22 Biosorption and bioaccumulation of chromium VI by different fungal species 333 Dhara Shukla and Padma S. Vankar Chapter 23 Fungal biomolecules in plant growth promotion 345 Hexon Angel Contreras?]Cornejo, Lourdes Macias?]Rodriguez and Jose Lopez?]Bucio Chapter 24 Fungal biomolecules and their implications 363 Andleeb Zehra, Manish Kumar Dubey, Arti Tiwari, Mukesh Meena, Punam Kumari, Vivek Kumar Singh, Vijai Kumar Gupta and R. S. Upadhyay Index 377
£128.20
John Wiley & Sons Inc Preparative Chromatography for Separation of
Book SynopsisPreparative Chromatography for Separation of Proteins addresses a wide range of the most current modeling techniques, strategies, and case studies of industrial separation of proteins and peptides to aid in the efficiency and efficacy of this broadly-used technique in the purification of biopharmaceuticals.Table of ContentsList of Contributors xv Series Preface xix Preface xxi 1 Model-Based Preparative Chromatography Process Development in the QbD Paradigm 1Arne Staby, Satinder Ahuja, and Anurag S. Rathore 1.1 Motivation 1 1.2 Regulatory Context of Preparative Chromatography and Process Understanding 1 1.3 Application of Mathematical Modeling to Preparative Chromatography 6 Acknowledgements 8 References 8 2 Adsorption Isotherms: Fundamentals and Modeling Aspects 11Jørgen M. Mollerup 2.1 Introduction 11 2.2 Definitions 12 2.3 The Solute Velocity Model 14 2.4 Introduction to the Theory of Equilibrium 17 2.5 Association Equilibria 21 2.6 The Classical Adsorption Isotherm 24 2.7 The Classical Ion Exchange Adsorption Isotherm 26 2.8 Hydrophobic Adsorbents, HIC and RPC 38 2.9 Protein–Protein Association and Adsorption Isotherms 47 2.10 The Adsorption Isotherm of a GLP-1 Analogue 51 2.11 Concluding Remarks 59 Appendix 2.A Classical Thermodynamics 60 References 77 3 Simulation of Process Chromatography 81Bernt Nilsson and Niklas Andersson 3.1 Introduction 81 3.2 Simulation-Based Prediction of Chromatographic Processes 82 3.3 Numerical Methods for Chromatography Simulation 94 3.4 Simulation-Based Model Calibration and Parameter Estimation 96 3.5 Simulation-Based Parametric Analysis of Chromatography 97 3.6 Simulation-Based Optimization of Process Chromatography 101 3.7 Summary 106 Acknowledgement 107 References 108 4 Simplified Methods Based on Mechanistic Models for Understanding and Designing Chromatography Processes for Proteins and Other Biological Products 111Noriko Yoshimoto and Shuichi Yamamoto 4.1 Introduction 111 4.2 HETP and Related Variables in Isocratic Elution 114 4.3 Linear Gradient Elution (LGE) 120 4.4 Applications of the Model 130 4.5 Summary 145 Appendix 4.A Mechanistic Models for Chromatography 149 Appendix 4.B Distribution Coefficient and Binding Sites [20- 149 References 152 5 Development of Continuous Capture Steps in Bioprocess Applications 159Frank Riske and Tom Ransohoff 5.1 Introduction 159 5.2 Economic Rationale for Continuous Processing 160 5.3 Developing a Continuous Capture Step 162 5.4 The Operation of MCC Systems 165 5.5 Modeling MCC Operation 167 5.6 Processing Bioreactor Feeds on a Capture MCC 169 5.7 The Future of MCC 171 References 172 6 Computational Modeling in Bioprocess Development 177Francis Insaidoo, Suvrajit Banerjee, David Roush, and Steven Cramer 6.1 Linkage of Chromatographic Thermodynamics (Affinity, Kinetics, and Capacity) 177 6.2 Binding Maps and Coarse-Grained Modeling 180 6.3 QSPR for Either Classification or Quantification Prediction 188 6.4 All Atoms MD Simulations for Free Solution Studies and Surfaces 192 6.5 Ensemble Average and Comparison of Binding of Different Proteins in Chromatographic Systems 204 6.6 Antibody Homology Modeling and Bioprocess Development 205 6.7 Summary of Gaps and Future State 209 Acknowledgment 212 References 212 7 Chromatographic Scale-Up on a Volume Basis 227Ernst B. Hansen 7.1 Introduction 227 7.2 Theoretical Background 229 7.3 Proof of Concept Examples 232 7.4 Design Applications: How to Scale up from Development Data 233 7.5 Discussion 240 7.6 Recommendations 242 References 245 8 Scaling Up Industrial Protein Chromatography: Where Modeling Can Help 247Chris Antoniou, Justin McCue, Venkatesh Natarajan, Jörg Thömmes, and Qing Sarah Yuan 8.1 Introduction 247 8.2 Packing Quality: Why and How to Ensure Column Packing Quality Across Scales 248 8.3 Process Equipment: Using CFD to Describe Effects of Equipment Design on Column Performance 257 8.4 Long-Term Column Operation at Scale: Impact of Resin Lot-to-Lot Variability 264 8.5 Closing Remarks 265 References 265 9 High-Throughput Process Development 269Silvia M. Pirrung and Marcel Ottens 9.1 Introduction to High-Throughput Process Development in Chromatography 269 9.2 Process Development Approaches 271 9.3 Case Descriptions 279 9.4 Future Directions 286 References 286 10 High-Throughput Column Chromatography Performed on Liquid Handling Stations 293Patrick Diederich and Jürgen Hubbuch 10.1 Introduction 293 10.2 Chromatographic Methods 299 10.3 Results and Discussion 300 10.4 Summary and Conclusion 328 Acknowledgements 329 References 330 11 Lab-Scale Development of Chromatography Processes 333Hong Li, Jennifer Pollard, and Nihal Tugcu 11.1 Introduction 333 11.2 Methodology and Proposed Workflow 336 11.3 Conclusions 377 Acknowledgments 377 References 377 12 Problem Solving by Using Modeling 381Martin P. Breil, Søren S. Frederiksen, Steffen Kidal, and Thomas B. Hansen 12.1 Introduction 381 12.2 Theory 382 12.3 Materials and Methods 385 12.4 Determination of Model Parameters 385 12.5 Optimization In Silico 388 12.6 Extra-Column Effects 390 Abbreviations 397 References 398 13 Modeling Preparative Cation Exchange Chromatography of Monoclonal Antibodies 399Stephen Hunt, Trent Larsen, and Robert J. Todd 13.1 Introduction 399 13.2 Theory 401 13.3 Model Development 403 13.4 Model Application 413 13.5 Conclusions 424 Nomenclature 425 Greek letters 425 References 426 14 Model-Based Process Development in the Biopharmaceutical Industry 429Lars Sejergaard, Haleh Ahmadian, Thomas B. Hansen, Arne Staby, and Ernst B. Hansen 14.1 Introduction 429 14.2 Molecule—FVIII 430 14.3 Overall Process Design 431 14.4 Use of Mathematical Models to Ensure Process Robustness 432 14.5 Experimental Design of Verification Experiments 435 14.6 Discussion 438 14.7 Conclusion 439 Acknowledgements 439 Appendix 14.A Practical MATLAB Guideline to SEC 439 Appendix 14.B Derivation of Models Used for Column Simulations 449 References 455 15 Dynamic Simulations as a Predictive Model for a Multicolumn Chromatography Separation 457Marc Bisschops and Mark Brower 15.1 Introduction 457 15.2 BioSMB Technology 459 15.3 Protein A Model Description 460 15.4 Fitting the Model Parameters 463 15.5 Case Studies 464 15.6 Results for Continuous Chromatography 469 15.7 Conclusions 475 References 476 16 Chemometrics Applications in Process Chromatography 479Anurag S. Rathore and Sumit K. Singh 16.1 Introduction 479 16.2 Data Types 480 16.3 Data Preprocessing 481 16.4 Modeling Approaches 485 16.5 Case Studies of Use of Chemometrics in Process Chromatography 490 16.6 Guidance on Performing MVDA 495 References 497 17 Mid-UV Protein Absorption Spectra and Partial Least Squares Regression as Screening and PAT Tool 501Sigrid Hansen, Nina Brestrich, Arne Staby, and Jürgen Hubbuch 17.1 Introduction 501 17.2 Mid-UV Protein Absorption Spectra and Partial Least Squares Regression 503 17.3 Spectral Similarity and Prediction Precision 511 17.4 Application as a Screening Tool: Analytics for High-Throughput Experiments 516 17.5 Application as a PAT Tool: Selective In-line Quantification and Real-Time Pooling 518 17.6 Case Studies 523 17.7 Conclusion and Outlook 532 References 532 18 Recent Progress Toward More Sustainable Biomanufacturing: Practical Considerations for Use in the Downstream Processing of Protein Products 537Milton T. W. Hearn 18.1 Introduction 537 18.2 The Impact of Individualized Unit Operations versus Integrated Platform Technologies on Sustainable Manufacturing 543 18.3 Implications of Recycling and Reuse in Downstream Processing of Protein Products Generated by Biotechnological Processes: General Considerations 549 18.4 Metrics and Valorization Methods to Assess Process Sustainability 553 18.5 Conclusions and Perspectives 573 Acknowledgment 573 References 574 Index 583
£153.85
John Wiley & Sons Inc Computational Toxicology
Book SynopsisA key resource for toxicologists across a broad spectrum of fields, this book offers a comprehensive analysis of molecular modelling approaches and strategies applied to risk assessment for pharmaceutical and environmental chemicals. Provides a perspective of what is currently achievable with computational toxicology and a view to future developments Helps readers overcome questions of data sources, curation, treatment, and how to model / interpret critical endpoints that support 21st century hazard assessment Assembles cutting-edge concepts and leading authors into a unique and powerful single-source reference Includes in-depth looks at QSAR models, physicochemical drug properties, structure-based drug targeting, chemical mixture assessments, and environmental modeling Features coverage about consumer product safety assessment and chemical defense along with chapters on open source toxicology and big data Table of ContentsList of Contributors xvii Preface xxi Acknowledgments xxiii Part I Computational Methods 1 1 AccessibleMachine Learning Approaches for Toxicology 3Sean Ekins, Alex M. Clark, Alexander L. Perryman, Joel S. Freundlich, Alexandru Korotcov, and Valery Tkachenko 1.1 Introduction 3 1.2 Bayesian Models 5 1.2.1 CDD Models 7 1.3 Deep LearningModels 13 1.4 Comparison of Different Machine LearningMethods 16 1.4.1 Classic Machine LearningMethods 17 1.4.1.1 Bernoulli Naive Bayes 17 1.4.1.2 Linear Logistic Regression with Regularization 18 1.4.1.3 AdaBoost Decision Tree 18 1.4.1.4 Random Forest 18 1.4.1.5 Support Vector Machine 19 1.4.2 Deep Neural Networks 19 1.4.3 Comparing Models 20 1.5 FutureWork 21 Acknowledgments 21 References 21 2 Quantum Mechanics Approaches in Computational Toxicology 31Jakub Kostal 2.1 Translating Computational Chemistry to Predictive Toxicology 31 2.2 Levels of Theory in Quantum Mechanical Calculations 33 2.3 Representing Molecular Orbitals 38 2.4 Hybrid Quantum and Molecular Mechanical Calculations 39 2.5 Representing System Dynamics 40 2.6 Developing QM Descriptors 42 2.6.1 Global Electronic Parameters 42 2.6.1.1 Electrostatic Potential, Dipole, and Polarizability 43 2.6.1.2 Global Electronic Parameters Derived from Frontier Molecular Orbitals (FMOs) 45 2.6.2 Local (Atom-Based) Electronic Parameters 47 2.6.2.1 Parameters Derived from Frontier Molecular Orbitals (FMOs) 48 2.6.2.2 Partial Atomic Charges 51 2.6.2.3 Hydrogen-Bonding Interactions 51 2.6.2.4 Bond Enthalpies 53 2.6.3 Modeling Chemical Reactions 53 2.6.4 QM/MM Calculations of Covalent Host-Guest Interactions 56 2.6.5 Medium Effects and Hydration Models 59 2.7 Rational Design of Safer Chemicals 61 References 64 Part II Applying Computers to Toxicology Assessment: Pharmaceutical, Industrial and Clinical 69 3 Computational Approaches for Predicting hERG Activity 71Vinicius M. Alves, Rodolpho C. Braga, and Carolina Horta Andrade 3.1 Introduction 71 3.2 Computational Approaches 73 3.3 Ligand-Based Approaches 73 3.4 Structure-Based Approaches 77 3.5 Applications to Predict hERG Blockage 77 3.5.1 Pred-hERGWeb App 79 3.6 Other Computational Approaches Related to hERG Liability 82 3.7 Final Remarks 83 References 83 4 Computational Toxicology for Traditional Chinese Medicine 93Ni Ai and Xiaohui Fan 4.1 Background, Current Status, and Challenges 93 4.2 Case Study: Large-Scale Prediction on Involvement of Organic Anion Transporter 1 in Traditional Chinese Medicine-Drug Interactions 99 4.2.1 Introduction to OAT1 and TCM 99 4.2.2 Construction of TCM Compound Database 101 4.2.3 OAT1 Inhibitor Pharmacophore Development 101 4.2.4 External Test Set Evaluation 102 4.2.5 Database Searching 102 4.2.6 Results: OAT1 Inhibitor Pharmacophore 103 4.2.7 Results: OAT1 Inhibitor Pharmacophore Evaluation 104 4.2.8 Results: TCM Compound Database Searching Using OAT1 Inhibitor Pharmacophore 104 4.2.9 Discussion 110 4.3 Conclusion 114 Acknowledgment 114 References 114 5 PharmacophoreModels for Toxicology Prediction 121Daniela Schuster 5.1 Introduction 121 5.2 Antitarget Screening 125 5.3 Prediction of Liver Toxicity 125 5.4 Prediction of Cardiovascular Toxicity 127 5.5 Prediction of Central Nervous System (CNS) Toxicity 128 5.6 Prediction of Endocrine Disruption 130 5.7 Prediction of ADME 135 5.8 General Remarks on the Limits and Future Perspectives for Employing Pharmacophore Models in Toxicological Studies 136 References 137 6 Transporters in Hepatotoxicity 145Eleni Kotsampasakou, Sankalp Jain, Daniela Digles, and Gerhard F. Ecker 6.1 Introduction 145 6.2 Basolateral Transporters 146 6.3 Canalicular Transporters 148 6.4 Data Sources for Transporters in Hepatotoxicity 148 6.5 In Silico Transporters Models 150 6.6 Ligand-Based Approaches 150 6.7 OATP1B1 and OATP1B3 150 6.8 NTCP 154 6.9 OCT1 154 6.10 OCT2 154 6.11 MRP1, MRP3, and MRP4 155 6.12 BSEP 155 6.13 MRP2 156 6.14 MDR1/P-gp 156 6.15 MDR3 157 6.16 BCRP 157 6.17 MATE1 158 6.18 ASBT 159 6.19 Structure-Based Approaches 159 6.20 Complex Models Incorporating Transporter Information 160 6.21 In Vitro Models 160 6.22 Multiscale Models 161 6.23 Outlook 162 Acknowledgments 164 References 164 7 Cheminformatics in a Clinical Setting 175Matthew D. Krasowski and Sean Ekins 7.1 Introduction 175 7.2 Similarity Analysis Applied to Drug of Abuse/Toxicology Immunoassays 177 7.3 Similarity Analysis Applied toTherapeutic Drug Monitoring Immunoassays 187 7.4 Similarity Analysis Applied to Steroid Hormone Immunoassays 191 7.5 Cheminformatics Applied to "Designer Drugs" 195 7.6 Relevance to Antibody-Ligand Interactions 202 7.7 Conclusions and Future Directions 203 Acknowledgment 204 References 204 Part III Applying Computers to Toxicology Assessment: Environmental and Regulatory Perspectives 211 8 Computational Tools for ADMET Profiling 213Denis Fourches, Antony J.Williams, Grace Patlewicz, Imran Shah, Chris Grulke, JohnWambaugh, Ann Richard, and Alexander Tropsha 8.1 Introduction 213 8.2 Cheminformatics Approaches for ADMET Profiling 214 8.2.1 Chemical Data Curation Prior to ADMET Modeling 215 8.2.2 QSAR Modelability Index 217 8.2.3 Predictive QSAR Model DevelopmentWorkflow 218 8.2.4 Hybrid QSAR Modeling 220 8.2.4.1 Simple Consensus 223 8.2.4.2 Mixed Chemical and Biological Features 223 8.2.4.3 Two-Step HierarchicalWorkflow 224 8.2.5 Chemical Biological Read-Across 226 8.2.6 Public Chemotype Approach to Data-Mining 229 8.3 Unsolved Challenges in Structure Based Profiling 230 8.3.1 Biological Data Curation 231 8.3.2 Identification and Treatment of Activity and Toxicity Cliffs 233 8.3.3 In Vitro to In Vivo Continuum in the Context of AOP 233 8.4 Perspectives 234 8.4.1 Profilers on the Go with Mobile Devices 235 8.4.2 Structure–Exposure–Activity Relationships 236 8.5 Conclusions 237 Acknowledgments 237 Disclaimer 237 References 238 9 Computational Toxicology and Reach 245Emilio Enfenati, Anna Lombardo, and Alessandra Roncaglioni 9.1 A Theoretical and Historical Introduction to the Evolution Toward Predictive Models 245 9.2 Reach and the Other Legislations 247 9.3 Annex XI of Reach for QSARModels 248 9.3.1 The First Condition of Annex XI and QMRF 249 9.3.2 The Second Condition and the Applicability Domain 251 9.3.3 TheThird Condition of Annex XI, and the Use of the QSAR Models 252 9.3.4 Adequate and Reliable Documentation of the Applied Method 254 9.4 The ECHA Guidelines and the Use of QSAR Models within ECHA 255 9.4.1 Example of Bioconcentration Factor (BCF) 255 9.4.2 Example of Mutagenicity (Reverse-Mutation Assay) Prediction 260 9.5 Conclusions 266 References 266 10 Computational Approaches to Predicting Dermal Absorption of Complex Topical Mixtures 269Jim E. Riviere and Jason Chittenden 10.1 Introduction 269 10.2 Principles of Dermal Absorption 270 10.3 Dermal Mixtures 274 10.4 Model Systems 275 10.5 Local Skin Versus Systemic Endpoints 277 10.6 QSAR Approaches to Model Dermal Absorption 278 10.7 PharmacokineticModels 281 10.8 Conclusions 284 References 285 Part IV New Technologies for Toxicology, Future Perspectives 291 11 Big Data in Computational Toxicology: Challenges and Opportunities 293Linlin Zhao and Hao Zhu 11.1 Big Data Scenario of Computational Toxicology 293 11.2 Fast-Growing Chemical Toxicity Data 295 11.3 The Use of Big Data Approaches in Modern Computational Toxicology 299 11.3.1 Profiling the Toxicants with Massive Biological Data 299 11.3.2 Read-Across Study to Fill Data Gap 301 11.3.3 Unstructured Data Curation 302 11.4 Challenges of Big Data Research in Computational Toxicology and Relevant Forecasts 303 References 304 12 HLA-Mediated Adverse Drug Reactions: Challenges and Opportunities for Predictive Molecular Modeling 313George van Den Driessche and Denis Fourches 12.1 Introduction 313 12.2 Human Leukocyte Antigens 314 12.2.1 HLA Proteins 314 12.2.2 ADR–HLA Associations 316 12.2.3 HLA-Drug-Peptide Proposed T-Cell Signaling Mechanisms 321 12.3 Structure-Based Molecular Docking to Study HLA-Mediated ADRs 322 12.3.1 Structure-Based Docking 324 12.3.2 Case Study: Abacavir with B*57:01 326 12.3.3 Limitations 332 12.4 Perspectives 334 References 335 13 Open Science Data Repository for Toxicology 341Valery Tkachenko, Richard Zakharov, and Sean Ekins 13.1 Introduction 341 13.2 Open Science Data Repository 342 13.3 Benefits of OSDR 344 13.3.1 Chemically and Semantically Enabled Scientific Data Repository 344 13.3.2 Chemical Validation and Standardization Platform 346 13.3.3 Format Adapters 347 13.3.4 Open Platform for Data Acquisition, Curation, and Dissemination 350 13.3.5 Dataledger 350 13.4 Technical Details 351 13.5 FutureWork 353 13.5.1 Implementation of Ontology-Based Properties 356 13.5.2 Implementation of an Advanced Search System 357 13.5.3 Implementation of a Scientist Profile, Advanced Security, Data Sharing Capabilities and Notifications Framework 357 References 358 14 Developing Next Generation Tools for Computational Toxicology 363Alex M. Clark, Kimberley M. Zorn, Mary A. Lingerfelt, and Sean Ekins 14.1 Introduction 363 14.2 Developing Apps for Chemistry 364 14.3 Green Chemistry 364 14.3.1 Green Solvents and Lab Solvents 367 14.3.2 Green Lab Notebook 370 14.4 Polypharma and Assay Central 374 14.4.1 Future Efforts with Assay Central 380 14.5 Conclusion 382 Acknowledgments 383 References 383 Index 389
£140.55
John Wiley & Sons Inc Molecular Tools for the Detection and
Book SynopsisA guide to state-of-the-art molecular tools for monitoring and managing the toxigenicity of cyanobacteria Runaway eutrophication and climate change has made the monitoring and management of toxigenic organisms in the world s bodies of water more urgent than ever.Table of ContentsList of Contributors xix About the Editors xxiii About the Book xxvii Preface xxix Acknowledgments xxxi 1 Introduction 1Rainer Kurmayer, Kaarina Sivonen, and Nico Salmaso 1.1 A Brief Historical Overview 1 1.2 The Genetic Basis of Toxin Production 2 1.2.1 Microcystin and Nodularin 2 1.2.2 Cylindrospermopsin 5 1.2.3 Saxitoxin 6 1.2.4 Anatoxin 8 1.3 Application of Molecular Tools 8 1.4 Laboratory Safety Issues 13 1.5 References 14 2 Sampling and Metadata 19Rainer Kurmayer, Guntram Christiansen, Konstantinos Kormas, Wim Vyverman, Elie Verleyen, Vitor Ramos, Vitor Vasconcelos, and Nico Salmaso 2.1 Introduction 19 2.2 Handling of Samples 20 2.3 Sample Contamination 21 2.4 Sampling 21 2.4.1 Quantitative Depth-Integrated and Discrete Sampling 21 2.4.2 Qualitative Plankton Net Sampling 22 2.4.3 Surface (Scum Material) Sampling 22 2.4.4 Benthic (Terrestrial) Cyanobacteria Sampling 22 2.4.5 Food Supplement Sampling 22 2.4.6 Isolation of Single Colonies/Filaments 22 2.5 Subsampling Food Supplement Samples 23 2.6 Sampling of Nucleic Acids 23 2.7 General Conclusions 24 2.8 References 24 SOP 2.1 Sampling and Filtration (DNA) 26Rainer Kurmayer and Konstantinos Kormas SOP 2.1.1 Introduction 26 SOP 2.1.2 Experimental 26 SOP 2.1.3 Procedure 27 SOP 2.1.4 Notes 28 SOP 2.1.5 References 29 SOP 2.2 Sampling of Benthic Cyanobacteria 29Wim Vyverman and Elie Verleyen SOP 2.2.1 Introduction 29 SOP 2.2.2 Experimental 30 SOP 2.2.3 Procedure 30 SOP 2.2.4 Notes 31 SOP 2.2.5 References 31 SOP 2.3 Isolation of Single Cyanobacteria Colonies/Filaments 32 Rainer Kurmayer SOP 2.3.1 Introduction 32 SOP 2.3.2 Experimental 32 SOP 2.3.3 Procedure 33 SOP 2.3.4 Notes 33 SOP 2.3.5 References 33 SOP 2.4 Sampling Food Supplements 34Vitor Ramos, Cristiana Moreira, and Vitor Vasconcelos SOP 2.4.1 Introduction 34 SOP 2.4.2 Experimental 35 SOP 2.4.3 Procedure (Fig. 8.3) 35 SOP 2.4.4 Notes 36 SOP 2.4.5 References 36 SOP 2.5 Sampling and Filtration (RNA) 37Rainer Kurmayer and Guntram Christiansen SOP 2.5.1 Introduction 37 SOP 2.5.2 Experimental 37 SOP 2.5.3 Procedure 38 SOP 2.5.4 Notes 38 SOP 2.5.5 References 38 SOP 2.6 Sampling of Abiotic and Biotic Data and Recording Metadata 39Elie Verleyen, Maxime Sweetlove, Dagmar Obbels, and Wim Vyverman SOP 2.6.1 Introduction 39 SOP 2.6.2 Experimental 39 SOP 2.6.3 Type of Metadata and Additional Biotic and Abiotic Data 40 SOP 2.6.4 Notes 41 SOP 2.6.5 References 42 3 Isolation, Purification, and Cultivation of Toxigenic Cyanobacteria 43Sigrid Haande, Iwona Jasser, Muriel Gugger, Camilla H.C. Hagman, Annick Wilmotte, and Andreas Ballot 3.1 Introduction 43 3.2 Methodical Principles for Cyanobacterial Isolation, Purification, and Cultivation 44 3.2.1 Sampling, Identification, and Treatments Prior to the Isolation of Cyanobacteria 44 3.2.2 Traditional Techniques for the Isolation and Purification of Cyanobacteria 45 3.2.3 Culture Media Preparation 47 3.2.4 Cultivation Conditions 48 3.3 General Conclusions 49 3.4 References 49 SOP 3.1 Isolation, Purification, and Clonal Isolate Testing 51Sigrid Haande, Camilla H.C. Hagman, and Andreas Ballot SOP 3.1.1 Introduction 51 SOP 3.1.2 Experimental 51 SOP 3.1.3 Procedure 52 SOP 3.1.4 Notes 54 SOP 3.1.5 References 54 SOP 3.2 Isolation of Picocyanobacterial Cells by Flow Cytometer (FCM) Sorting 55Ewa Koz³owska and Iwona Jasser SOP 3.2.1 Introduction 55 SOP 3.2.2 Experimental 56 SOP 3.2.3 Procedure 56 SOP 3.2.4 Notes 58 SOP 3.2.5 References 59 SOP 3.3 Axenization 60Muriel Gugger SOP 3.3.1 Introduction 60 SOP 3.3.2 Experimental 60 SOP 3.3.3 Procedure 61 SOP 3.3.4 Notes 63 SOP 3.3.5 References 63 SOP 3.4 Culture Media (Solid and Liquid) 64Sigrid Haande, Camilla H.C. Hagman, and Andreas Ballot SOP 3.4.1 Introduction 64 SOP 3.4.2 Experimental 64 SOP 3.4.3 Procedure 65 SOP 3.4.4 Notes 68 SOP 3.4.5 References 68 SOP 3.5 Strain Maintenance (Living Cultures) 69Sigrid Haande, Camilla H.C. Hagman, and Andreas Ballot SOP 3.5.1 Introduction 69 SOP 3.5.2 Experimental 69 SOP 3.5.3 Procedure 70 SOP 3.5.4 Notes 72 SOP 3.5.5 References 73 SOP 3.6 Cryopreservation and Recovery 73Muriel Gugger SOP 3.6.1 Introduction 73 SOP 3.6.2 Experimental 74 SOP 3.6.3 Procedure 75 SOP 3.6.4 Notes 78 SOP 3.6.5 References 78 4 Taxonomic Identification of Cyanobacteria by a Polyphasic Approach 79Annick Wilmotte, H. Dail Laughinghouse IV, Camilla Capelli, Rosmarie Rippka, and Nico Salmaso 4.1 Introduction 79 4.2 Nomenclature and Classification of Cyanobacteria 82 4.3 Microscopy 84 4.3.1 Light Microscopy 84 4.3.2 Autofluorescence Microscopy 86 4.4 Molecular Markers: Single Loci 87 4.5 Molecular Markers: Multiple Loci 94 4.5.1 Multilocus Sequence Typing (MLST) and Multilocus Sequence Analysis (MLSA) 94 4.5.2 Genome-Based Extension of MLST and MLSA 96 4.6 Molecular Typing Methods Based on Gel Electrophoresis 96 4.7 Denaturing Gradient Gel Electrophoresis (DGGE) 97 4.8 Taxonomic and Molecular Databases 97 4.9 The Polyphasic Approach 98 4.10 Final Considerations 105 4.11 References 106 SOP 4.1 Taxonomic Identification by Light Microscopy 120Nico Salmaso, Rosmarie Rippka, and Annick Wilmotte SOP 4.1.1 Introduction 120 SOP 4.1.2 Experimental 121 SOP 4.1.3 References 124 SOP 4.2 Polyphasic Approach on Cyanobacterial Strains 125Nico Salmaso, Camilla Capelli, Rosmarie Rippka, and Annick Wilmotte SOP 4.2.1 Introduction 125 SOP 4.2.2 Experimental 126 SOP 4.2.3 References 131 5 Nucleic Acid Extraction 135Elke Dittmann, Anne Rantala-Ylinen, Vitor Ramos, Vitor Vasconcelos, Guntram Christiansen, and Rainer Kurmayer 5.1 Introduction 135 5.2 Specific Extraction Procedures and Storage 137 5.2.1 DNA Extraction from Laboratory Strains 137 5.2.2 DNA Extraction from Field Samples 137 5.2.3 DNA Extraction from Food Supplements 137 5.2.4 RNA Extraction from Laboratory Strains 138 5.2.5 RNA Extraction from Field Samples 138 5.2.6 Single Colony and Filament Analysis 138 5.2.7 Whole Genome Amplification 139 5.2.8 Nucleic Acid Storage 139 5.3 References 139 SOP 5.1 Standard DNA Isolation Technique for Cyanobacteria 140Elke Dittmann SOP 5.1.1 Introduction 140 SOP 5.1.2 Experimental 140 SOP 5.1.3 Procedure 141 SOP 5.1.4 Notes 141 SOP 5.1.5 References 142 SOP 5.2 DNA Isolation Protocol for Cyanobacteria with Extensive Mucilage 143Guntram Christiansen, Elisabeth Entfellner, and Rainer Kurmayer SOP 5.2.1 Introduction 143 SOP 5.2.2 Experimental 143 SOP 5.2.3 Procedure 144 SOP 5.2.4 Notes 145 SOP 5.2.5 References 145 SOP 5.3 Quantitative DNA Isolation from Filters 145Rainer Kurmayer SOP 5.3.1 Introduction 146 SOP 5.3.2 Experimental 146 SOP 5.3.3 Procedure 147 SOP 5.3.4 Notes 148 SOP 5.3.5 References 148 SOP 5.4 Genomic DNA Extraction from Single Filaments/Colonies for Multiple PCR Analyses 149Guntram Christiansen, Chen Qin, and Rainer Kurmayer SOP 5.4.1 Introduction 149 SOP 5.4.2 Experimental 149 SOP 5.4.3 Procedure 150 SOP 5.4.4 Notes 151 SOP 5.4.5 References 151 SOP 5.5 Whole Genome Amplification Using Bacteriophage Phi29 DNA Polymerase 151Guntram Christiansen and Rainer Kurmayer SOP 5.5.1 Introduction 151 SOP 5.5.2 Experimental 152 SOP 5.5.3 Procedure 152 SOP 5.5.4 Notes 152 SOP 5.5.5 Reference 153 SOP 5.6 DNA Extraction from Food Supplements 153Vitor Ramos, Cristiana Moreira, and Vitor Vasconcelos SOP 5.6.1 Introduction 153 SOP 5.6.2 Experimental 153 SOP 5.6.3 Procedure 154 SOP 5.6.4 Notes 155 SOP 5.6.5 References 156 SOP 5.7 RNA Extraction from Cyanobacteria 156Guntram Christiansen and Rainer Kurmayer SOP 5.7.1 Introduction 156 SOP 5.7.2 Experimental 156 SOP 5.7.3 Procedure 158 SOP 5.7.4 Notes 158 SOP 5.7.5 References 159 SOP 5.8 cDNA Synthesis 159Guntram Christiansen and Rainer Kurmayer SOP 5.8.1 Introduction 159 SOP 5.8.2 Experimental 159 SOP 5.8.3 Procedure 160 SOP 5.8.4 Notes 161 SOP 5.8.5 References 161 6 Conventional PCR 163Elke Dittmann, Anne Rantala-Ylinen, Kaarina Sivonen, Ilona Ga²ga³a, Joanna Mankiewicz-Boczek, Samuel Cirés, Andreas Ballot, Guntram Christiansen, Rainer Kurmayer, Vitor Ramos, Vitor Vasconcelos, and Martin Saker 6.1 Introduction 163 6.2 Principle of PCR and Available Enzymes 164 6.2.1 Primer Development 165 6.2.2 Setup of PCR Conditions for DNA and Single Colony Analysis 168 6.2.3 Gel Electrophoresis and Documentation 168 6.2.4 Troubleshooting of PCR Results 168 6.2.5 PCR Product Downstream Processing (RFLP, Cloning, Sequencing) 169 6.3 Special Notes 170 6.4 References 170 SOP 6.1 PCR Detection of Microcystin Biosynthesis Genes Combined with RFLP Differentiation of the Producing Genus 172Elke Dittmann SOP 6.1.1 Introduction 172 SOP 6.1.2 Experimental 172 SOP 6.1.3 Procedure 173 SOP 6.1.4 Notes 174 SOP 6.1.5 Reference 174 SOP 6.2 PCR Detection of Microcystin and Nodularin Biosynthesis Genes in the Cyanobacterial Orders Oscillatoriales, Chroococcales, Stigonematales, and Nostocales 175Elke Dittmann, Joanna Mankiewicz-Boczek, and Ilona Ga²ga³a SOP 6.2.1 Introduction 175 SOP 6.2.2 Experimental 175 SOP 6.2.3 Procedure 177 SOP 6.2.4 Notes 177 SOP 6.2.5 References 178 SOP 6.3 Genus-Specific PCR Detection of Microcystin Biosynthesis Genes in Anabaena/Nodularia and Microcystis and Planktothrix, Respectively 179Anne Rantala-Ylinen and Kaarina Sivonen SOP 6.3.1 Introduction 179 SOP 6.3.2 Experimental 179 SOP 6.3.3 Procedure 181 SOP 6.3.4 Notes 181 SOP 6.3.5 References 181 SOP 6.4 PCR Detection of Anatoxin Biosynthesis Genes Combined with RFLP Differentiation of the Producing Genus 182Anne Rantala-Ylinen and Kaarina Sivonen SOP 6.4.1 Introduction 182 SOP 6.4.2 Experimental 182 SOP 6.4.3 Procedure 183 SOP 6.4.4 Notes 184 SOP 6.4.5 Reference 184 SOP 6.5 PCR Detection of the Saxitoxin Biosynthesis Genes, sxtA, sxtX, sxtH, sxtG, and sxtI 185Andreas Ballot and Samuel Cirés SOP 6.5.1 Introduction 185 SOP 6.5.2 Experimental 187 SOP 6.5.3 Procedure 187 SOP 6.5.4 Notes 188 SOP 6.5.5 References 189 SOP 6.6 PCR Detection of the Cylindrospermopsin Biosynthesis Gene cyrJ 189Samuel Cirés and Andreas Ballot SOP 6.6.1 Introduction 189 SOP 6.6.2 Experimental 190 SOP 6.6.3 Procedure 191 SOP 6.6.4 Notes 191 SOP 6.6.5 References 192 SOP 6.7 PCR from Single Filament of Toxigenic Planktothrix 193Qin Chen, Guntram Christiansen, and Rainer Kurmayer SOP 6.7.1 Introduction 193 SOP 6.7.2 Experimental 193 SOP 6.7.3 Procedure 194 SOP 6.7.4 Notes 195 SOP 6.7.5 References 195 SOP 6.8 Analysis of Microcystin Biosynthesis Gene Subpopulation Variability in Planktothrix 196Rainer Kurmayer SOP 6.8.1 Introduction 196 SOP 6.8.2 Experimental 196 SOP 6.8.3 Procedure 197 SOP 6.8.4 Notes 197 SOP 6.8.5 References 198 SOP 6.9 PCR Detection of Microcystin Biosynthesis Genes from Food Supplements 199Vitor Ramos, Cristiana Moreira, and Vitor Vasconcelos SOP 6.9.1 Introduction 199 SOP 6.9.2 Experimental 199 SOP 6.9.3 Procedure 201 SOP 6.9.4 Notes 202 SOP 6.9.5 References 203 7 Quantitative PCR 205Anne Rantala-Ylinen, Henna Savela, Kaarina Sivonen, and Rainer Kurmayer 7.1 Introduction 205 7.2 Primer/Probe Design 206 7.3 Optimization 208 7.4 Absolute Quantification 208 7.5 Relative Quantification 209 7.6 Calibration of qPCR Results 209 7.7 General Conclusions 210 7.8 References 210 SOP 7.1 Optimization of qPCR Assays 211Rainer Kurmayer SOP 7.1.1 Introduction 211 SOP 7.1.2 Experimental 211 SOP 7.1.3 Procedure 212 SOP 7.1.4 Notes 213 SOP 7.1.5 References 213 SOP 7.2 Calibration of qPCR Results 214Rainer Kurmayer SOP 7.2.1 Introduction 214 SOP 7.2.2 Experimental 214 SOP 7.2.3 Procedure 215 SOP 7.2.4 Notes 217 SOP 7.2.5 References 217 SOP 7.3 Quantification of Potentially Microcystin/Nodularin-Producing Anabaena, Microcystis, Planktothrix, and Nodularia 218Anne Rantala-Ylinen, Kaarina Sivonen, and Rainer Kurmayer SOP 7.3.1 Introduction 218 SOP 7.3.2 Experimental 219 SOP 7.3.3 Procedure 219 SOP 7.3.4 Notes 221 SOP 7.3.5 References 221 SOP 7.4 Relative Quantification of Microcystis or Planktothrix mcy Genotypes Using qPCR 222Rainer Kurmayer SOP 7.4.1 Introduction 222 SOP 7.4.2 Experimental 222 SOP 7.4.3 Procedure 224 SOP 7.4.4 Notes 225 SOP 7.4.5 References 225 SOP 7.5 Quantification of Transcript Amounts of mcy Genes in Planktothrix 226Guntram Christiansen and Rainer Kurmayer SOP 7.5.1 Introduction 226 SOP 7.5.2 Experimental 226 SOP 7.5.3 Procedure 227 SOP 7.5.4 Notes 228 SOP 7.5.5 References 228 SOP 7.6 Quantification of Potentially Cylindrospermopsin-Producing Chrysosporum ovalisporum 229Rehab El-Shehawy and Antonio Quesada SOP 7.6.1 Introduction 229 SOP 7.6.2 Experimental 229 SOP 7.6.3 Procedure 230 SOP 7.6.4 Notes 231 SOP 7.6.5 References 231 SOP 7.7 qPCR Detection of the Paralytic Shellfish Toxin Biosynthesis Gene sxtB 231Henna Savela SOP 7.7.1 Introduction 231 SOP 7.7.2 Experimental 232 SOP 7.7.3 Procedure 233 SOP 7.7.4 Notes 234 SOP 7.7.5 References 234 SOP 7.8 Application of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) Guidelines to Quantitative Analysis of Toxic Cyanobacteria 234Henna Savela SOP 7.8.1 Introduction 234 SOP 7.8.2 Sampling 235 SOP 7.8.3 Sample Preparation and DNA Extraction 235 SOP 7.8.4 Target Information and Oligonucleotide Design 235 SOP 7.8.5 qPCR Protocol 238 SOP 7.8.6 qPCR Validation 239 SOP 7.8.7 Data Analysis 239 SOP 7.8.8 Reference 239 8 DNA (Diagnostic) and cDNA Microarray 241Anne Rantala-Ylinen, Kaarina Sivonen, and Annick Wilmotte 8.1 DNA (Diagnostic) Microarray 241 8.1.1 Introduction 241 8.1.2 Methodological Principles 242 8.1.3 General Conclusions 243 8.1.4 References 243 8.2 cDNA Microarray for Cyanobacteria 244Hans C.P. Matthijs and J. Merijn Schuurmans 8.2.1 Introduction 244 8.2.2 Principles of Microarray Use 244 8.2.3 Considerations for Experimental Design 245 8.2.4 Microarray: Practical Approach 246 8.2.5 Microarray: Data Analysis 246 8.2.6 References 246 SOP 8.1 DNA-Chip Detection of Potential Microcystin and Nodularin Producing Cyanobacteria in Environmental Water Samples 248Anne Rantala-Ylinen and Kaarina Sivonen SOP 8.1.1 Introduction 248 SOP 8.1.2 Experimental 249 SOP 8.1.3 Procedure 250 SOP 8.1.4 Notes 253 SOP 8.1.5 References 253 SOP 8.2 cDNA Microarrays for Cyanobacteria 254J. Merijn Schuurmans and Hans C.P. Matthijs SOP 8.2.1 Introduction 254 SOP 8.2.2 Experimental 254 SOP 8.2.3 Procedure 256 SOP 8.2.4 Notes 259 SOP 8.2.5 Reference 261 9 Analysis of Toxigenic Cyanobacterial Communities through Denaturing Gradient Gel Electrophoresis 263Iwona Jasser, Aleksandra Bukowska, Jean-Francois Humbert, Kaisa Haukka, and David P. Fewer 9.1 Introduction 263 9.2 Main Applications of the Method 264 9.3 Possible Applications 264 9.4 DGGE Procedure 265 9.5 General Conclusions Including Pros and Cons of the Method 267 9.6 Optimization of the Method and Troubleshooting 267 9.7 References 268 SOP 9.1 DGGE-mcyA Conditions 270Aleksandra Bukowska and Iwona Jasser SOP 9.1.1 Introduction 270 SOP 9.1.2 Experimental 270 SOP 9.1.3 Procedure 272 SOP 9.1.4 Notes 275 SOP 9.1.5 References 275 10 Monitoring of Toxigenic Cyanobacteria Using Next-Generation Sequencing Techniques 277Li Deng, Maxime Sweetlove, Stephan Blank, Dagmar Obbels, Elie Verleyen, Wim Vyverman, and Rainer Kurmayer 10.1 Introduction 277 10.2 Specific Procedures 279 10.2.1 16S rRNA Gene Amplicon Library Preparation 279 10.2.2 Amplicon Purification, Quantification and Pooling 280 10.2.3 Sequencing 280 10.2.4 Bioinformatic Exploration of Sequencing Results 281 10.2.5 General Conclusions Including Pros and Cons of the Method 281 10.2.6 References 281 10.3 Bioinformatic Processing of Amplicon Sequencing Datasets 283Maxime Sweetlove, Dagmar Obbels, Elie Verleyen, Igor S. Pessi, Annick Wilmotte, and Wim Vyverman 10.3.1 Introduction 283 10.3.2 Sequencing Platforms 283 10.3.3 Data Formats 284 10.3.4 Error Associated with NGS Data 285 10.3.5 OTU Delineation: Choosing a Similarity Threshold 286 10.3.6 Conclusions 286 10.4 References 286 SOP 10.1 Standard Technique to Generating 16S rRNA PCR Amplicons for NGS 288Li Deng, Stephan Blank, Guntram Christiansen, and Rainer Kurmayer SOP 10.1.1 Introduction 288 SOP 10.1.2 Experimental 288 SOP 10.1.3 Procedure 289 SOP 10.1.4 Notes 290 SOP 10.1.5 References 290 SOP 10.2 Bioinformatics Analysis for NGS Amplicon Sequencing 291Maxime Sweetlove, Dagmar Obbels, Elie Verleyen, Igor S. Pessi, Annick Wilmotte, and Wim Vyverman SOP 10.2.1 Introduction 291 SOP 10.2.2 Experimental 291 SOP 10.2.3 Practical Tips and Alternatives for Quality Filtering 298 SOP 10.2.4 References 298 11 Application of Molecular Tools in Monitoring Cyanobacteria and Their Potential Toxin Production 301Vitor Ramos, Cristiana Moreira, Joanna Mankiewicz-Boczek, and Vitor Vasconcelos 11.1 Introduction 301 11.2 Possible Applications 303 11.3 Checklist of Publications, Applications and Lessons from Practice 315 11.3.1 Molecular-Based Studies on (Toxic) Cyanobacteria: Overview of Methods Being Used, and Generic Findings and Concerns 315 11.3.2 The Need for Complementary Approaches 316 11.3.3 Interpreting Results 316 11.3.4 Choice of Molecular Tools for Toxigenicity Assessment 317 11.3.5 Common and Possible Applications of Molecular Tools 318 11.4 General Conclusions 321 11.5 Acknowledgments 324 11.6 References 324 Appendix: Supplementary Tables 335 Cyanobacterial Species Cited in the Book 376 Glossary 379 Index 393
£124.40
John Wiley & Sons Inc Biochemistry An Integrative Approach
Book SynopsisTable of Contents1 The Chemical Foundations of Biochemistry 1 Chemistry in Context 1 1.1 General Chemical Principles 2 1.1.1 The basic principles of thermodynamics describe all systems 2 1.1.2 Equilibrium describes a specific thermodynamic state 7 1.1.3 Kinetics describes the rate of chemical reactions 8 1.1.4 Thermodynamics, equilibrium, and kinetics are used together to describe biochemical reactions and systems 9 1.2 Fundamental Concepts of Organic Chemistry 11 1.2.1 Chemical properties and reactions can be sorted by functional groups 11 1.2.2 The solubility and polarity of a molecule can be determined from its structure 12 1.2.3 Reaction mechanisms attempt to explain how a reaction occurs 13 1.2.4 Many biochemical molecules are polymers 14 1.3 The Chemistry of Water 15 1.3.1 The structure of water provides clues about its properties 16 1.3.2 Hydrogen bonding among water molecules is one of the most important weak forces in biochemistry 17 1.3.3 Water can ionize to acids and bases in biochemical systems 18 2 Nucleic Acids 26 Nucleic Acids in Context 26 2.1 Nucleic Acids Have Distinct Structures 27 2.1.1 Nucleic acids can be understood at the chemical level 28 2.1.2 The complex shapes of nucleic acids are the result of numerous weak forces 30 2.2 Nucleic Acids Have Many Cellular Functions 37 2.2.1 Replication is the process by which cells copy DNA 37 2.2.2 Transcription is the copying of DNA into an RNA message 40 2.2.3 Translation is the synthesis of proteins by ribosomes using an mRNA code 41 2.2.4 Regulation of replication, transcription, and translation is critical to an organism’s survival and propagation 42 2.2.5 Viruses and retroviruses use the cell’s own machinery to reproduce 43 2.3 The Manipulation of Nucleic Acids Has Transformed Biochemistry 45 2.3.1 DNA can be easily manipulated and analyzed in vitro 45 2.3.2 DNA can be used to drive protein expression 53 2.3.3 Techniques can be used to silence genes in organisms 59 3 Proteins I: An Introduction to Protein Structure and Function 67 Proteins in Context 67 3.1 Amino Acid Chemistry 69 3.1.1 The structure of amino acids dictates their chemical properties 69 3.1.2 The side chains of amino acids impart unique properties 70 3.1.3 Amino acids have various roles in biochemistry 72 3.2 Proteins Are Polymers of Amino Acids 74 3.2.1 Both peptides and proteins are polymers of amino acids 74 3.2.2 The peptide bond has special characteristics 76 3.2.3 Many proteins require inorganic ions or small organic molecules to function 76 3.2.4 Amino acids can be modified within proteins 77 3.3 Proteins Are Molecules of Defined Shape and Structure 79 3.3.1 The primary structure of a protein is its amino acid sequence 79 3.3.2 The secondary structure of a protein is comprised of a few conserved structures 81 3.3.3 The tertiary structure of a protein is the organization of secondary structures into conserved motifs 84 3.3.4 The quaternary structure of a protein describes how individual subunits interact 88 3.4 Examples of Protein Structures and Functions 89 3.4.1 Aquaporin, a transmembrane pore 90 3.4.2 Chymotrypsin, an enzyme 90 3.4.3 Collagen, a structural protein 91 3.4.4 Hemoglobin, a transport protein 92 3.4.5 Immunoglobulins, binding proteins 92 3.4.6 Insulin, a signaling protein 93 3.4.7 Myosin, a molecular motor 94 4 Proteins II: Enzymes 101 Enzymes in Context 101 4.1 Regarding Enzymes 103 4.1.1 Enzymes are protein catalysts 103 4.1.2 Enzymatically catalyzed reactions can be categorized 105 4.1.3 How do enzymes work? 106 4.2 Enzymes Increase Reaction Rate 108 4.2.1 A review of chemical rates 108 4.2.2 The Michaelis-Menten equation relates enzymatic rates to measurable parameters 109 4.2.3 The Michaelis constant has several meanings 111 4.2.4 Kinetic data can be graphically analyzed 112 4.2.5 kcat/KM is a measure of catalytic efficiency 112 4.2.6 Some enzymes approach catalytic perfection 112 4.2.7 Enzymatic reactions may be inhibited through one of several different mechanisms 113 4.2.8 Many reactions have more than one substrate 116 4.3 The Mechanism of an Enzyme Can Be Deduced from Structural, Kinetic, and Spectral Data 117 4.3.1 Enzymatically catalyzed reactions have common properties 118 4.3.2 Examining examples of enzymatic reaction mechanisms illustrates underpinning principles 119 4.3.3 Mechanisms are elucidated using a combination of experimental techniques 125 4.4 Examples of Enzyme Regulation 127 4.4.1 Covalent modifications are a common means of enzyme regulation 127 4.4.2 Allosteric regulators bind at sites other than the active site 129 5 Membranes and an Introduction to Signal Transduction 138 Biochemistry in Context 138 5.1 Membrane Structure and Function 139 5.1.1 The chemical properties of the membrane components dictate the characteristics of the membrane 140 5.1.2 Other aspects of membrane structure 145 5.1.3 Membrane fusion and membrane budding 146 5.2 Signal Transduction 149 5.2.1 General principles underlie signal transduction 149 5.2.2 The protein kinase A (PKA) signaling pathway is activated by cyclic AMP 150 5.2.3 Insulin is an important metabolic regulator and growth factor 153 5.2.4 The AMP kinase (AMPK) signaling pathway coordinates metabolic pathways in the cell and in the body 154 6 Carbohydrates I: Mono- and Disaccharides, Glycolysis, Gluconeogenesis, and the Fates of Pyruvate 161 Carbohydrates in Context 161 6.1 Properties, Nomenclature, and Biological Functions of Monosaccharides 163 6.1.1 Monosaccharides are the simplest carbohydrates 163 6.1.2 Monosaccharides form hemiacetals and hemiketals 165 6.1.3 Monosaccharides form heterocyclic structures 165 6.1.4 Monosaccharides can be chemically modified 167 6.1.5 Carbohydrates can be classified as reducing sugars or nonreducing sugars 168 6.2 Properties, Nomenclature, and Biological Functions of Complex Carbohydrates 170 6.2.1 Common disaccharides include lactose, sucrose, and maltose 170 6.2.2 Trisaccharides and oligosaccharides contain three or more monosaccharide units bound by glycosidic linkages 173 6.2.3 Common polysaccharides function to store energy or provide structure 174 6.3 Glycolysis and an Introduction to Metabolic Pathways 177 6.3.1 Metabolic pathways describe how molecules are built up or broken down 178 6.3.2 Glycolysis is the process by which glucose is broken into pyruvate 180 6.4 Gluconeogenesis 193 6.4.1 Gluconeogenesis differs from glycolysis at four reactions 193 6.4.2 The regulation of gluconeogenesis takes place at several different levels 195 6.5 The Fates of Pyruvate 196 6.5.1 Pyruvate can be decarboxylated to acetyl-CoA by pyruvate dehydrogenase 197 6.5.2 Pyruvate can be converted to lactate by lactate dehydrogenase 200 6.5.3 Pyruvate can be transaminated to alanine 201 6.5.4 Pyruvate can be carboxylated to oxaloacetate by pyruvate carboxylase 201 6.5.5 Microbes can decarboxylate pyruvate into acetaldehyde 201 7 The Common Catabolic Pathway: Citric Acid Cycle, the Electron Transport Chain, and ATP Biosynthesis 209 Electron Transport in Context 209 7.1 The Citric Acid Cycle 211 7.1.1 There are eight reactions in the citric acid cycle 212 7.1.2 The citric acid cycle is regulated at multiple places and by several different mechanisms 218 7.1.3 Anaplerotic reactions of the citric acid cycle replenish intermediates 219 7.2 The Electron Transport Chain 223 7.2.1 Electron transport occurs through a series of redox active centers from higher to lower potential energy 224 7.2.2 Complex I (NADH dehydrogenase) transfers electrons from NADH to ubiquinone via a series of iron-sulfur centers 229 7.2.3 Complex II is the citric acid cycle enzyme succinate dehydrogenase 231 7.2.4 Complex III is ubiquinone/cytochrome c reductase 233 7.2.5 Cytochrome c is a soluble electron carrier 235 7.2.6 In complex IV, oxygen is the terminal electron carrier 235 7.2.7 The entire complex working as one: the respirasome 238 7.3 ATP Biosynthesis 241 7.3.1 The structure of ATP synthase underlies its function 241 7.3.2 ATP synthase acts as a molecular machine driving the assembly of ATP molecules 243 7.3.3 Other ATPases serve as ion pumps 245 7.3.4 Inhibitors of the ATPases can be powerful drugs or poisons 246 8 Carbohydrates II: Glycogen Metabolism, the Pentose Phosphate Pathway, Glycoconjugates, and Extracellular Matrices 253 Polysaccharides in Context 253 8.1 Glycogen Metabolism 255 8.1.1 Glycogenesis is glycogen biosynthesis 256 8.1.2 Glycogenolysis is glycogen breakdown 257 8.1.3 The regulation of glycogenesis and glycogenolysis 259 8.2 The Pentose Phosphate Pathway 264 8.2.1 The oxidative phase of the pentose phosphate pathway produces NADPH and ribulose-5- phosphate 264 8.2.2 The nonoxidative phase of the pentose phosphate pathway results in rearrangement of monosaccharides 266 8.2.3 Regulation of the pentose phosphate pathway 267 8.2.4 The pentose phosphate pathway in health and disease 268 8.2.5 Xylulose-5-phosphate is a master regulator of carbohydrate and lipid metabolism 271 8.3 Carbohydrates in Glycoconjugates 273 8.3.1 Glycoproteins 273 8.3.2 Glycolipids 276 8.3.3 Proteoglycans and non-proteoglycan polysaccharides 279 8.3.4 Peptidoglycans 282 8.4 Extracellular Matrices and Biofilms 284 8.4.1 Eukaryotic extracellular matrix proteins 284 8.4.2 Biofilms are composed of microbes living in a secreted matrix 290 9 Lipids I: Fatty Acids, Steroids, and Eicosanoids; Beta-Oxidation and Fatty Acid Biosynthesis 300 Lipids in Context 300 9.1 Properties, Nomenclature, and Biological Functions of Lipid Molecules 302 9.1.1 Fatty acids are a common building block of many lipids 302 9.1.2 Neutral lipids are storage forms of fatty acids or cholesterol 305 9.1.3 Phospholipids are important in membrane formation 306 9.1.4 All steroids and bile salts are derived from cholesterol 309 9.1.5 Eicosanoids are potent signaling molecules derived from 20-carbon polyunsaturated fatty acids 310 9.2 Fatty Acid Catabolism 311 9.2.1 Fatty acids must be transported into the mitochondrial matrix before catabolism can proceed 312 9.2.2 Fatty acids are oxidized to acetyl-CoA by β-oxidation 312 9.2.3 Beta-oxidation is regulated at two different levels 316 9.3 Fatty Acid Biosynthesis 317 9.3.1 Two major enzyme complexes are involved in fatty acid biosynthesis 318 9.3.2 Elongases and desaturases in the endoplasmic reticulum increase fatty acid diversity 326 9.3.3 The formation of malonyl-CoA by acetyl-CoA carboxylase is the regulated and rate-determining step of fatty acid biosynthesis 327 9.4 Ketone Body Metabolism 329 9.4.1 Ketone bodies are made from acetyl-CoA 330 9.4.2 Ketone bodies can be thought of as a water-soluble fuel source used in the absence of carbohydrates 330 9.5 Steroid Metabolism 332 9.5.1 Cholesterol is synthesized in the liver through the addition of energetically activated isoprene units 332 9.5.2 Steroid hormones are derived from cholesterol 336 9.5.3 Bile salts are steroid detergents used in the digestion of fats 337 9.6 Eicosanoid and Endocannabinoid Metabolism 339 9.6.1 Eicosanoids are classified by the enzymes involved in their synthesis 339 9.6.2 Endocannabinoids such as anandamide are also arachidonate derivatives 341 10 Lipids II: Metabolism and Transport of Complex Lipids 351 Complex Lipids in Context 351 10.1 Phospholipid Metabolism 353 10.1.1 Glycerophospholipids are derived from phosphatidate or diacylglycerol using activated carriers 354 10.1.2 Sphingolipids are synthesized from ceramide 355 10.1.3 Phospholipases and sphingolipases cleave at specific sites 358 10.2 Digestion of Triacylglycerols 361 10.2.1 Triacylglycerol digestion begins in the gastrointestinal tract 361 10.2.2 Dietary lipids are absorbed in the small intestine and pass into lymph before entering the circulation 363 10.2.3 Several molecules affect neutral lipid digestion 365 10.3 Transport of Lipids in the Circulation 367 10.3.1 Lipoproteins have a defined structure and composition, and transport lipids in the circulation 367 10.3.2 The trafficking of lipoproteins in the blood can be separated conceptually into three different paths 369 10.3.3 Brain lipids are transported on apo E-coated discs 372 10.3.4 Fatty acids and hydrophobic hormones are transported by binding to carrier proteins 374 10.4 Entry of Lipids into the Cell 377 10.4.1 Fatty acids can enter the cell via diffusion or by protein-mediated transport 377 10.4.2 Lipoprotein particles and many other complexes enter the cell via receptor-mediated endocytosis 377 10.5 Neutral Lipid Biosynthesis 380 10.5.1 Triacylglycerols are synthesized by different pathways depending on the tissue 380 10.5.2 Triacylglycerol metabolism and phosphatidate metabolism are enzymatically linked 382 10.6 Lipid Storage Droplets, Fat Storage, and Mobilization 384 10.6.1 Bulk neutral lipids in the cell are stored in a specific organelle, the lipid storage droplet 384 10.6.2 Specific phosphorylation of lipases and lipid droplet proteins regulate lipolysis (triacylglycerol breakdown) 384 10.6.3 Triacylglycerol metabolism is regulated at several levels 387 10.7 Lipid Rafts as a Biochemical Entity 388 10.7.1 Lipid rafts are loosely associated groups of sphingolipids and cholesterol found in the plasma membrane 388 10.7.2 Lipid rafts have been broadly grouped into two categories: caveolae and non-caveolar rafts 388 11 Amino Acid and Amine Metabolism 397 Amine Metabolism in Context 397 11.1 Digestion of Proteins 399 11.1.1 Protein digestion begins in the stomach 399 11.1.2 Protein digestion continues in the small intestine, aided by proteases 401 11.1.3 Amino acids are absorbed in the small intestine 401 11.1.4 Amino acids serve many biological roles in the organism 403 11.2 Transamination and Oxidative Deamination 404 11.2.1 Ammonia can be removed from an amino acid in two different ways 405 11.2.2 The glucose–alanine shuttle moves nitrogen to the liver and delivers glucose to tissues that need it 405 11.2.3 Glutamine is also important in nitrogen transport 406 11.3 The Urea Cycle 409 11.3.1 Ammonia detoxification begins with the synthesis of carbamoyl phosphate 409 11.3.2 The urea cycle synthesizes urea and other metabolic intermediates 409 11.3.3 Nitrogen metabolism is regulated at different levels 412 11.3.4 Mechanisms for elimination of nitrogenous wastes differ between mammals and non-mammals 412 11.3.5 Some mammals have adapted to high- or low-protein diets 413 11.4 Pathways of Amino Acid Carbon Skeleton Scavenging 414 11.4.1 Three-carbon skeletons produce pyruvate 416 11.4.2 Four-carbon skeletons produce oxaloacetate 417 11.4.3 Five-carbon skeletons produce α-ketoglutarate 418 11.4.4 Methionine, valine, and isoleucine produce succinyl-CoA 418 11.4.5 Other amino acids produce acetyl-CoA, acetoacetate, or fumarate 418 11.5 The Detoxification of Other Amines and Xenobiotics 423 11.5.1 Phase I metabolism makes molecules more hydrophilic through oxidative modification 424 11.5.2 Phase II metabolism couples molecules to bulky hydrophilic groups 427 11.6 The Biochemistry of Renal Function 429 11.6.1 Molecules smaller than proteins are filtered out of the blood by the glomerulus 430 11.6.2 Water, glucose, and electrolytes are reabsorbed in the proximal convoluted tubule, loop of Henle, and distal convoluted tubule 431 12 Regulation and Integration of Metabolism 440 Metabolism in Context 440 12.1 A Review of the Pathways and Crossroads of Metabolism 442 12.1.1 The pathways of metabolism are interconnected 442 12.1.2 Several metabolites are at the intersection of multiple pathways 443 12.2 Organ Specialization and Metabolic States 446 12.2.1 Different organs play distinct roles in metabolism 447 12.2.2 The organism shifts between different metabolic states depending on access to food 450 12.3 Communication between Organs 455 12.3.1 Organs communicate using hormones 455 12.3.2 Hormonal signals to the brain regulate appetite and metabolism 458 12.3.3 Transcription factors and histone acetylases and deacetylases regulate metabolism in the longer term 460 12.4 Metabolic Disease 463 12.4.1 Diseases of excess: obesity, diabetes, and metabolic syndrome 463 12.4.2 Diseases of absence: starvation, cachexia, and cancer 467 12.4.3 Diseases of indulgence: alcohol overconsumption 468 12.4.4 Other metabolic states 469 Techniques 477 solutions 493 Glossary 509 Index I-1
£128.66
St. Martin's Press A Taste for Poison
Book SynopsisA fascinating tale of poisons and poisonous deeds which both educates and entertains. --Kathy ReichsA brilliant blend of science and crime, A TASTE FOR POISON reveals how eleven notorious poisons affect the body--through the murders in which they were used. As any reader of murder mysteries can tell you, poison is one of the most enduringand popularweapons of choice for a scheming murderer. It can be slipped into a drink, smeared onto the tip of an arrow or the handle of a door, even filtered through the air we breathe. But how exactly do these poisons work to break our bodies down, and what can we learn from the damage they inflict? In a fascinating blend of popular science, medical history, and true crime, Dr. Neil Bradbury explores this most morbidly captivating method of murder from a cellular level. Alongside real-life accounts of murderers and their crimessome notorious, some forgotten, some still unsolvedare the equally compelling storie
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St. Martin's Griffin A Taste for Poison
Book SynopsisA fascinating tale of poisons and poisonous deeds which both educates and entertains. --Kathy ReichsA brilliant blend of science and crime, A Taste for Poison reveals how eleven notorious poisons affect the body--through the murders in which they were used. As any reader of murder mysteries can tell you, poison is one of the most enduringand popularweapons of choice for a scheming murderer. It can be slipped into a drink, smeared onto the tip of an arrow or the handle of a door, even filtered through the air we breathe. But how exactly do these poisons work to break our bodies down, and what can we learn from the damage they inflict?In a fascinating blend of popular science, medical history, and true crime, Dr. Neil Bradbury explores this most morbidly captivating method of murder from a cellular level. Alongside real-life accounts of murderers and their crimessome notorious, some forgotten, some still unsolvedare the equally compelling
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Barcharts, Inc Biochemistry 2 QuickStudy Laminated Reference
Book SynopsisA further examination of how molecules function in cellular processes. Vitamins and minerals are critical for human health, and yet few people know why they are so important for our bodies. Hormones control everything from sugar metabolism (diabetes), to sexual maturation (estrogen and testosterone), to bone density and growth (BMPs), but how these key chemicals control cells is often misunderstood. This guide will explain these topics in molecular detail for everyone interested in nutrition, molecular biology, medicine, and health. Sections include Enzymes & Enzyme Regulation, Energetics & Metabolic Pathways, Hormones, Membranes & Signaling, and Replication & Central Dogma. 6-page laminated guide includes: Enzymes & Enzyme Regulation Enzyme Terms Catalytic Models Drugs & Inhibition Enzyme Regulation Vitamins & Minerals Energetics & Metabolic Pathways ATP Reduction & Oxidation Oxidation of Glucose Gluconeogenesis 5-Carbon Sugar Biosynthesis Lipid Metabolism & Fatty Acid Biosynthesis A
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DK Easy Keto Meal Prep
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Robert D. Reed Publishers MIRACLES ARE MADE: A Real-Life Guide to Autism
Book SynopsisMiracles Are Made is a real-life guide written from the happenings of real life. It is a How To on living with and healing autism.Lynette Louise began life's journey first as an individual, then as a mother, and eventually as a grandmother reaching into the heart of this disorder and helping first herself and then her children to become independent. Lynette's journey, challenging as it was, taught her many lessons on the very real possibilities and limitations buried within the diagnosis.In Miracles Are Made Lynette not only shares stories from her personal and professional life but also illuminates the whys and the wherefores of the social climate parents find themselves in when coping with autism. She does this by educating us on the history of science and social awareness in relation to this disorder. She then teaches us how to make the best of what is possible and recreate the healings she has been fortunate enough to facilitate. You will come away understanding how to understand autism.You will come away knowing what to do.
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World Health Organization Strontium and Strontium Compounds
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