Science: general issues Books

Book SynopsisTemperature and Plant Development provides a detailed analysis of the role of temperature fluctuations and stressors in plant development. Renowned experts in plant biology outline plant adaptation to high and low temperature stress, whole plant psychological adaptations, and temperature-regulated gene networks.Table of ContentsContributors xi Preface xiii 1 Temperature sensing in plants 1 Steven Penfield and Dana MacGregor 1.1 Introduction 1 1.2 Passive and active temperature responses in plants 1 1.3 Temperature sensing during transcriptional regulation 3 1.4 Sensing cold: A role for plasma membrane calcium channels in plants 8 1.5 A role for membrane fluidity as an upstream temperature sensor? 11 1.6 Temperature sensing by proteins 12 1.7 Summary 14 2 Plant acclimation and adaptation to cold environments 19 Bob Baxter 2.1 Introduction 19 2.2 Chilling and freezing injury 20 2.3 Freezing avoidance and tolerance at the structural and physiological level 21 2.4 Freezing tolerance 26 2.5 Cold deacclimation (dehardening) and reacclimation (rehardening) 32 2.6 Spatial and temporal considerations of plant responses to low temperature 34 2.7 The survival of cold and freezing stress in a changing climate 38 2.8 Plant cold acclimation and adaptation in an agricultural context 42 2.9 Summary 42 3 Plant acclimation and adaptation to warm environments 49 Martijn van Zanten, Ralph Bours, Thijs L. Pons, and Marcel C.G. Proveniers 3.1 Introduction 49 3.2 Implications of high temperature for agriculture and natural ecosystems 51 3.3 Temperature perception and signaling pathways 52 3.4 Photosynthesis 53 3.5 Respiration and carbon balance 57 3.6 Growth and allocation of biomass 58 3.7 Architectural changes in response to high temperature 58 3.8 Hormonal regulation of thermotolerance 62 3.9 Functional implications of plant architectural changes to high temperature 63 3.10 Interactions between drought and high temperature 64 3.11 Carbohydrate status control of plant acclimation to high temperature 65 3.12 Thermoperiodic effects on plant growth and architecture 66 3.13 High-temperature effects on the floral transition 68 4 Vernalization: Competence to flower provided by winter 79 Dong-Hwan Kim and Sibum Sung 4.1 Introduction 79 4.2 Vernalization requirement in Arabidopsis 80 4.3 The molecular mechanism of vernalization 84 4.4 Resetting of FLC repression during meiosis 88 4.5 Vernalization in other plant species 89 4.6 Concluding remarks 91 5 Temperature and light signal integration 97 Harriet G. McWatters, Gabriela Toledo-Ortiz, and Karen J. Halliday 5.1 Introduction 97 5.2 Convergence points for light and temperature sensing 101 5.3 Phytochrome-Interacting Factors as signal integrators 102 5.4 ELONGATED HYPOCOTYL 5 (HY5): A cool operator 105 5.5 Light and temperature converge at the circadian oscillator 107 5.6 Photoperiodic and thermal control of flowering 113 5.7 Light-dependent circadian gating of cold-acclimation responses 115 5.8 Temperature and light regulation of cell membrane fatty acid composition 117 5.9 Concluding thoughts: Implications for a changing future 118 6 Temperature and the circadian clock 131 Kathleen Greenham and C. Robertson McClung 6.1 Introduction 131 6.2 Temperature compensation 136 6.3 Temperature entrainment 142 6.4 Cold tolerance 146 6.5 Splicing 150 6.6 Concluding remarks 151 7 Temperature and plant immunity 163 Jian Hua 7.1 Introduction 163 7.2 Plant immunity 164 7.3 Temperature effects on plant disease resistance 167 7.4 The molecular basis for temperature sensitivity in plant immunity 170 7.5 Evolution of the temperature sensitivity of immunity 174 7.6 Concluding remarks 176 8 Temperature, climate change, and global food security 181 Robert J. Redden, Jerry L. Hatfield, P.V. Vara Prasad, Andreas W. Ebert, Shyam S. Yadav, and Garry J. O’Leary 8.1 Introduction 181 8.2 Climate change on a global basis 181 8.3 The impact of temperature on crop water relations 183 8.4 The influence of high temperature on crop physiology and yield processes 186 8.5 The interaction of climate change factors on crop development 188 8.6 The impact of global climate change on food quality and plant nutrient demand 190 8.7 Breeding high-temperature stress tolerance using crop wild relatives 190 8.8 Global food production and food security 191 8.9 Crop nutritional content 194 8.10 Discussion 196 8.11 Conclusions 197 Index 203 Color plate section is located between pages 130 and 131.

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Book SynopsisThe highly successful Fieser & Fieser series has provided several generations of professional chemists and students with an timely survey of the reagent literature. Providing an up-to-date, A-to-Z listing of reagents cited in synthetic literature, Fiesers'' Reagents for Organic Synthesis, Volume 27 encompasses chemical literature from the end of 2009 to the end of 2011. Listed by common name, each entry feature a concise description, illustrations of chemical reactions, selected examples of applications, how to make it or buy it, what it is good for, and where to find complete details.Table of ContentsPreface vii Foreword ix General Abbreviations xi Reference Abbreviations xv Reagents 1 Author Index 527 Subject Index 618

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Book SynopsisHorticultural Reviews presents state-of-the-art reviews on topics in horticultural science and technology covering both basic and applied research. Topics covered include the horticulture of fruits, vegetables, nut crops, and ornamentals. These review articles, written by world authorities, bridge the gap between the specialized researcher and the broader community of horticultural scientists and teachers.Table of ContentsContributors ix Dedication: John Reuben Clark xiii Chad E. Finn 1. Postharvest Biology and Technology of Cut Flowers and Potted Plants 1 Michael S. Reid and Cai-Zhong Jiang I. Introduction 3 II. The Ornamental Industry 4 III. Factors Affecting the Postharvest Life of Ornamentals 5 IV. Biology of Flower Senescence 29 V. Transgenic Strategies for Extending Floral Life 36 VI. Future Prospects 42 Literature Cited 44 2. Water Relations of Cut Flowers: An Update 55 Wouter G. van Doorn I. Introduction 57 II. Water Supply to Flowers 57 III. Water Loss: Influence of Stomata 58 IV. Water Uptake: Xylem Blockage 63 V. Small and Coalescing Air Bubbles Form in Cut Stems, in the Absence of Cavitation 88 VI. Water Flow Rate in the Xylem as Affected by Ions in the Water 89 VII. Use of An Artificial Tap Water as a Standard Vase Solution? 90 VIII. Water Stress and Ethylene 93 IX. Conclusions 96 Acknowledgments 97 Literature Cited 97 3. Factors Involved in Fruit Calcium Deficiency Disorders 107 Sergio Tonetto de Freitas and Elizabeth J. Mitcham I. Introduction 109 II. Physiology of Calcium Deficiency in Fruit Tissue 109 III. Calcium Translocation at the Whole Plant Level 111 IV. Calcium at the Fruit Level 116 V. Calcium at the Cellular Level 118 VI. Role of Abiotic Stress in Calcium Deficiency Disorders 125 VII. Role of Growth Regulators in Calcium Deficiency Disorders 127 VIII. Proposed Mechanisms Controlling Fruit Susceptibility to Calcium Deficiency Disorders 135 Literature Cited 137 4. Rhubarb: Botany, Horticulture, and Genetic Resources 147 Danny L. Barney and Kim E. Hummer I. Introduction 148 II. Historical 149 III. Botany 156 IV. Horticulture 164 V. World Genetic Resources 170 VI. The Future 178 Acknowledgments 178 Literature Cited 179 Manuscripts 182 5. Ancient Dates and their Potential Use in Breeding 183 Shimshon Ben-Yehoshua and Liat Josefsberg Ben-Yehoshua I. Introduction 184 II. Dates and Health 189 III. Historical Review 190 IV. Remnants of Dates and Their Potential Uses 203 V. Conclusions 210 Acknowledgments 210 Literature Cited 210 6. The Cucurbits and Nightshades of Renaissance England: John Gerard and William Shakespeare 215 Jules Janick, Harry S. Paris, and Marie-Christine Daunay I. Introduction 216 II. John Gerard 217 III. William Shakespeare 246 IV. The Connection Between Gerard and Shakespeare 251 V. Conclusion 252 Literature Cited 255 7. Greenhouse Cover Technology 259 Johannes F. J. Max, Ulrich Schurr, Hans-Jürgen Tantau, Urbanus N. Mutwiwa, Thomas Hofmann, and Andreas Ulbrich I. Introduction 263 II. Greenhouse Superstructures 267 III. Materials Used for Covering Greenhouses 286 IV. Material Combinations 346 V. Plant Response to Greenhouse Covers 350 VI. Comparison and Economic Assessment 368 VII. Conclusions and Prospects 378 Acknowledgments 381 Literature Cited 381 Subject Index 397 Cumulative Subject Index 399 Cumulative Contributor Index 427

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Book SynopsisPlant Breeding Reviews presents state-of-the-art reviews on plant genetics and the breeding of all types of crops by both traditional means and molecular methods. Many of the crops widely grown today stem from a very narrow genetic base; understanding and preserving crop genetic resources is vital to the security of food systems worldwide. The emphasis of the series is on methodology, a fundamental understanding of crop genetics, and applications to major crops. It is a serial title that appears in the form of one or two volumes per year.Table of ContentsContributors ix 1. Dedication: Rodomiro Ortiz Plant Breeder, Catalyst for Agricultural Development 1 Jonathan H. Crouch I. Preamble 2 II. Early Years 4 III. Research Career 10 IV. The Man 51 V. The Scientist 53 VI. The Mentor, Inspirer, Manager, and Multiplier 54 VII. The Future 57 Acknowledgments 59 Publications of Rodomiro Ortiz 59 Germplasm Registrations 84 2. Phenotyping, Genetic Dissection, and Breeding for Drought and Heat Tolerance in Common Wheat: Status and Prospects 85 P. K. Gupta, H. S. Balyan, V. Gahlaut, and P. L. Kulwal I. Introduction 89 II. Target Environments 90 III. Traits and Parameters to Measure Drought and Heat Tolerance and Their Genetic Dissection in Wheat 95 IV. Synergy Among Stress-Adaptive Traits 126 V. Crop Modeling for Drought and Heat Tolerance 127 VI. High-Throughput Phenotyping 129 VII. Strategies for Developing Drought- and Heat-Tolerant Wheat Genotypes 133 VIII. Outlook 144 Acknowledgments 147 Literature Cited 147 3. Nutritionally Enhanced Staple Food Crops 169 Sangam L. Dwivedi, Kanwar L. Sahrawat, Kedar N. Rai, Matthew W. Blair, Meike S. Andersson, and Wolfgang Pfeiffer I. Introduction 173 II. Biomarkers for Assessing Nutritional Status 178 III. Micronutrient Bioavailability 180 IV. Phenotypic Screens 192 V. Mining Germplasm Collections for Natural Variation for Seed Iron, Zinc, and Phytate 205 VI. Exploiting Natural Genetic Variation to Breed for Seed Mineral-Dense Cultivars 215 VII. Enhancing Seed Iron, Zinc, and B-Carotene Using Transgene(S) 242 VIII. Outlook 258 Acknowledgments 261 Literature Cited 261 4. Genetic Management of Virus Diseases in Peanut 293 S. N. Nigam, R. D.V. J. Prasada Rao, Pooja Bhatnagar-Mathur,and K. K. Sharma I. Introduction 297 II. Virus Diseases 298 III. Breeding for Resistance to Virus Diseases 307 IV. The Future 340 Literature Cited 341 5. Common Bean Breeding in the Tropics 357 Steven Beebe I. Introduction 359 II. A Brief History 361 III. The Tropical Context 364 IV. Origins and Genetic Resources 369 V. Biotic Constraints 374 VI. Abiotic Constraints 385 VII. Yield Potential 398 VIII. Nutritional Quality 400 IX. Climbing Beans 402 X. Progress by Market Classes 403 XI. The Institutional Context 408 XII. Future Priorities, Challenges, and Opportunities 410 Acknowledgments 412 Literature Cited 412 6. New Approaches to Cassava Breeding 427 Herna´n Ceballos, Clair Hershey, and Luis Augusto Becerra-Lopez- Lavalle I. Introduction 429 II. Genetic Resources 438 III. Cassava Breeding 445 IV. Conventional and Molecular Genetics 475 V. Future Prospects 484 Literature Cited 489 Subject Index 505 Cumulative Subject Index 507 Cumulative Contributor Index 529

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Book SynopsisShelf life, a term recognised in EU/UK food legislation, may be defined as the period of time for which a food product will remain safe and fit for use, provided that it is kept in defined storage conditions. During this period, the product should retain its desired sensory, chemical, physical, functional and microbiological characteristics, as well as accurately comply with any nutritional information printed on the label. ?Shelf life? therefore refers to a number of different aspects; each food product has a microbiological shelf life, a chemical shelf life, and a sensory (or organoleptic) shelf life. These categories reflect the different ways in which a food product will deteriorate over time. Ultimately the shelf life of a food product is intended to reflect the overall effect of these different aspects. Shelf life has always been an important facet of industrial food preparation and production, as food and drink are often produced in one area and then distributed Table of ContentsPreface to the Second Edition ix Preface to the First Edition xi Section 1 Introduction to shelf life of foods – Frequently asked questions 1 1.1 What is shelf life? 1 1.2 Why are food safety and shelf life related? 2 1.3 Who should be interested in shelf life of foods? 5 1.4 Who is responsible for determining shelf life? 6 1.5 Is it illegal to give a wrong shelf life to a food product? 7 1.6 How long a shelf life should my product have? 10 1.7 What is accelerated shelf life testing? 12 1.8 What are the resources required for determining shelf life? 15 1.9 How is the end of shelf life normally decided? 16 1.10 How do we ensure that the shelf lives established for our products are accurate and reproducible? 17 1.11 Can mathematical/computer models help in shelf life determinations? 20 1.12 What is challenge testing? 30 1.13 Can the shelf life of my product be extended? 31 1.14 How are storage tests and trials set up for determining shelf life? 36 1.14.1 Objective of the storage trial 36 1.14.2 Storage conditions 36 1.14.3 Samples for storage trials 37 1.14.4 Sampling schedule 38 1.14.5 Shelf life tests 38 1.15 Food waste and shelf life: What is the problem? 39 1.16 Summary 40 Section 2 The ways food deteriorates and spoils 41 2.1 Mechanisms of food deterioration and spoilage 41 2.1.1 Physical changes and mechanisms 41 2.1.2 Chemical and/or biochemical changes 46 2.1.3 Light‐induced changes 57 2.1.4 Microbiological changes 58 2.2 Factors influencing the shelf life of foods 62 2.2.1 Intrinsic factors 62 2.2.2 Extrinsic factors 71 2.2.3 Interaction between intrinsic and extrinsic factors 76 2.2.4 Consumer handling and use 76 2.2.5 Commercial considerations 77 2.3 Summary 77 Section 3 Determining shelf life in practice 79 3.1 Case study 1 – chilled recipe dish 79 3.1.1 The product 79 3.1.2 The process 79 3.1.3 Food safety 80 3.1.4 Mechanism(s) of shelf life deterioration 81 3.1.5 Shelf life determination – storage trials 81 3.1.6 Predicting shelf life 82 3.1.7 Assurance of assigned shelf life – the HACCP approach 82 3.2 Case study 2 – savoury potato snack 83 3.2.1 The product 83 3.2.2 The process 83 3.2.3 Food safety 83 3.2.4 Mechanism(s) of shelf life deterioration 84 3.2.5 Shelf life determination – storage trials 85 3.2.6 Assurance of assigned shelf life – the HACCP approach 86 3.3 Case study 3 – carbonated soft drink 86 3.3.1 The product 86 3.3.2 The process 87 3.3.3 Food safety 88 3.3.4 Mechanism(s) of shelf life determination 88 3.3.5 Shelf life determination – storage trials 88 3.3.6 Assurance of assigned shelf life – the HACCP approach 89 3.4 Case study 4 – condiment sauce 91 3.4.1 The product 91 3.4.2 The process 91 3.4.3 Food safety 91 3.4.4 Mechanism(s) of shelf life deterioration 91 3.4.5 Shelf life determination – storage trials 93 3.4.6 Assurance of assigned shelf life – the HACCP approach 94 3.5 Case study 5 – frozen baked cake 95 3.5.1 The product 95 3.5.2 The process 95 3.5.3 Food safety 95 3.5.4 Mechanisms(s) of shelf life deterioration 95 3.5.5 Shelf life determination – storage trials 96 3.5.6 Assurance of assigned shelf life – the HACCP approach 97 3.6 Summary 98 Epilogue 101 Appendix A: The Arrhenius model 109 Appendix B: The CIMSCEE formulae for microbiological safety and stability 111 References 115 Index 131

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Book SynopsisReaders of this accessible book now in a revised and updated new edition are taken on a conceptual journey which passes every milestone and important feature of the HACCP landscape at a pace which is comfortable and productive. The information and ideas contained in the book will enable food industry managers and executives to take their new-found knowledge into the workplace for use in the development and implementation of HACCP systems appropriate for their products and manufacturing processes. The material is structured so that the reader can quickly assimilate the essentials of the topic. Clearly presented, this HACCP briefing includes checklists, bullet points, flow charts, schematic diagrams for quick reference, and at the start of each section the authors have provided useful key points summary boxes. HACCP: a Food Industry Briefing is an introductory-level text for readers who are unfamiliar with the subject either because they have never come across it or beTable of ContentsDisclaimer ix Preface xi Section 1 Introduction to HACCP 1 Frequently asked questions 2 1.1 What is HACCP? 2 1.2 Where did it come from? 2 1.3 How does it work? 3 1.4 What are the seven HACCP principles? 3 1.5 Is it difficult to use? 4 1.6 Why use it? 4 1.7 What type of company would use HACCP? 5 1.8 Are there any common misconceptions? 9 1.9 How do we know HACCP works? 10 1.10 What actually gets implemented in the workplace? 11 1.11 How does a HACCP plan get written? 11 1.12 Who carries out the HACCP study? 12 1.13 What is the regulatory position of HACCP? 12 1.14 Are there other driving forces for the use of HACCP? 14 1.15 What does it cost? 15 1.16 What is third]party certification? 16 1.17 Is there anything more that I should know? 16 Section 2 The HACCP system explained 17 2.1 HACCP system overview – How does it all fit together? 18 2.2 HACCP in the context of other management systems – What is HACCP and what is not? 21 2.2.1 Business management practices 22 2.2.2 Prerequisite programmes 25 2.2.3 Quality management systems for effective operation and process control 29 2.3 How do you get started with HACCP – The preparation and planning stage 32 2.3.1 Management commitment, personnel and training 33 2.3.2 Baseline audit 36 2.3.3 Planning the HACCP project 37 Section 3 HACCP in practice 41 3.1 Preparation for the HACCP plan development 42 3.1.1 Terms of reference 43 3.1.2 Describe the product and intended use 45 3.1.3 Construction and validation of a process flow diagram 49 3.2 Applying the principles 50 3.2.1 Principle 1: Conduct a hazard analysis – What can go wrong? 50 3.2.2 Principle 2: Determine the Critical Control Points (CCPs) – At what stage in the process is control essential? 62 3.2.3 Principle 3: Establish critical limit(s) – What criteria must be met to ensure product safety? 68 3.2.4 Principle 4: Establish a system to monitor control of the CCP – What checks will indicate thatsomething is going wrong? 69 3.2.5 Principle 5: Establish the corrective action to be taken when monitoring indicates that a particular CCP is not under control – If something does go wrong what action needs to be taken? 73 3.2.6 Principle 6: Establish procedures for verification to confirm that the HACCP system is workingeffectively – How can you make sure that the system is working in practice? 75 3.2.7 Principle 7: Establish appropriate documentation concerning all procedures and records appropriateto those principles and their application – How can you demonstrate (if challenged) that the system works? 79 3.3 Implementation of the HACCP plan 82 3.4 Maintenance of the HACCP system 87 3.5 Third]party certification of food safety management systems 89 3.6 Conclusion 89 Epilogue 91 Appendix A: Case study: Chilled and frozen cheesecake production 103 Appendix B: Acronyms and glossary 153 References 159 HACCP Resources 161 Index 165

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Book SynopsisPlant Breeding Reviews presents state-of-the-art reviews on plant genetics and the breeding of all types of crops by both traditional means and molecular methods. Many of the crops widely grown today stem from a very narrow genetic base; understanding and preserving crop genetic resources is vital to the security of food systems worldwide.Table of ContentsContributors ix 1. Bikram Gill: Cytogeneticist and Wheat Man 1 W. John Raupp and Bernd Friebe I. Early Life: Emergence of a Cytogeneticist 2 II. Research 4 III. International Collaborations 23 IV. Educator 24 V. Champion of WheatWorkers 27 VI. The Man 27 VII. Epilogue 29 Acknowledgments 29 Literature Cited 30 2. Synthetic Hexaploids: Harnessing Species of the Primary Gene Pool for Wheat Improvement 35 Francis C. Ogbonnaya, Osman Abdalla, Abdul Mujeeb-Kazi, Alvina G. Kazi, Steven S. Xu, Nick Gosman, Evans S. Lagudah, David Bonnett, Mark E. Sorrells, and Hisashi Tsujimoto I. Introduction 39 II. Production and Utilization of Synthetic Hexaploid Wheat 42 III. Impact of Synthetic Hexaploid in Wheat Improvement 58 IV. Conclusions and Future Prospects 100 Acknowledgments 105 Literature Cited 105 3. Breeding Early and Extra-Early Maize for Resistance to Biotic and Abiotic Stresses in Sub-Saharan Africa 123 B. Badu-Apraku and M. A. B. Fakorede I. Introduction 126 II. Development of Breeding Populations 131 III. S1 Recurrent Selection Program for Striga Resistance 146 IV. Adaptation 164 V. Development of QPM Populations and Cultivars 169 VI. Breeding for Combined Tolerance/Resistance to Multiple Stresses in Early and Extra-Early Maize 179 VII. Inbred-Hybrid Development Program 180 VIII. Traits for Indirect Selection for Stress Tolerance/Resistance in Contrasting Environments 188 IX. Future Challenges and Perspectives 193 Acknowledgments 197 Literature Cited 197 4. Almond Breeding 207 Thomas M. Gradziel and Pedro Martýnez-Gomez I. Introduction 209 II. Botany 211 III. Genetic Diversity 221 IV. Genetic Improvement 226 V. Molecular Approaches 238 VI. Future Progress 248 Literature Cited 249 5. Breeding Loquat 259 Maria L. Badenes, Jules Janick, Shunquan Lin, Zhike Zhang, Guolu L. Liang, and Weixing Wang I. Introduction 261 II. Germplasm 262 III. Reproductive Physiology 270 IV. Breeding Objectives 275 V. Breeding Methods 276 VI. Future Progress 290 Literature Cited 291 6. Prognostic Breeding: A New Paradigm for Crop Improvement 297 Vasilia A. Fasoula I. Introduction 298 II. Genetic Components of Crop Yield Potential 303 III. A New General Response Equation 305 IV. Prognostic Equations for Single Plants and Sibling Lines 307 V. The Advantages of Prognostic Breeding 335 VI. The Marriage of Phenotyping with Genotyping 338 VII. Outlook 339 Literature Cited 342 Subject Index 349 Cumulative Subject Index 351 Cumulative Contributor Index 373

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Book SynopsisThis book shows scientists how to apply their analysis and synthesis skills to overcoming the challenge of how to write, as well as what to write, to maximise their chances of publishing in international scientific journals. The book uses analysis of the scientific article genre to provide clear processes for writing each section of a manuscript, starting with clear story' construction and packaging of results. Each learning step uses practical exercises to develop writing and data presentation skills based on reader analysis of well-written example papers. Strategies are presented for responding to referee comments, and for developing discipline-specific English language skills for manuscript writing and polishing. The book is designed for scientists who use English as a first or an additional language, and for individual scientists or mentors or a class setting. In response to reader requests, the new edition includes review arTrade Review“This volume will be useful for upper-level undergraduates, ESL students, and graduate students who need assistance in writing for publication. Summing Up: Recommended. Upper-division undergraduates and graduate students.” (Choice, 1 November 2013) “As was the case with its predecessor, the second edition of Writing Scientific Research Articles will be of most value to early-career scientists with little writing experience. It should also be read by research scientists who do not have English as their first language. The book could also serve as a refresher in scientific writing for experienced scientists, and it contains a lot of sound advice that should be heeded by English-speaking researchers.” (Aquaculture International, 1 August 2013)"I liked many aspects of this book. The text is well written and easy to read, as you would hope with a book on writing. The tone is formal, and I had no trouble imagining the authors presenting the material in a series of lectures." ( Bulletin of the Entomological Society of Canada 2013)Table of ContentsPreface to the second edition ix Preface to the first edition xi Section 1: A framework for success 1 1 How the book is organized, and why 3 1.1 Getting started with writing for international publication 3 1.2 Publishing in the international literature 4 1.3 What do you need to know to select your target journal? 6 1.4 Aims of this book 7 1.5 How the book is structured 8 2 Research article structures 11 2.1 Conventional article structures: AIMRaD (Abstract, Introduction, Materials and methods, Results, and Discussion) and its variations 11 3 Reviewers’ criteria for evaluating manuscripts 17 3.1 Titles as content signposts 18 Section 2: When and how to write each article section 21 4 Results as a “story”: the key driver of an article 23 5 Results: turning data into knowledge 25 5.1 Figure, table, or text? 26 5.2 Designing figures 26 5.3 Designing tables 29 5.4 Figure legends and table titles 31 6 Writing about results 33 6.1 Structure of Results sections 33 6.2 Functions of Results sentences 34 6.3 Verb tense in Results sections 34 7 The Methods section 37 7.1 Purpose of the Methods section 37 7.2 Organizing Methods sections 38 7.3 Use of passive and active verbs 39 8 The Introduction 43 8.1 Argument stages towards a compelling Introduction 43 8.2 Stage 1: Locating your project within an existing field of scientific research 43 8.3 Using references in Stages 2 and 3 47 8.4 Avoiding plagiarism when using others’ work 50 8.5 Indicating the gap or research niche 51 8.6 Stage 4: The statement of purpose or main activity 52 8.7 Stages 5 and 6: Highlighting benefit and mapping the article 52 8.8 Suggested process for drafting an Introduction 53 8.9 Editing for logical flow 54 9 The Discussion section 59 9.1 Important structural issues 59 9.2 Information elements to highlight the key messages 60 9.3 Negotiating the strength of claims 62 10 The title 65 10.1 Strategy 1: Provide as much relevant information as possible, but be concise 65 10.2 Strategy 2: Use keywords prominently 65 10.3 Strategy 3: Choose strategically: noun phrase, statement, or question? 66 10.4 Strategy 4: Avoid ambiguity in noun phrases 67 11 The Abstract 69 11.1 Why Abstracts are so important 69 11.2 Selecting additional keywords 69 11.3 Abstracts: typical information elements 69 12 Writing review articles 73 12.1 What editors want to publish 75 12.2 The “take-home-message” of a review 75 12.3 The structure of review articles 83 12.4 Visual elements in review articles: tables, figures, and boxes 84 12.5 Checklist for review article manuscripts 86 12.6 Submission and revision of review articles 86 Section 3: Getting your manuscript published 89 13 Submitting a manuscript 91 13.1 Five practices of successful authors 91 13.2 Understanding the peer-review process 92 13.3 Understanding the editor’s role 93 13.4 The contributor’s covering letter 93 13.5 Understanding the reviewer’s role 94 13.6 Understanding the editor’s role (continued) 97 14 How to respond to editors and reviewers 99 14.1 Rules of thumb 99 14.2 How to deal with manuscript rejection 99 14.3 How to deal with “conditional acceptance” or “revise and resubmit” 101 15 A process for preparing a manuscript 109 15.1 Initial preparation steps 109 15.2 Editing procedures 110 15.3 A pre-review checklist 113 Section 4: Developing your writing and publication skills further 115 16 Skill-development strategies for groups and individuals 117 16.1 Journal clubs 117 16.2 Writing groups 118 16.3 Selecting feedback strategies for different purposes 118 16.4 Becoming a reviewer 120 16.5 Training for responding to reviewers 121 17 Developing discipline-specific English skills 123 17.1 Introduction 123 17.2 Error types and editor expectations of language use 123 17.3 Strategic (and acceptable!) language re-use: sentence templates 125 17.4 More about noun phrases 128 17.5 Concordancing: a tool for developing your discipline-specific English 129 17.6 Using the English articles (a/an, the) appropriately in science writing 133 17.7 Using “which” and “that” 136 18 Writing funding proposals 139 18.1 Introduction 139 18.2 A process for preparing and submitting a funding proposal 140 18.3 Easy mistakes to make 143 Section 5: Provided example articles 145 19 PEA1: Kaiser et al. (2003) 147 20 PEA2: Britton-Simmons and Abbott (2008) 159 21 PEA3: Ganci et al. (2012) 171 Answer pages 185 Appendix: Measures of journal impact and quality 213 A.1 Journal impact 213 A.2 Using indices of journal quality 214 References 217 Index 219

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Book SynopsisPlant Cell Wall Patterning and Cell Shape is among the first books to take a holistic look at the cell wall?s complex role in plant growth and development. This study examines how cell walls dictate cell shape, their effects on plant development, and researchers? latest perceptions of cell wall pattering.Table of ContentsList of Contributors vii Preface xiii Section 1 Factors Controlling Plant Cell Wall Patterning 1 1 The Biosynthesis and Function of Polysaccharide Components of the Plant Cell Wall 3 Ryusuke Yokoyama, Naoki Shinohara, Rin Asaoka, Hideki Narukawa and Kazuhiko Nishitani 2 Regulation of Cell Wall Formation by Membrane Traffic 35 Clara Sánchez-Rodríguez and Staffan Persson 3 A Blueprint for Cellulose Biosynthesis, Deposition, and Regulation in Plants 65 Ian S. Wallace and Chris R. Somerville 4 Cortical Microtubule Array Organization and Plant Cell Morphogenesis 97 Sidney L. Shaw and Laura Vineyard 5 Actin Filament Dynamics and their Role in Plant Cell Expansion 127 Jiejie Li, Ruthie Arieti and Christopher J. Staiger Section 2 Cellular Mechanisms Underlying Various Cell Shapes 163 6 The Regulation of Cell Shape Formation by ROP-dependent Auxin Signaling 165 Shingo Nagawa and Zhenbiao Yang 7 Xylem Cell Wall Pattern Formation Regulated by Microtubule-associated Proteins and ROP GTPases 191 Yoshihisa Oda and Hiroo Fukuda 8 ROP Signaling and the Cytoskeleton in Pollen Tube Growth 215 Lei Zhu and Ying Fu 9 Phosphoinositide Signaling in Root Hair Tip Growth 239 Hiroaki Kusano, Rumi Tominaga, Takuji Wada, Mariko Kato and Takashi Aoyama 10 Arabidopsis Trichome Morphogenesis and the Role of Microtubules in Controlling Trichome Branch Formation 269 M. David Marks 11 Transfer Cells: Novel Cell Types with Unique Wall Ingrowth Architecture Designed for Optimized Nutrient Transport 287 David W. McCurdy Section 3 Developmental Regulations of Cell Shape 319 12 Regulation of Guard Cell Formation by Integration of Transcriptional and Signaling Regulation 321 Chin-Min Kimmy Ho and Dominique C. Bergmann 13 Transcriptional Regulation of Biosynthesis of Cell Wall Components during Xylem Differentiation 351 Ruiqin Zhong and Zheng-Hua Ye 14 Phloem Cell Development 379 Raffael Lichtenberger, Kaori Furuta-Miyashima, Eva Hellmann and Ykä Helariutta Index 401

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Book SynopsisThis latest volume in the Horticultural Reviews Series presents the most recent analyses of innovations in horticultural science and technology. Covering both basic and applied research, Volume 41 incorporates a wide variety of horticultural topics including the horticulture of fruits, vegetables, nut crops, and ornamentals. Specialized researchers and the broader community of horticultural scientists and student may benefit from this research tool.Table of ContentsContributors ix Dedication: Philipp W. Simon xiiIrwin Goldman 1. Circadian Regulation of Horticultural Traits: Integration of Environmental Signals 1Marcos Egea-Cortines, Fabiola Ruiz-Ramon, and Julia Weiss I. Introduction 2 II. General Structure of the Plant Circadian Clock 3 III. Environmental Inputs 10 IV. Control of Plant Growth and Morphogenesis 13 V. Adaptation to Biotic and Abiotic Stress 29 VI. Summary and Conclusions 33 Acknowledgments 34 Literature Cited 34 2. Response of Perennial Horticultural Crops to Climate Change 47D. Michael Glenn, Soo-Hyung Kim, Julian Ramirez-Villegas, and Peter Laderach I. Introduction 51 II. Response of Perennial Horticultural Crops with Abiotic Factors Associated with Climate Change 54 III. Case Studies 57 IV. Adapation 91 V. Future Research Needs 109 Acknowledgments 112 Literature Cited 112 3. Nonchilling Physiological Rind Disorders in Citrus Fruit 131Lembe Samukelo Magwaza, Umezuruike Linus Opara, Paul J. R. Cronje, Sandra Landahl, Leon A. Terry, and Bart M. Nicolay I. Introduction 133 II. Citrus Rind Disorders 134 III. Rind Anatomy and Histological Characteristics 143 IV. Causes of Physiological Rind Disorders of Citrus Fruit 145 V. Molecular and Physiological Basis of PhysiologicalRind Disorders 158 VI. Techniques for Inducing Rind Disorders 161 VII. Prospects for Future Research 162 VIII. Conclusions 164 Acknowledgments 166 Literature Cited 166 4. Fruit Splitting in Citrus 177Paul J. R. Cronje, Ockert P. J. Stander, and Karen I. Theron I. Introduction 179 II. Physiology of Citrus Fruit Splitting 183 III. Causes of Citrus Fruit Splitting 187 IV. Reducing Citrus Fruit Splitting 191 V. Conclusions 195 Acknowledgments 197 Literature Cited 197 5. Postharvest Biology and Technology of Ber Fruit 201Sunil Pareek and Elhadi M. Yahia I. Introduction 203 II. Fruit Composition and Nutritional Variability 208 III. Physiological and Biochemical Changes During Maturation and Ripening 210 IV. Preharvest Treatments to Extend Shelf Life 218 V. Postharvest Handling and Technology 220 VI. Postharvest Diseases and Disorders 227 VII. Summary and Future Prospects 229 Literature Cited 231 6. Peach Texture 241Paul Sandefur, John R. Clark, and Cameron Peace I. Introduction 243 II. Fruit Texture 245 III. Peach Texture 249 IV. Peach Flesh Types 258 V. Ripening and the Enzymatic Effects on Peach Texture 269 VI. Production and Handling Effects on Peach Texture 276 VII. Summary 285 Literature Cited 286 7. High-Density Olive Plantations 303Luis Rallo, Diego Barranco, Sergio Castro-Garcya, David J. Connor, Marya Gomez del Campo, and Pilar Rallo I. Introduction: Olive Growing in a Time of Change 305 II. Typologies of Olive Plantations 307 III. Effects of Density on Plant Performance 318 IV. Critical Factors for High-Density Orchards 325 V. Orchard Establishment Costs, Management Costs, and Economical Indices 362 VI. The Future 365 Acknowledgments 370 Literature Cited 370 8. The Carob Tree: Botany, Horticulture, and Genetic Resources 385Joan Tous, Agusti Romero, and Ignasi Batlle I. Introduction 387 II. Botany 395 III. Horticulture 407 IV. Variability and Genetic Resources 419 V. Properties and Uses 434 VI. Concluding Remarks 442 Acknowledgments 445 Literature Cited 446 9. Snake Gourd and Pointed Gourd: Botany andHorticulture 457L. K. Bharathi, T. K. Behera, A. K. Sureja, K. Joseph John, and Todd C. Wehner I. Introduction 459 II. The Genus Trichosantes 459 III. Snake Gourd 467 IV. Pointed Gourd 475 V. Future Prospects 484 Literature Cited 485 Subject Index 497 Cumulative Subject Index 499 Cumulative Contributor Index 533

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Book SynopsisThe development of recombinant DNA methods has changed the face of the food industry over the last 50 years. Crops which have been genetically modified are being cultivated in more and more countries and this process is likely to accelerate as desirable traits are identified and transferred to appropriate organisms, and they are cleared by the regulatory authorities. However, the technique has its critics who claim that modification of the genome of the plant (or animal) in this way may pose unknown and unacceptable risks to the human consumer. Genetic Modification and Food Quality: A Down to Earth Analysis is the first comprehensive text on how GM production methods influence the quality of foods and feeds, based on a complete and unbiased assessment of the scientific findings. It presents a balanced analysis of the benefits and drawbacks of gene-modified food sources in the human diet. Chapters approach the topic with regard to different food types such as cereal grains, oilseed cropTrade Review"Genetic Modification and Food Quality: A Down to Earth Analysis is the first comprehensive text on how GM production methods influence the quality of foods and feeds, based on a complete and unbiased assessment of the scientific findings. It presents a balanced analysis of the benefits and drawbacks of gene-modified food sources in the human diet." (South African Food Science and Technology July 2017)Table of Contents1 Introduction 1 2 International regulations 4 3 Microorganisms 20 4 Cereals 35 5 Oilseed crops 81 6 Fruits and vegetables 141 7 Fish and other animals 174 8 Animal products 181 9 Overall assessment of the safety of GM foods and feeds 200 10 Overall assessment of the nutritional value of GM foods and feeds 211 11 Addressing consumer issues 250 12 Overall conclusions 262 Index 271

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Book SynopsisTRY (FREE for 14 days), OR RENT this title: www.wileystudentchoice.com Europe is the second-smallest of the continents, yet it is the third most populatedand its rich history has played out on the world''s maps for centuries. The region''s borders have undergone near-continuous evolution through the rise and fall of nations, rebellions, and civilizations, and the paths these borders take have repercussions around the globe. This book presents a systematic survey of Europe and individual country-by-country coverage based on the most current data. From the core of the European Union to the lesser-known corners of the continent, this book provides in-depth examination of the physical, cultural, economic, and political geography of this powerful region. Fresh perspective sheds new light on recent events including Brexit, Russia''s takeover of Crimea, terrorist attacks in France, and the EU''s newest members, while the European Union''s future is explored in light ofTable of ContentsIntroduction: The European Union 1 Present Issues 1 The Coal and Steel Community (1951) and the European Economic Community (1957) 2 EFTA: The European Free Trade Association (1960) 2 Enlargement of the European Economic Community (EEC) 2 European Union (1993) 4 Origins of the European Union 4 World War II 4 Western European Defense Needs 5 The Truman Doctrine, The Marshall Plan, and NATO 5 Agreeing on a European Framework 5 The Suez Canal Crisis 6 Jean Monnet 6 The Coal and Steel Community 7 Rome to Maastricht 7 EU Expansion and Expansion Fatigue 9 EU Issues 9 The EU Today 9 A Multicultural EU 10 The European Union and North America 10 Organization of the Text 11 Further Reading 11 Part I Systematic Survey 1 Physical Environments 14 Environmental Concerns 14 A View from Space 14 Climate and Weather 15 The Variability of European Weather 16 General Climate Considerations 17 Natural Vegetation 21 Topography: Mountains, Rivers, and Plains 23 Human Impact on the Environment 28 Further Reading 30 2 Cultural and Historical Geography 31 Introduction 31 A Mosaic of Cultures 32 Languages 32 Religions 40 Culture Contrasts 45 Further Reading 46 3 Population, Distribution, Density, Migration, and Aging 47 Introduction 47 Thomas Robert Malthus 48 Demographic History 48 The Demographic Transition 50 Distribution of Population 55 EU Population Trends 60 Further Reading 63 4 Rural and Urban Settlements 64 Introduction 64 The Network of Roman Towns 66 The Medieval City 66 The Renaissance City 70 The Industrial City 76 Rural Settlement 79 Settlements in the Modern Era 83 Ethnicity in European Cities 90 Summary 92 Further Reading 93 5 Economic Geography: Agriculture, Industry, and Services 94 Introduction 94 Sectors of the Economy 96 Agriculture 97 Industrialization 102 The Stages of European Economic Growth 109 The Impact of the EU on Agriculture, Industry, and Services 113 Human Development Index 115 Further Reading 115 6 Political Geography 116 Friedrich Ratzel 116 Mackinder 116 World War I 116 Ideas for a United Europe 121 Totalitarian Regimes and Economic Autarky 122 The New Order in Europe 125 New European Boundaries after World War II 126 The Cold War 128 Economic Cooperation in Western Europe 129 EU Enlargement (1995) Linked to Soviet Collapse (1991) 135 Widening versus Deepening 138 Summary 140 Further Reading 140 Part II The Core of the European Union 7 France and the Benelux Countries 142 Introduction 142 Belgium 156 The Netherlands 161 Luxembourg 166 Further Reading 168 8 Germany and Italy 169 Introduction 169 Germany 169 Italy 183 Summary 197 Further Reading 198 Part III Enlargement of EU 9 The United Kingdom, Denmark, and Ireland 200 Introduction 200 The United Kingdom 200 Regions of Britain: Scotland, Wales, Northern Ireland, and England 203 A United Kingdom? 219 Denmark 221 Ireland 225 Summary 230 Further Reading 230 10 Southern Europe: Greece, Spain, and Portugal 232 Greece 232 The Iberian Peninsula—Spain and Portugal 240 Further Reading 250 11 Austria, Switzerland, Sweden, Norway, Iceland, and Finland 251 Introduction 251 Austria 251 Switzerland 256 Sweden 263 Norway 268 Iceland 274 Finland 278 Summary 281 Further Reading 281 Part IV Enlargement in the 21st Century 12 Eastward Expansion 2004: The Baltics, Poland, The Czech Republic, Slovakia, Hungary, and Slovenia 284 Introduction 284 The Baltic States: Estonia, Latvia, Lithuania 285 Poland 289 The Czech Republic 296 Slovakia 303 Hungary 305 Slovenia 311 East Europe Summary 312 Further Reading 312 13 Eastward Expansion 2007–2013: The Balkans 314 Introduction: The Balkans 314 Romania 315 Bulgaria 319 Croatia 322 Serbia 324 Montenegro 327 Bosnia-Herzegovina 328 Macedonia 331 Albania 332 Balkan Summary 334 Further Reading 335 Part V Regional Survey: Russia and Former Soviet Socialist Republics 14 Belarus, the Ukraine, Moldova, Georgia, and Russia 338 Introduction 338 Belarus and the Ukraine 338 Moldova 344 Georgia 346 Russia 349 Summary 367 Further Reading 367 Part VI The Mediterranean Fringe 15 Turkey, Cyprus, Malta, and Gibraltar 370 Introduction 370 Turkey 370 Turkey, The Middle East, and Europe 376 Cyprus, Malta, and Gibraltar 377 Cyprus 377 Malta 381 Gibraltar 388 The EU in Africa 391 Islas Canarias 391 Further Reading 392 16 European Union Future? 394 EU External Relations 395 The Common Agricultural Policy in World Affairs 395 Imperial Pasts 396 Decolonization 396 Turkey 396 Summary 397 Glossary 398 Index 404

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Book SynopsisOver 7 billion people demand water from resources that the changing climate is making more and more difficult to harness. Water scarcity and shortage are increasingly common and conditions are becoming more extreme. Inadequate and inappropriate management of water is already taking its toll on the environment and on the quality of life of millions of people. Modern water professionals have a duty to develop sound water science and robust evidence to lobby and influence national and regional development policy and investment priorities. We need to be bold and brave to challenge the status quo, argue the case for change, and create a New Water Architecture. Water Resources: A New Water Architecture takes a unique approach to the challenges of water management. The stress caused by our desire to live, eat, and consume is examined in the context of Governance, the role of policy, and the commercial world. The authors share their nine-step vision for a New Water ArchitecturTrade Review"This is a well written book on a subject of ever increasing importance, it seems, at best, very unlikely that water stress will go away anytime soon and is highly recommended. I'm delighted to have it on my shelves and imagine that it might be rather well thumbed in a few years' time." Geoscientist OnlineTable of ContentsSeries Editor Foreword – Challenges in Water Management xi Foreword xiii Preface xv Acknowledgements xvii List of Abbreviations xix Units and Conversion xxi Glossary xxiii Part I Setting the Scene 1 1 Water Resources in the Twenty-First Century 3 1.1 A Looming Crisis 3 1.2 Human Interactions with Water in the Biosphere 4 1.3 An Inspiring Challenge 6 References 6 2 Fundamentals of Water Management 7 2.1 The Planetary Picture 7 2.1.1 The Blue Planet 7 2.1.2 Water and the Biosphere 8 2.1.3 Distinguishing between Hydrology and Water Resources 10 2.2 Evolution of Water Resource Systems 11 2.2.1 Hydroclimates and Water Resources 12 2.2.2 Mechanisms of Human Interactions with Water Fluxes 18 2.2.3 Anthropogenic Influence: The Traditional Urban Water Cycle 20 2.2.4 Anthropogenic Influence: Advancements in the Urban Water Cycle 24 2.2.5 Anthropogenic Influence: Agriculture 25 2.3 Water, Society and the Biosphere 26 2.3.1 Water and Civilisation 26 2.3.2 The Human Right to Water 27 2.3.3 Population Growth and Mobility 29 2.3.4 Disparity between Water Resources and Population 30 2.3.5 Ability to Access Local Water Resources 30 2.3.6 Different Types of Water Scarcity 32 2.3.7 Ability to Access Distant Water Resources 33 2.3.8 Modern Water Politics 33 References 37 Part II Stresses and Strains 41 3 Key Concepts 43 3.1 Water Fluxes in Space and Time 43 3.2 Mechanisms of Human Interaction with Water Fluxes 45 3.3 Water Stress and Water Scarcity 47 3.4 Virtual Water and the Water Footprint 49 3.5 Live, Eat, Consume: The Conceptual Framework of Water Stress and Virtual Water 58 References 61 4 Live 63 4.1 Introduction 63 4.2 Water and Energy 63 4.2.1 The Nexus of Water and Energy 63 4.2.2 Energy Use in Water Management 65 4.2.3 Water Use in Energy Production 72 4.3 Urbanisation 86 4.3.1 The Rise of the City 86 4.3.2 Peri]Urban Communities 88 4.3.3 Traditional Approaches to the Management of Urban Water Supply and Demand 90 4.3.4 Alternative Approaches to Urban Water Supply 91 4.3.5 Demand Management and the Role of Water Pricing 97 4.3.6 Using Water to Meet Urban Demands for Other Resources 100 4.3.7 Flooding in Urban Environments 102 4.3.8 Opportunities and Challenges of Urban Water Management 106 References 110 5 Eat 117 5.1 The Hidden Water in Food 118 5.1.1 How Much Water is Hidden in Food? 118 5.1.2 The Impact of Water Use in the Global Food System 120 5.2 An Increasingly Important Problem 124 5.2.1 Population Growth 124 5.2.2 Changing Diet 126 5.2.3 Food Waste 129 5.2.4 Food as a Globalised Commodity 131 5.2.5 Climate Change 133 5.3 How to Respond to the Water/Food Conundrum 135 5.3.1 Improving the Efficiency of Water Use in the Global Food System 135 5.3.2 The Importance of Consumer Education 145 5.3.3 Improve Governance of Water Use for Food Production 148 References 150 6 Consume 156 6.1 Impact of Consumerism on Water Management 156 6.1.1 Water as the Essential Economic Ingredient 156 6.1.2 Hidden Demand 157 6.2 Water Use in Industry: Which Sectors Use the Most? 158 6.3 Water Use in Industry: Which Activities Use the Most? 161 6.3.1 Agriculture: Water to Produce Non]Food Goods 161 6.3.2 Mining for Minerals 166 6.3.3 Manufacturing 169 6.4 Water Risk: Recognising the Magnitude of the Problem 170 6.5 Water Risk: Defining and Quantifying the Risk 173 6.5.1 Physical Risks 173 6.5.2 Geopolitical Risks 175 6.5.3 Reputational Risks 178 6.5.4 Social and Community Risks and Impacts 179 6.5.5 Regulatory Risks 179 6.5.6 Financial Implications of Water Risks 181 6.6 Managing Risks and Seizing Opportunities: The Path to Maturity 181 6.6.1 The Age of Taking Water for Granted 182 6.6.2 The Age of Water Reduction 184 6.6.3 The Age of Water Stewardship 186 References 190 Part III Existing Water Architecture 195 7 Existing Management of Water Resources 197 7.1 Governance 197 7.2 Structure of Water Management 198 7.3 The Role of Policy in Decision Making 201 7.4 Types of Policy and their Development 202 7.4.1 Water Policy for Domestic Supply 203 7.4.2 Water Policy for Agriculture 206 7.4.3 Water Policy for Industry 208 7.5 The Rise of Decentralisation and Consultation 209 7.6 Regulation of Water Management 210 7.6.1 Regulating Sources of Water 211 7.6.2 Regulating Drinking Water and Non]Potable Quality 214 7.6.3 Managing Demands for Water and Enforcing Best Practice 215 7.6.4 Regulating Wastewater Treatment and Disposal 216 7.6.5 Regulating Environmental Conditions 217 7.7 Regulatory Models 218 7.8 Regulatory Phases: Unregulated versus Highly Regulated 219 7.8.1 The Unregulated or Lightly Regulated Phase 220 7.8.2 The Over]Regulated Phase 221 7.8.3 The Mature Phase 222 7.9 Governance Silos 223 7.10 Breaking the Silos and Integrating Water Supply Policy 224 7.11 Evolution of Integrated Water Resource Management 227 7.12 Traditional Water Planning Responsibilities versus a Corporate-Driven ‘Water Risk’ Agenda 231 7.13 Summary 231 References 232 8 Ownership and Investment 237 8.1 Public versus Private Ownership Models 237 8.1.1 A New Era of Privatisation 238 8.1.2 A Backlash Against Privatisation 239 8.1.3 Reflections on the Public versus Private Debate 240 8.2 Investment Models and the Economics of Water Management 241 8.2.1 Current and Future Forecast Levels of Investment 241 8.2.2 Meeting Investment Needs 243 8.3 Summary 246 References 246 Part IV Moving to a New Water Architecture 249 9 Challenges and Opportunities 251 9.1 A New Water Architecture: An Introduction 251 9.2 Challenges 252 9.2.1 Stresses and Strains 252 9.2.2 Current Architecture of Water Management 254 9.3 Opportunities 255 9.3.1 Emergence of Virtual Water Concepts in Water Policy 255 9.3.2 Emergence of Multi]Stakeholder Approaches to Water Policy 257 9.3.3 Reform of Water Policy as Opportunity 258 9.4 A Systems Approach to Water Management 260 9.4.1 Principles of Systems Thinking 260 9.4.2 Integrated Management of Water at a Catchment Scale 261 9.4.3 Cyclical Management and Allocation of Water Resources 264 References 265 10 Conceptual Integration 266 10.1 Societal View of the Value of Water 267 10.1.1 The ‘Free’ Resource 267 10.1.2 Price Signals in Drinking Water Supply 267 10.1.3 Price Signals Related to Water in Food and Other Goods 268 10.2 Water as an Under-Valued Resource: The Consequences 269 10.2.1 Profligacy 269 10.2.2 Poor Water Management and Decision Making 269 10.3 Moving to Conceptual Integration 270 10.3.1 A New Appreciation of the Role and Value of Water 270 10.3.2 The Role of Water Professionals 271 References 272 11 Institutional Integration 273 11.1 Requirements for Delivering Integrated Solutions 273 11.1.1 Vertical Integration 274 11.1.2 Horizontal Integration 275 11.2 The Challenges of Delivering Integrated Solutions 276 11.2.1 The State of Play 276 11.2.2 Causes and Barriers 276 11.3 The Role of Governments 277 11.4 The Importance of Education 281 11.5 The Role of Private Organisations 283 11.6 The Importance of Knowledge Transfer and the Benefits of the Digital Revolution 285 11.7 The Role of Non-Governmental Organisations 287 11.8 How to Finance Change 287 11.9 Conclusions: Institutional Enablers 289 References 290 12 Physical Integration 293 12.1 The Need for Change 294 12.1.1 Existing Limitations 294 12.1.2 Barriers to Change 297 12.1.3 Overcoming the Barriers 298 12.2 Integrating Green and Grey Infrastructure to Slow Down Water 299 12.3 The Storage Continuum 301 12.4 Creating Hybrid Water Management Systems 305 12.4.1 The Challenge of Maintenance and Long]Term Responsibility 307 12.5 Circular Systems that Transform ‘Wastes’ to ‘Resources’ 308 12.6 Conclusions 312 References 313 13 A Way Forward 316 13.1 Conceptual Integration 316 13.2 Institutional Integration 318 13.3 Physical Integration 319 13.4 Summary 320 Index 321

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Book SynopsisThe determination of food authenticity is a vital component of quality control. Its importance has been highlighted in recent years by high-profile cases in the global supply chain such as the European horsemeat scandal and the Chinese melamine scandal which led to six fatalities and the hospitalisation of thousands of infants. As well as being a safety concern, authenticity is also a quality criterion for food and food ingredients. Consumers and retailers demand that the products they purchase and sell are what they purport to be. This book covers the most advanced techniques used for the authentication of a vast number of products around the world. The reader will be informed about the latest pertinent analytical techniques. Chapters focus on the novel techniques & markers that have emerged in recent years. An introductory section presents the concepts of food authentication while the second section examines in detail the analytical techniques for the detection of fraud relTable of ContentsList of Contributors xv Preface xix Part A Introduction and Status 1 1 Introduction, Definitions and Legislation 3 Demetrios G. Sotirchos, Georgios P. Danezis and Constantinos A. Georgiou 1.1 Introduction 3 1.2 Definitions 4 1.2.1 Food Origin 4 1.2.2 Label 4 1.2.3 Adulteration and Fraud 4 1.3 Geographical Indications 5 1.3.1 PDO, PGI, and TSG 6 1.3.2 Wines 8 1.4 Organics 11 1.5 Conclusion 14 References 14 Legislation Acts 16 2 Food Authentication by Numbers 19 Georgios P. Danezis and Constantinos A. Georgiou 2.1 Introduction 19 2.2 Research Trends 19 2.3 Analytical Techniques 20 2.4 Countries 22 2.5 Journals 24 References 24 Part B Consumer Attitudes Towards Authentic Food and Market Analysis 25 3 The Concept of Authenticity and its Relevance to Consumers: Country and Place Branding in the Context of Food Authenticity 27 Athanasios Krystallis 3.1 Introduction: The Challenge of Authenticity 27 3.1.1 The Origin of Authenticity and its Marketing Relevance 27 3.1.2 The Philosophy of Authenticity 29 3.2 Countries as Brands: The Country-of-Origin (COO) Effect on Product Choices 30 3.2.1 Do Places get the Reputation they Deserve? 30 3.2.2 Countries as Brands 31 3.2.3 Impact of Country Names on Attitudes Towards Products 33 3.3 Place Branding: Geographic Indication Labels and their Effect on Food Choice 42 3.3.1 Mediterranean Diet: A Typical Place Marketing Paradigm 42 3.3.2 Regulatory Initiatives of Place Branding: Designation of Origin Labelled (DOL) Food and the PDO/PGI/TSG Schemes 50 3.3.3 The Industry’s Response: Is Place Branding a Panacea? 62 3.4 Conclusion: Towards a Definiton of Authenticity in a Business Context 75 Acknowledgements 77 References 78 Part C Geographical, Botanical, and Species Origin, Method of Production and Food Frauds Detection 83 4 Elemental Fingerprinting 85 Georgios P. Danezis, Constantinos A. Papachristidis and Constantinos A. Georgiou 4.1 Introduction 85 4.2 Elemental Techniques 86 4.2.1 ICP‐MS 86 4.2.1.1 Operation Principle: Main Features 86 4.2.1.2 Mass Analyzers 87 4.2.1.3 Interferences 90 4.2.1.4 ICP‐MS versus Other Techniques 92 4.2.2 ICP‐AES and Other Techniques 94 4.3 Sample Preparation: Pretreatment 95 4.3.1 Digestion 95 4.3.2 Direct Solid Sampling Analysis 97 4.3.3 Sampling Problems and Remedies 97 4.3.3.1 Wines and Beverages 97 4.3.3.2 Food Waste Water 98 4.3.3.3 Vegetables and Mushrooms 98 4.3.3.4 Fruits 98 4.3.3.5 Cereals 98 4.3.3.6 Fats and Oils 98 4.3.3.7 Meat 99 4.3.3.8 Seafood 99 4.3.3.9 Dairy Products 99 4.3.3.10 Honey 99 4.4 Applications 99 4.4.1 Elemental Fingerprinting Rational and Trends 99 4.4.2 Elemental Fingerprinting Authenticates Various Food Products 101 4.4.2.1 Wines 103 4.4.2.2 Beverages 103 4.4.2.3 Fruits and Vegetables 103 4.4.2.4 Oils 104 4.4.2.5 Cereals – Pulses 105 4.4.2.6 Dairy Products 105 4.4.2.7 Meat 106 4.4.2.8 Fish and Fish Products 106 4.4.2.9 Honey 107 4.4.2.10 Coffee and Tea 107 4.4.2.11 Spices – Food Ingredients 108 4.4.2.12 Organic Foods 108 4.4.3 Chemometrics 109 4.5 Conclusions and Outlook 111 References 111 5 Isotopic Fingerprinting 117 5.1 Light Isotopes 118 Dana Alina Magdas and Gabriela Cristea 5.1.1 Introduction 118 5.1.2 Application of Stable Isotope Ratios in Food Control 119 5.1.2.1 Fruit Juices 119 5.1.2.2 Wines and Sparkling Wines 121 5.1.2.3 Mineral Waters 122 5.1.2.4 Vanilla 124 5.1.2.5 Spices 125 5.1.2.6 Fish 125 5.1.2.7 Beef 126 References 127 5.2 Heavy Isotopes 131 Andrea Marchetti, Caterina Durante and Lucia Bertacchini 5.2.1 Introduction 131 5.2.2 Quality vs. Geographical Traceability 132 5.2.3 The Isotopic Approach to Food Traceability 134 5.2.3.1 Traceability Models Based on the Use of 87Sr/86Sr 136 5.2.3.2 Mass Bias 137 5.2.3.3 Correction of the Mass‐Dependent Bias 138 5.2.4 Bioavailability 141 5.2.4.1 Applications 142 5.2.4.2 Case Study: Extra Virgin Olive Oils 147 5.2.4.2.1 Sampling and Sample Treatment 148 5.2.4.2.2 Soil Sampling and Treatment 149 5.2.4.2.3 Branch and Olive Treatment 150 5.2.4.2.4 Analytical Determination: Strontium Isotope Ratio 150 5.2.4.2.5 Instrumentation 151 5.2.4.2.6 Accuracy and Precision Evaluation 152 5.2.4.2.7 87Sr/86 Sr for Soil, Branch and Olive Samples 152 5.2.4.3 Case Study: Lambruschi PDO 155 5.2.4.3.1 Sampling and Sample Treatment 156 5.2.4.3.2 Lambrusco Winemaking Sampling 157 5.2.4.3.3 Soil, Branch and Juice Sampling 159 5.2.4.3.4 Soil, Branch and Juice Pretreatments 160 5.2.4.3.5 87Sr/86 Sr in Lambrusco Winemaking 160 5.2.4.3.6 87Sr/86 Sr from Soils to Lambrusco Wines 161 References 165 Legislation 176 6 Nuclear Magnetic Resonance – Metabolomics 177 Donatella Capitani, Anatoly P. Sobolev and Luisa Mannina 6.1 Introduction 177 6.2 Olive Oils 179 6.3 NMR for Investigating Fruit Metabolomics 182 6.3.1 NMR Metabolomics Applied to Kiwifruits 183 6.3.2 NMR Metabolomics Applied to Blueberries 188 6.4 NMR Metabolomics of Transgenic Vegetable Food 190 References 193 7 Chromatography 199 7.1 Introduction to Chromatography – Techniques 200 Joana Santos and M. Beatriz P.P. Oliveira 7.1.1 Introduction 200 7.1.2 Chromatography 202 7.1.2.1 HPLC and Hyphenated Techniques 203 7.1.2.1.1 Liquid Chromatography–Mass Spectrometry 210 7.1.2.2 GC and Hyphenated Techniques 215 7.1.2.2.1 Gas Chromatography–Mass Spectrometry 223 Acknowledgements 224 References 225 7.2 Chromatography – Applications 233 Ana I. Ruiz‐Matute, M. Luz Sanz, F. Javier Moreno and Marta Corzo‐Martínez 7.2.1 Introduction 233 7.2.2 Carbohydrates 233 7.2.3 Food Proteins and Peptides 240 7.2.4 Fatty Acids and Triacylglicerols 246 7.2.5 Volatile Compounds 249 7.2.6 Phenolic Compounds 256 7.2.7 Organic Acids 258 7.2.8 Conclusions 258 Acknowledgements 259 References 259 8 Vibrational and Fluorescence Spectroscopy 277 8.1 Vibrational Spectroscopy 278 Daniel Cozzolino 8.1.1 Introduction 278 8.1.2 Instrumentation and Software 280 8.1.3 Applications of Vibrational Spectroscopy in Food Authenticity 284 8.1.3.1 Fish and Seafood 284 8.1.3.2 Fish and Meat By‐Products 284 8.1.3.3 Wine 285 8.1.3.4 Cereal grains 287 8.1.3.5 Honey 288 8.1.3.6 Meat and Meat Products 291 8.1.4 Concluding Remarks and Future Perspectives 291 References 292 8.2 Fluorescence Spectroscopy 298 Georgios Mousdis and Fotini Mellou 8.2.1 Fluorescence 298 8.2.1.1 Basic Principles 298 8.2.1.2 Instrumentation 299 8.2.1.3 Types of Fluorescence Spectra 301 8.2.1.4 Factors Affecting Fluorescence Intensity 302 8.2.1.4.1 Concentration and Inner Filter Effect 302 8.2.1.4.2 Quenching 303 8.2.1.4.3 Scatter 303 8.2.1.4.4 Molecular Environment 303 8.2.2 Chemometrics 303 8.2.3 Applications in Foods and Drinks 305 8.2.3.1 Edible Oils 305 8.2.3.2 Meat and Meat Products 307 8.2.3.3 Fish and Fish Products 308 8.2.3.4 Eggs 309 8.2.3.5 Caviar 309 8.2.3.6 Milk and Cheese Products 309 8.2.3.7 Cereals 311 8.2.3.8 Honey, Sugar, and Syrups 312 8.2.3.9 Fruits 313 8.2.3.10 Alcoholic Beverages 313 8.2.4 Conclusions and Perspectives 315 References 315 9 Molecular Techniques – Genomics and Proteomics 325 Ignacio Ortea, Karola Böhme, Pilar Calo‐Mata and Jorge Barros‐Velázquez 9.1 Introduction 325 9.2 DNA‐Based Methods 326 9.2.1 Randomly Amplified Polymorphic DNA (RAPD) 328 9.2.2 Simple Sequence Repeats (SSR) 328 9.2.3 DNA Sequencing 330 9.2.4 Multiplex PCR with Species‐Specific Primers 331 9.2.5 Real‐Time PCR 331 9.2.6 PCR‐SSCP 333 9.2.7 PCR‐RFLP 333 9.2.8 DNA Hybridization and Microarrays 335 9.2.9 Peptide Nucleic Acid (PNA) ‐Based Approaches 335 9.3 Proteomics for Species and Geographical Origin Authentication 336 9.3.1 Gel‐Based Methods 337 9.3.2 MS‐Based Methods 341 9.3.3 MS/MS‐Based Methods 342 9.3.4 Directed Approaches 342 9.4 Future Trends 343 References 344 10 Immunological Techniques 355 Yun‐Hwa Peggy Hsieh and Jack Appiah Ofori 10.1 Introduction 355 10.2 Immunoassays 356 10.3 Meat Speciation 357 10.4 Fish and Shellfish Authentication 362 10.5 Fruit Juices 364 10.6 Botanical Origin of Honey 365 10.7 Irradiated and Genetically Modified Foods 366 10.7.1 Detection of Irradiated Foods 367 10.7.2 Detection of GM Foods 368 10.8 Conclusions 369 References 369 11 Sensory Analysis 377 Laura Aceña, Montserrat Mestres, Olga Busto and Ricard Boqué 11.1 Introduction 377 11.2 Organoleptic Evaluation and Food Quality 377 11.3 Human Sensory Panels: Response and Subjectivity 378 11.4 Instrumental Sensory Analysis 378 11.4.1 Looking for Objectivity 378 11.4.2 Gas Chromatography‐Olfactometry (GCO) 379 11.4.2.1 GCO Device: How it Works 379 11.4.2.2 Olfactometric Techniques 380 11.4.2.3 Applications 380 11.4.3 Electronic Nose 381 11.4.3.1 Emulating the sense of smell 381 11.4.3.2 Types of Electronic Noses: Instrumental Aspects 381 11.4.3.3 Applications of E‐Noses in Food Analysis 382 11.4.4 Electronic Tongue 382 11.4.4.1 Emulating the Sense of Taste 382 11.4.4.2 Types of Electronic Tongues 382 11.4.5 Multivariate Data Analysis 384 11.5 Future Trends 386 References 387 12 MALDI Mass Spectrometry: A Promising Non-Chromatographic Technique 393 Cosima D. Calvano, Antonio Monopoli and Carlo G. Zambonin 12.1 Introduction 393 12.2 MALDI MS Principles 394 12.3 MALDI-TOF-MS for Food Proteins and Peptides Analysis 396 12.4 MALDI-TOF-MS for Lipids Analysis 397 12.5 MALDI-TOF-MS for Illegal Mixture Detection 397 12.5.1 Hazelnut Oil in Olive Oil: Lipid Analysis 397 12.5.2 Hazelnut Oil in Olive Oil: Protein Analysis 399 12.5.3 Cow Milk in Goat and Sheep Milk: Protein Analysis 399 12.5.4 Powder Milk in Liquid Milk: Protein and Lipid Analysis 401 12.6 MALDI-TOF-MS for Microbial Contamination Detection 402 Acknowledgements 404 References 404 13 Detection of Food Processing Techniques 413 Aristidis S. Tsagkaris, Georgios P. Danezis and Constantinos A. Georgiou 13.1 Introduction 413 13.2 Freezing–Thawing 414 13.2.1 Methods of Detection 414 13.3 Irradiation 415 13.3.1 Physical Methods for Irradiation Detection 417 13.3.2 Chemical Methods for Irradiation Detection 418 13.3.3 Biological Methods for Irradiation Detection 418 13.4 Heating Techniques 418 13.4.1 Methods of Detection 419 13.5 Conclusion 420 References 420 14 Adulteration Stories 423 Aristidis S. Tsagkaris, Constantinos A. Papachristidis, Georgios P. Danezis and Constantinos A. Georgiou 14.1 Introduction 423 14.2 A Flashback 424 14.3 Food Fraud Incidents 425 14.3.1 Bootleg Liquor, India, 2015 425 14.3.2 Horse Meat Scandal, EU, 2013 425 14.3.3 Adulteration with Melamine, China, 2008 and 2007 427 14.3.4 Food Extension in the ConAgra Incident, USA, 1997 427 14.3.5 Low‐Cost Mixture Marketed as 100% Pure Apple Juice in the Beech‐nut Incident, USA, 1987 427 14.3.6 Arsenic in Beer, UK, 1880 and 1900 428 14.3.7 Bright Poisonous Inorganic Colors for Sweets, UK, 1858 428 14.3.8 Adulteration of Bread with Alum in London, UK, 1839 429 14.4 Conclusions 429 References 429 15 Organic Foods 431 Yolanda Picó 15.1 Introduction 431 15.2 Biochemical Markers and Analytical Platforms 432 15.3 Sampling 433 15.4 Sample Preparation and Extraction 440 15.5 Instrumental Analysis 441 15.5.1 Multi‐Elemental Composition 441 15.5.2 Stable Isotope Analysis 441 15.5.3 Biocrystallisation 443 15.5.4 Infrared Spectroscopy 443 15.5.5 Proton Transfer Reaction Mass Spectrometry (PTR‐MS) 444 15.5.6 Gas Chromatography–Mass Spectrometry (GC‐MS) 444 15.5.7 Liquid Chromatography–Mass Spectrometry (LC-MS) 445 15.5.8 Direct Analysis in Real‐Time High‐Resolution Mass Spectrometry (DART‐HRMS) 446 15.5.9 Biological Methods 447 15.6 Data Analysis 447 15.7 Conclusions and Future Trends 448 References 449 16 Screening and High-Throughput Multi-Contaminants Methods 453 Natasa P. Kalogiouri and Nikolaos S. Thomaidis 16.1 Introduction 453 16.2 Sample Preparation 454 16.2.1 Sample Extraction 454 16.2.1.1 Solid‐Phase Micro‐Extraction 454 16.2.1.2 Matrix Solid‐Phase Dispersion Extraction 460 16.2.1.3 Supercritical Fluid Extraction 460 16.2.1.4 Accelerated Solvent Extraction 461 16.2.1.5 Liquid–Liquid Extraction 461 16.2.1.6 QuEChERS 461 16.2.1.7 Microwave‐Assisted Extraction 462 16.2.2 Sample Clean‐Up 462 16.2.2.1 Gel Permeation Chromatography 463 16.2.2.2 Solid‐Phase Extraction 463 16.2.2.3 Dispersive Solid‐Phase Extraction 463 16.3 Separation and Detection 464 16.3.1 Gas Chromatography Coupled to Conventional Detectors and Mass Spectrometry 464 16.3.2 Liquid Chromatography–Mass Spectrometry 465 16.3.3 Ambient Mass Spectrometry 468 16.3.4 Immunoassays 468 16.3.5 Biosensors 469 16.4 Conclusions 469 References 470 17 Chemometrics – Bioinformatics 481 Marina Cocchi, Mario Li Vigni and Caterina Durante 17.1 The Role of Chemometrics in Food Authentication 481 17.1.1 Authenticity Issues 482 17.1.2 Nature and Challenge of Datasets Arising from Fingerprinting Techniques 482 17.2 Methodology 483 17.2.1 Exploratory Data Analysis 484 17.2.1.1 PCA in Practice 488 17.2.2 Classification and Discrimination 489 17.2.2.1 PLS‐DA 492 17.2.2.2 SIMCA 493 17.2.2.3 Assessing Classification Performance 494 17.2.2.4 Assessing Model Dimensionality 495 17.2.2.5 Case Study 496 17.2.3 Multiway Techniques 497 17.2.3.1 An Illustrative Example 500 17.2.4 Assessing Feature Relevance 500 17.2.4.1 PCA Models 500 17.2.4.2 PLS, PLS‐DA Models 503 17.2.4.3 SIMCA Model 506 17.2.5 Data Fusion 506 17.2.5.1 DF Application Example 507 17.2.6 ANN‐Based Methodology 508 17.2.6.1 A Few Hints About ANN Methodology 509 17.2.6.2 A Working Example 511 References 513 18 Conclusions and Prospects 519 Georgios P. Danezis and Constantinos A. Georgiou References 521 Index 527

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Book SynopsisTechnical ideas may be solid or even groundbreaking, but if these ideas cannot be clearly communicated, reviewers of technical documents are likely to reject the argument for advancing these ideas. This book presents a scientific approach to writing that mirrors the sensibilities of scientists and engineers.Table of ContentsA Note from the Series Editor, xiii Acknowledgments, xv Foreword, xvii Preface, xxi 1 Introduction to the Approach 1 PART I Sentences 9 2 Qualifiers Used in Sentences 11 3 Subordinate Clauses Used as Qualifiers 21 4 Explanatory Phrases, Participle Phrases, and Major Prepositional Phrases 31 5 Infinitive Phrases, and the General Rule for Punctuating Qualifiers 45 6 Sentences with Two Qualifiers 55 7 Higher Orders of Punctuation 69 8 Strategies to Improve Sentences with Qualifiers 77 PART II Lists 89 9 Two-Item Lists 91 10 Multiple-Item Lists 103 11 Strategies for Writing Better Lists 111 PART III Word Choice and Placement 119 12 Adjectives and Adverbs 121 13 Precision in Word Usage 135 PART IV Beyond Sentences 149 14 Paragraphs 151 15 Arguments 163 16 Justification of Arguments 173 17 Organization and Presentation 181 References, 193 About the Author, 207 Index, 209

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Book SynopsisPlants are forced to adapt for a variety of reasons protection, reproductive viability, and environmental and climatic changes. Computational tools and molecular advances have provided researchers with significant new insights into the molecular basis of plant adaptation.Table of ContentsList of Contributors ix Preface xiii 1 Technological Advances in Studies of Plant Adaptation 1José G. Vallarino and Sonia Osorio Introduction 1 Next-Generation Sequencing Technologies 2 Applications of Next-Generation Sequencing 7 Proteome Analysis in Understanding Plant Adaptation 12 Applications of Proteomics 16 Metabolome Analysis in Plant Adaptation 17 Applications of Metabolic Profiling 18 Concluding Remarks and Future Prospects 21 Acknowledgments 22 References 22 2 Use of Natural Variation in Arabidopsis thaliana to Study Adaptation 31Lisa M. Smith and Roosa A. E. Laitinen Introduction 31 Genetic Natural Variation 33 Epigenetic Natural Variation 37 Natural Variation and Metabolites 42 Use of A. thaliana Hybrids in Understanding Evolution 46 Conclusion 49 Acknowledgments 50 References 50 3 Seed Dormancy, Longevity and Their Adaptation 61Thu-Phuong Nguyen and Leónie Bentsink Introduction 61 The Induction of Seed Dormancy and Seed Longevity 62 Factors Affecting Seed Dormancy and Seed Longevity 63 Seed Dry Storage 64 Genetics of Seed Dormancy and Seed Longevity 67 The Relation Between Seed Dormancy and Seed Longevity and its Ecological Significance 70 Ecological Role 70 The Trade-off Between Seed Dormancy and Seed Longevity 73 Conclusions 74 References 74 4 The “Gatekeeper” Concept: Cell-Type Specific Molecular Mechanisms of Plant Adaptation to Abiotic Stress 83SamW. Henderson and Matthew Gilliham Introduction 83 The “Gatekeeper” Concept 85 Single Cell TypesWithin Plant Roots 86 Root Hairs – Tolerance to Phosphorus Deficiency 88 Epidermal Cells of the Root Apex – Aluminum Tolerance 91 Xylem Parenchyma Cells – Salinity Tolerance 94 Pericycle Cells – Nitrogen Starvation 99 Endodermal Cells – ABA Signaling Under Abiotic Stress 102 Beyond Gatekeepers – Conclusions and Perspectives 103 References 105 5 Regulatory and Biosynthetic Mechanisms Underlying Plant Chemical Defense Responses to Biotic Stresses 117William R. Chezem and Nicole K. Clay Introduction 117 Defensive Phenylpropanoids 119 Defense-Related Regulators of Phenylpropanoid Metabolism 124 Defensive Aromatic Alkaloids 126 Defense-Related Regulators of Aromatic Alkaloid Metabolism 131 Conclusion 134 References 135 6 Role of Small RNAs in Regulation of Plant Responses to Stress 147Luis A.A. Toledo-Filho and Sascha Laubinger Introduction 147 miRNAs Biogenesis and Function 148 Evolution of miRNAs 149 siRNAs Biogenesis and Function 150 sRNA Stress Responses 151 sRNA in Abiotic Stress Responses 157 Conclusions and Future Prospects 162 References 163 7 Adaptation of Flower Form: An Evo-Devo Approach to Study Adaptive Evolution in Flower Morphology 169Roxana Yockteng, Ana M.R. Almeida, Alma Pi ˜neyro-Nelson, and Chelsea D. Specht Introduction 169 Flower Developmental Genetics: (A)BCs and Beyond 171 Approaches to the Study of Evolution of Floral Morphology 172 Using GRNs to Investigate Adaptive Evolution of Floral Form: SEP3 as a Case Study 176 Conclusions 184 Acknowledgments 185 References 185 8 Computational Approaches to Dissect and Understand Mechanisms of Adaptation 191Sabrina Kleessen and Zoran Nikoloski Introduction 191 Experimental Set-Ups for Data Acquisition to Reveal Trade-Offs via Correlations 193 Pareto Front Approaches 195 The Triangulation Criterion 195 Ranking of Genotypes 197 From Models to Elements Contributing to Adaptation 199 Cellular Tasks Involved in Adaptation 202 Minimal Network Adjustments Upon Perturbations 202 Investigation of Network Adjustments by Integrating High-Throughput Data 204 Non-Steady State Behavior and Metabolic Network Adjustments 205 Future Challenges and Perspectives 207 References 208 9 From the Greenhouse to the Real World – Arabidopsis Field Trials and Applications 215Karin Köhl and Roosa A.E. Laitinen Introduction 215 Field Experiments in A. thaliana 216 How to do Field Trials? 220 From Arabidopsis to Crops 228 Future Prospects 230 References 230 Index 235

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Book SynopsisSpray drying is a well-established method for transforming liquid materials into dry powder form. Widely used in the food and pharmaceutical industries, this technology produces high quality powders with low moisture content, resulting in a wide range of shelf stable food and other biologically significant products. Encapsulation technology for bioactive compounds has gained momentum in the last few decades and a series of valuable food compounds, namely flavours, carotenoids and microbial cells have been successfully encapsulated using spray drying. Spray Drying Technique for Food Ingredient Encapsulation provides an insight into the engineering aspects of the spray drying process in relation to the encapsulation of food ingredients, choice of wall materials, and an overview of the various food ingredients encapsulated using spray drying. The book also throws light upon the recent advancements in the field of encapsulation by spray drying, i.e., nanospray dryers forTable of ContentsAbout the authors xiv Preface xv Acknowledgments xvi 1 Introduction to spray drying 1 1.1 Introduction 1 1.2 Stage 1: Atomization 2 1.2.1 Principle of atomization 3 1.2.2 Classification of atomizers 4 1.2.2.1 Rotary atomizers 4 1.2.2.2 Pressure nozzle (or hydraulic) atomizer 6 1.2.2.3 Two-fluid nozzle atomizer 7 1.2.2.4 Ultrasonic atomizers 8 1.2.2.5 Electrohydrodynamic atomizers 9 1.3 Stage 2: Spray-air contact 11 1.4 Stage 3: Evaporation of moisture 13 1.5 Stage 4: Particle separation 15 1.5.1 Cyclone separator 15 1.5.2 Bag filter 15 1.5.3 Electrostatic precipitator 17 1.6 Morphology of spray dried particles 17 1.6.1 Skin-forming morphology with hollow internal structure 19 1.6.2 Blow-hole formation 20 1.6.3 Agglomerate 21 1.6.4 Formation of dented structure and presence of small particles within large particles 21 1.7 Spray-drying process parameters and their influence on product quality 22 1.7.1 Atomization parameters 22 1.7.1.1 Atomization pressure 22 1.7.1.2 Feed flow rate 23 1.7.1.3 Feed viscosity 23 1.7.1.4 Feed surface tension 23 1.8 Parameters of spray-air contact and evaporation 24 1.8.1 Aspirator flow rate (or speed) 24 1.8.2 Inlet temperature 24 1.8.3 Outlet temperature 25 1.8.4 Glass transition temperature (Tg) 27 1.8.5 Residence time of particles in the spray chamber 27 1.9 Types of spray dryer 27 1.9.1 Open cycle spray dryer 28 1.9.2 Closed cycle spray dryer 28 1.9.3 Semi-closed cycle spray dryer 28 1.9.4 Single-stage spray dryer 29 1.9.5 Two-stage spray dryer 29 1.9.6 Short-form 30 1.9.7 Tall-form 30 1.10 Applications and advantages of spray drying 31 References 33 2 Introduction to encapsulation of food ingredients 37 2.1 Introduction 37 2.2 Encapsulation of food ingredients 37 2.3 The core and wall for encapsulation 40 2.3.1 Carbohydrates 42 2.3.2 Proteins 42 2.3.3 Lipids 43 2.4 Encapsulation techniques 43 2.4.1 Chemical encapsulation processes 44 2.4.1.1 Coacervation 44 2.4.1.2 Inclusion complexation 45 2.4.1.3 Liposome entrapment 47 2.4.2 Mechanical or physical encapsulation processes 48 2.4.2.1 Emulsification 48 2.4.2.2 Spray chilling, spray cooling and fluidized bed drying 50 2.4.2.3 Freeze drying 50 2.4.2.4 Extrusion 52 2.4.2.5 Electrohydrodynamic technique for microencapsulation: electrospraying and electrospinning 53 2.4.2.6 Spray drying 54 2.5 The lexicon of encapsulation 59 References 60 3 Spray drying for encapsulation 65 3.1 Introduction 65 3.2 Principle of encapsulation by spray drying 65 3.3 Process steps and parameters of encapsulation by spray drying 67 3.3.1 Emulsion formation 67 3.3.1.1 Rationale of emulsification step 67 3.3.1.2 Emulsion parameters influencing encapsulation efficiency 68 3.3.2 Spray drying of emulsion 70 3.3.2.1 Atomization of the emulsion and influencing parameters 70 3.3.2.2 Drying of the emulsion droplets and influencing parameters 71 3.4 Food ingredients encapsulated by spray drying 71 3.4.1 Microorganisms 72 3.4.2 Flavors 72 3.4.3 Bioactive food components 73 References 74 4 Selection of wall material for encapsulation by spray drying 77 4.1 Introduction 77 4.2 Characteristics of wall materials for encapsulation by spray drying 77 4.2.1 Solubility 77 4.2.2 Emulsification property 78 4.2.3 Film-forming ability 78 4.2.4 Viscosity 78 4.2.5 Glass transition 79 4.2.6 Degree of crystallinity 79 4.3 Approaches to choosing wall materials for encapsulation 80 4.3.1 Estimation of drying kinetics and drying curve analysis for wall material selection 81 4.3.1.1 Isothermal drying method 81 4.3.1.2 Estimation of drying kinetics under simulated conditions of spray drying 82 4.3.2 Estimation of emulsification capacity 84 4.3.3 Analysis of viscosity and rheological characteristics of wall material dispersion 85 4.3.4 Determination of thermal properties of wall materials 86 4.4 Commonly used wall materials for encapsulation of food ingredients by spray drying 88 4.4.1 Gum Arabic 88 4.4.2 Maltodextrin 89 4.4.3 Whey protein (concentrate or isolate) 91 4.4.4 Gelatin 91 4.4.5 Sodium caseinate 92 4.4.6 Modified starches 92 4.4.7 Chitosan 93 References 98 5 Encapsulation of probiotics by spray drying 101 5.1 Introduction 101 5.2 Definition of probiotics and significance of probiotics encapsulation 101 5.3 Probiotic characteristics of importance to spray drying encapsulation 103 5.4 Criteria to decide suitability of wall material for encapsulation of probiotics 104 5.5 Selection of spray drying process parameters 106 5.5.1 Effect of atomization on probiotic cell viability 107 5.5.2 Effect of spray drying process conditions on probiotic cell survival 108 5.5.2.1 Thermal effect of spray drying process on cell viability 109 5.5.2.2 Dehydration effect of spray drying process on cell viability 112 5.6 Stability of spray dried probiotic microencapsulates to gastric environment 115 References 122 6 Encapsulation of flavors and specialty oils 126 6.1 Introduction 126 6.2 Selective diffusion theory and mechanisms of volatile retention during spray drying 127 6.3 Performance parameters of flavor encapsulation by spray drying 132 6.3.1 Encapsulation efficiency 133 6.3.1.1 Total oil analysis 133 6.3.1.2 Surface oil analysis 134 6.3.2 Lipid oxidation 134 6.3.2.1 Peroxide value determination 134 6.3.2.2 Active oxygen determination 135 6.3.3 Morphology and particle size 135 6.4 Factors influencing encapsulation of flavors and oils by spray drying 137 6.4.1 Emulsion-related factors 137 6.4.1.1 Wall material 137 6.4.1.2 Core 140 6.4.2 Spray drying-related factors 142 6.4.2.1 Atomization factors 142 6.4.2.2 Inlet and exit air temperatures 143 6.4.2.3 Feed temperature 145 References 153 7 Encapsulation of bioactive ingredients by spray drying 156 7.1 Introduction 156 7.2 Spray drying for encapsulation of polyphenols 156 7.2.1 Polyphenols and their functional properties 156 7.2.2 Rationale for encapsulation of polyphenols 157 7.2.3 Influence of core nature on encapsulation efficiency 157 7.2.4 Influence of wall material selection and spray drying process parameters on polyphenolic core retention 157 7.3 Spray drying encapsulation of vitamins 161 7.3.1 The functional benefits of vitamins 161 7.3.2 Vitamin stability and rationale for encapsulation of vitamins 161 7.3.3 Influence of wall material and feed composition on vitamin encapsulation 162 7.3.4 Influence of spray drying process parameters on vitamin encapsulation 163 7.4 Spray drying encapsulation of carotenoids 163 7.4.1 Carotenoids and their functional significance 163 7.4.2 Rationale for encapsulation of carotenoids 165 7.4.3 Effect of wall material selection and feed composition on encapsulation of carotenoids 165 7.4.4 Effect of spray drying process conditions on encapsulation of carotenoids 167 References 176 8 Spray drying for nanoencapsulation of food components 180 8.1 Introduction 180 8.2 Introduction to food nanoparticles and nanoencapsulation 181 8.3 Nano spray dryer 183 8.3.1 Operation principle of nano spray dryer 183 8.3.1.1 Piezo-electric driven vibrating mesh atomization 183 8.3.1.2 Heating mode, hot air flow pattern in and configuration of spray chamber 184 8.3.1.3 Product separation by electrostatic precipitator 186 8.4 Nanoencapsulation of food bioactive compounds by nano spray dryer 188 8.5 Analytical methods to characterize nanoencapsulates in foods 189 8.5.1 Electron microscopy 190 8.5.1.1 Scanning electron microscopy 190 8.5.1.2 Transmission electron microscopy 191 8.5.1.3 Atomic force microscopy 191 8.5.1.4 Atmospheric scanning electron microscopy 192 8.5.2 Quantification of nanoparticles’ size and mass by electron microscopy 193 References 195 9 Functional properties of spray dried encapsulates 198 9.1 Introduction 198 9.2 Controlled release of encapsulated bioactive compounds 198 9.2.1 Controlled release by dissolution 199 9.2.2 Controlled release by diffusion 199 9.3 Masking of off-taste by spray drying encapsulation 201 9.4 Improvement in stability of encapsulated bioactive compounds 202 References 208 10 Analysis of spray dried encapsulates 210 10.1 Introduction 210 10.2 Analysis of physical characteristics of spray dried encapsulates 211 10.2.1 Moisture content 211 10.2.2 Particle size 211 10.3 Analysis of the efficiency of spray drying encapsulation process 214 10.3.1 Estimation of encapsulation efficiency 214 10.3.1.1 Encapsulation efficiency of specialty oils 214 10.3.1.2 Encapsulation efficiency of vitamins and polyphenolic compounds 215 10.3.1.3 Encapsulation efficiency of flavors and other volatile compounds 215 10.3.1.4 Encapsulation efficiency of probiotic cells 216 10.4 Analysis of the stability of spray dried microencapsulates 216 10.4.1 Analysis of probiotic cell stability under simulated in vitro gastrointestinal conditions 217 10.4.2 Analysis of oxidative stability for lipophilic core compounds 217 10.4.2.1 Estimation of peroxide value by spectrophotometry method 217 10.4.2.2 Rancimat method for estimation of peroxide value 218 10.4.2.3 Gas chromatography method for analysis of oxidative stability 219 10.4.3 Analysis of the functional properties of spray dried encapsulates 220 10.4.3.1 Study of core release from microencapsulates 220 10.4.3.2 Taste-masking effects 221 References 222 11 Modeling approach for spray drying and encapsulation applications 224 11.1 Introduction 224 11.2 Computational fluid dynamics modeling 224 11.2.1 Conservation of mass equation 225 11.2.2 Conservation of momentum equation 225 11.2.3 Conservation of energy equation 225 11.3 Modeling of spray drying process – a theoretical perspective 229 11.3.1 Atomization 230 11.3.1.1 Boundary conditions for atomization models 230 11.3.2 Spray-air contact 232 11.3.2.1 Reference frames 235 11.3.2.2 Turbulence models 237 11.3.2.3 Droplet/particle trajectory 239 11.3.2.4 Droplet temperature 239 11.3.2.5 Droplet residence time 240 11.3.2.6 Particle impact position 241 11.3.3 Droplet drying and particle formation 243 11.4 Modeling of core release from encapsulates 245 References 249 12 Synergistic spray drying techniques for encapsulation 252 12.1 Introduction 252 12.2 Spray fluidized bed coating for encapsulation 252 12.2.1 Theory of fluidization 253 12.2.2 Fluid bed encapsulation – process steps and influential factors 253 12.2.2.1 Atomization 254 12.2.2.2 Droplet-particle interactions 258 12.2.2.3 Drying of coating material on particle surface 261 12.2.2.4 Food ingredient applications of spray fluidized bed coating 261 12.2.2.5 Challenges associated with spray fluidized bed coating 262 12.2.2.6 Recent advancements in spray fluidized bed coating 263 12.3 Spray-freeze-drying for encapsulation 263 12.3.1 Spray freezing 265 12.3.1.1 Spray freezing into vapor (SFV) 265 12.3.1.2 Spray freezing into vapor over liquid (SFV/L) 265 12.3.1.3 Spray freezing into liquid (SFL) 269 12.3.2 Freeze drying 270 12.3.2.1 Conventional freeze drying 270 12.3.2.2 Atmospheric freeze drying 271 12.3.3 Factors affecting the encapsulation efficiency of SFD process 271 References 273 13 Industrial relevance and commercial applications of spray dried active food encapsulates 275 13.1 Introduction 275 13.2 Applications of spray dried encapsulates in the food industries 276 13.2.1 Confectionery industry 276 13.2.2 Bakery industry 277 13.2.3 Other product categories 278 13.3 Cost analysis of the spray drying encapsulated active ingredient 278 13.4 Major industry players producing spray dried encapsulated food ingredients 281 13.4.1 Symrise 281 13.4.2 International Flavors & Fragrances (IFF) 281 13.4.3 Firmenich 281 13.4.4 Givaudan 282 13.4.5 Takasago International Corporation 282 13.4.6 TasteTech 282 13.4.7 Kievit 282 13.4.8 Synthite 282 13.5 Challenges and future scope of the spray drying encapsulation of food ingredients 283 References 284 Index 285

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Book SynopsisLactic acid bacteria (LAB) have historically been used as starter cultures for the production of fermented foods, especially dairy products. Over recent years, new areas have had a strong impact on LAB studies: the application of ?omics? tools; the study of complex microbial ecosystems, the discovery of new LAB species, and the use of LAB as powerhouses in the food and medical industries. This second edition of Biotechnology of Lactic Acid Bacteria: Novel Applications addresses the major advances in the fields over the last five years. Thoroughly revised and updated, the book includes new chapters. Among them: The current status of LAB systematics; The role of LAB in the human intestinal microbiome and the intestinal tract of animals and its impact on the health and disease state of the host; The involvement of LAB in fruit and vegetable fermentations; The production of nutraceuticals and aroma compounds by LAB; and Table of ContentsList of Contributors xiii Preface xviii1. Updates on Metabolism in Lactic Acid Bacteria in Light of “Omic” Technologies 1Magdalena Kowalczyk, Baltasar Mayo, María Fernández, and Tamara Aleksandrzak-Piekarczyk1.1. Sugar Metabolism 11.1.1. Practical Aspects of Sugar Catabolism 31.2. Citrate Metabolism and Formation of Aroma Compounds 41.2.1. Citrate Transport 41.2.2. Conversion of Citrate into Pyruvate and Production of Aroma Compounds 61.2.3. Conversion of Citrate into Succinate 61.2.4. Bioenergetics of Citrate Metabolism 61.3. The Proteolytic System of Lactic Acid Bacteria 61.3.1. Protein Degradation 71.3.2. Peptidases 81.3.3. Technological Applications of the Proteolytic System 101.3.4. Amino Acid Catabolism 101.4. LAB Metabolism in Light of Genomics Comparative Genomics and Metagenomics 121.5. Novel Aspects of Metabolism Regulation in the Post]genomic Age 121.6. Functional Genomics and Metabolism 161.6.1. Transcriptomics Proteomics and Metabolomics 161.6.2. Global Phenotypic Characterization of Microbial Cells 171.7. Systems Biology of LAB 17Acknowledgments 18References 182. Systematics of Lactic Acid Bacteria: Current Status 25Giovanna E. Felis, Elisa Salvetti, and Sandra Torriani2.1. Families and Genera of Lactic Acid Bacteria 252.2. A Focus on the Family Lactobacillaceae 272.3. Taxonomic Tools in the Genomic Era 29References 303. Genomic Evolution of Lactic Acid Bacteria: From Single Gene Function to the Pan]genome 32Grace L. Douglas, M. Andrea Azcarate-Peri,l and Todd R. Klaenhammer3.1. The Genomics Revolution 323.2. Genomic Adaptations of LAB to the Environment 333.2.1. LAB Evolution in the Dairy Environment 333.2.2. LAB Evolution in Vegetable and Meat Fermentations 343.2.3. Fast]evolving LAB 353.2.4. LAB in the GI Tract 353.3. “Probiotic Islands”? 363.4. Stress Resistance and Quorum Sensing Mechanisms 393.5. The Impact of Genome Sequencing on Characterization Taxonomy and Pan]genome Development of Lactic Acid Bacteria 403.6. Functional Genomic Studies to Unveil Novel LAB Utilities 453.7. Conclusions 47References 474. Lactic Acid Bacteria: Comparative Genomic Analyses of Transport Systems 55Graciela L. Lorca, Taylor A. Twiddy, and Milton H. Saier Jr.4.1. Introduction 554.2. Channel]forming Proteins 564.3. The Major Facilitator Superfamily 594.4. Other Large Superfamilies of Secondary Carriers 604.5. ABC Transporters 644.6. Heavy Metal Transporters 654.7. P-type ATPases in Prokaryotes 684.8. The Prokaryote-specific Phosphotransferase System (PTS) 684.9. Multidrug Resistance Pumps 714.10. Nutrient Transport in LAB 714.11. Conclusions and Perspectives 72Note 73Acknowledgments 73References 735. Novel Developments in Bacteriocins from Lactic Acid Bacteria 80Ingolf F. Nes, Christina Gabrielsen, Dag A. Brede, and Dzung B. Diep5.1. Introduction 805.2. Characteristics and Classification of Bacteriocins 805.2.1. Class Ia: Lantibiotics 815.2.2. Class II: The Non-lantibiotics 815.3. Mode of Action 845.4. Bacteriocin Resistance 865.5. Applications 885.5.1. Opportunities and Hurdles in Application of Bacteriocins 885.5.2. Application of Bacteriocins in Medical-related and Personal Hygiene Products 885.5.3. Bacteriocin]producing Probiotics 905.6. Future Perspectives 92References 936. Bacteriophages of Lactic Acid Bacteria and Biotechnological Tools 100Beatriz Martínez, Pilar García, Ana Rodríguez, Mariana Piuri, and Raúl R. Raya6.1. Introduction 1006.2. Bacteriophages of Lactic Acid Bacteria 1016.2.1. Classification of Lactococcal Phages 1036.3. Antiphage Strategies 1036.3.1. Natural Mechanisms of Phage Resistance 1036.3.2. Genetically Engineered Antiphage Systems 1056.4. Phage-Based Molecular Tools 1066.4.1. Phage Integrases and Integration Vectors 1066.4.2. CRISPR Applications 1086.4.3. Recombineering 1106.5. LAB Phages as Biocontrol Tools 1136.6. Conclusions 113References 1137. Lactic Acid Bacteria and the Human Intestinal Microbiome 120François P. Douillard and Willem M. de Vos7.1. Introduction 1207.2. Ecology of the Human Intestinal Tract 1217.2.1. The Human Microbiome in the Upper and Lower Intestinal Tract 1217.2.2. Lactic Acid Bacteria Associated with the Human Intestine 1227.2.3. Metagenomic Studies of the Intestine in Relation to LAB 1237.3. A Case Study: The Lactobacillus rhamnosus Species 1247.3.1. Genomic Diversity of Lact. rhamnosus and Intestinal Adaptation 1247.3.2. Lact. rhamnosus Metabolism and Adaptation to the Intestine 1267.3.3. Host Interaction Factors in Lact. rhamnosus 1277.3.4. The Lact. rhamnosus Species: Autochthonous or Allochthonous in the Human Intestine? 1277.4. Concluding Perspectives and Future Directions 129Acknowledgments 130References 1308. Probiotics and Functional Foods in Immunosupressed Hosts 134Ivanna Novotny Nuñez, Martin Manuel, Palomar Alejandra de Moreno de LeBlanc, Carolina Maldonado Galdeano, and Gabriela Perdigón8.1. Introduction 1348.2. Probiotic Fermented Milk in a Malnutrition Model 1358.3. Probiotic Administration in Stress Process 1388.4. Conclusions 140Acknowledgments 141References 1419. Lactic Acid Bacteria in Animal Production and Health 144Damien Bouchard, Sergine Even, and Yves Le Loir9.1. Introduction 1449.2. Lactic Acid Bacteria and Probiotics 1459.3. Classifications and Regulatory Criteria of Probiotics in Animal Health 1469.4. Probiotic LAB and Animal Production Sectors 1479.4.1. Probiotics in Ruminants 1479.4.2. Probiotics in Pigs 1509.4.3. Probiotics in Poultry 1529.5. Conclusions 154References 15410. Proteomics for Studying Probiotic Traits 159Rosa Anna Siciliano and Maria Fiorella Mazzeo10.1. Introduction 15910.2. Mass Spectrometric Methodologies in Proteomics 16010.2.1. The Classical Approach: 2-DE Separation and Protein Identification by Mass Spectrometry 16010.2.2. Gel-Free Proteomic Approaches 16010.3. Proteomics for Studying Molecular Mechanisms of Probiotic Action 16110.3.1. Adaptation Mechanisms to the GIT Environment 16110.3.2. Adhesion Mechanisms to the Host Mucosa 16210.3.3. Molecular Mechanisms of Probiotic Immunomodulatory Effects 16410.3.4. Probiotics and Prebiotics 16410.4. Concluding Remarks and Future Directions 165References 16611. Engineering Lactic Acid Bacteria and Bifidobacteria for Mucosal Delivery of Health Molecules 170Thibault Allain, Camille Aubry, Jane M. Natividad, Jean-Marc Chatel, Philippe Langella, and Luis G. Bermúdez-Humarán11.1. Introduction 17011.2. Lactococcus lactis: A Pioneer Bacterium 17111.3. Lactobacillus spp. as a Delivery Vector 17111.4. Bifidobacteria as a New Live Delivery Vehicle 17111.5. Engineering Genetic Tools for Protein and DNA Delivery 17211.5.1. Cloning Vectors 17211.5.2. Expression Systems 17311.6. Therapeutic Applications 17611.6.1. Inflammatory Bowel Disease (IBD) 17611.6.2. Anti-protease Enzyme-producing LAB: The Tole of Elafin 17611.6.3. Antioxidant Enzyme-producing Lactococci and Lactobacilli 17711.7. Allergy 17811.7.1. Use of LAB in Food Allergy 17811.7.2. Allergic Airways Diseases 17911.8. Autoimmune Diseases 18011.8.1. Type 1 Diabetes Mellitus 18011.8.2. Celiac Disease 18011.9. Infectious Diseases 18111.9.1. Mucosal Delivery of Bacterial Antigens 18111.9.2. Mucosal Delivery of Viral Antigens 18111.9.3. Parasitic Diseases 183References 18412. Lactic Acid Bacteria for Dairy Fermentations: Specialized Starter Cultures to Improve Dairy Products 191Domenico Carminati, Giorgio Giraffa, Miriam Zago, Mariángeles Briggiler Marcó, Daniela Guglielmotti, Ana Binetti, and Jorge Reinheimer12.1. Introduction 19112.2. Adjunct Cultures 19112.2.1. Ripening Cultures 19212.2.2. Protective Cultures 19312.2.3. Probiotic Cultures 19512.2.4. Exopolysaccharide-producing Starters 19612.3. Phage-Resistant Starters 19912.4. New Sources of Starter Strains 20112.5. Conclusions 202References 20313. Lactobacillus sakei in Meat Fermentation 209Marie-Christine Champomier-Vergès and Monique Zagorec13.1. Introduction 20913.2. Genomics and Diversity of the Species Lactobacillus sakei 21013.3. Post-genomic Vision of Meat Fitness Traits of Lactobacillus sakei 21213.3.1. Energy Sources 21213.3.2. Stress Response 21313.4. Conclusions 214References 21414. Vegetable and Fruit Fermentation by Lactic Acid Bacteria 216Raffaella Di Cagno, Pasquale Filannino, and Marco Gobbetti14.1. Introduction 21614.2. Lactic Acid Bacteria Microbiota of Raw Vegetables and Fruits 21614.3. Fermentation of Vegetable Products 21814.3.1. Spontaneous Fermentation 21814.3.2. The Autochthonous Starters 21814.4. Main Fermented Vegetable Products 22114.4.1. Sauerkrauts 22114.4.2. Kimchi 22214.4.3. Pickled Cucumbers 22314.5. Physiology and Biochemistry of LAB during Vegetable and Fruit Fermentation 22314.5.1. Metabolic Adaptation by LAB during Plant Fermentation 22414.6. Food Phenolic Compounds: Antimicrobial Activity and Microbial Responses 22414.6.1. Effect of Phenolics on the Growth and Viability of LAB 22414.6.2. Metabolism of Phenolics by LAB 22614.7. Health-promoting Properties of Fermented Vegetables and Fruits 22614.8. Alternative Sources of Novel Probiotics Candidates 22614.9. Vehicles for Delivering Probiotics 22814.10. Conclusions 229References 22915. Lactic Acid Bacteria and Malolactic Fermentation in Wine 231Aline Lonvaud-Funel15.1. Introduction 23115.2. The Lactic Acid Bacteria of Wine 23115.2.1. Origin 23115.2.2. Species 23215.2.3. Identification 23215.2.4. Typing at Strain Level 23315.2.5. Detection of Specific Strains 23315.3. The Oenococcus Oeni Species 23315.4. Evolution of Lactic Acid Bacteria during Winemaking 23415.4.1. Interactions between Wine Microorganisms 23515.4.2. Environmental Factors 23615.5. Lactic Acid Bacteria Metabolism and its Impact on Wine Quality 23715.5.1. Sugars 23715.5.2. Carboxylic Acids 23715.5.3. Amino Acids 24015.5.4. Other Metabolisms with Sensorial Impact 24115.6. Controlling the Malolactic Fermentation 24215.7. Conclusions 243References 24416. The Functional Role of Lactic Acid Bacteria in Cocoa Bean Fermentation 248Luc De Vuyst and Stefan Weckx16.1. Introduction 24816.2. Cocoa Crop Cultivation and Harvest 24916.3. The Cocoa Pulp or Fermentation Substrate 25016.4. Fresh Unfermented Cocoa Beans 25116.5. Cocoa Bean Fermentation 25216.5.1. Rationale 25216.5.2. Farming Practices 25316.6. Succession of Microorganisms during Cocoa Bean Fermentation 25616.6.1. The Spontaneous Three-phase Cocoa Bean Fermentation Process 25616.6.2. Yeast Fermentation 25716.6.3. LAB Fermentation 26016.6.4. AAB Fermentation 26416.7. Biochemical Changes in the Cocoa Beans during Fermentation and Drying 26616.8. Optimal Fermentation Course and End of Fermentation 26816.9. Further Processing of Fermented Cocoa Beans 26916.9.1. Drying of Fermented Cocoa Beans 26916.9.2. Roasting of Fermented Dry Cocoa Beans 27016.10. Use of Starter Cultures for Cocoa Bean Fermentation 27116.10.1. Rationale 27116.10.2. Experimental Use of Cocoa Bean Starter Cultures 27116.11. Concluding Remarks 273References 27317. B-Group Vitamins Production by Probiotic Lactic Acid Bacteria 279Jean Guy LeBlanc, Jonathan Emiliano Laiño, Marianela Juárez del Valle, Graciela Savoy de Giori, Fernando Sesma, and María Pía Taranto17.1. Introduction 27917.2. B-Group Vitamins 28017.2.1. Riboflavin (Vitamin B2 ) 28117.2.2. Folates (Vitamin B9) 28417.3. Probiotics In Situ 28617.3.1. Vitamin B12 (Cobalamin) 28817.3.2. Cobalamin Biosynthesis by Lactobacillus reuteri 28917.4. Conclusions 291Acknowledgments 292References 29218. Nutraceutics and High Value Metabolites Produced by Lactic Acid Bacteria 297Elvira M. Hebert, Graciela Savoy de Giori, and Fernanda Mozzi18.1. Introduction 29718.2. Nutraceutics 29818.2.1. Low-calorie Sugars 29818.2.2. Short-Chain Fatty Acids 30018.2.3. Conjugated Linoleic Acid (CLA) 30118.2.4. Bioactive Peptides 30118.2.5. Gamma-aminobutyric Acid (GABA) 30318.2.6. Vitamins 30518.3. Exopolysaccharides 30618.4. Commodity Chemicals 30718.5. Conclusions 308References 30819. Production of Flavor Compounds by Lactic Acid Bacteria in Fermented Foods 314Anne Thierry, Tomislav Pogačic, Magalie Weber, and Sylvie Lortal19.1. Introduction 31419.2. Flavor and Aroma Compounds 31519.2.1. Volatile Compounds: Diversity Analytical Methods 31519.2.2. Contribution of Volatile Aroma Compounds to Flavor 31619.2.3. Origin of Aroma Compounds 31619.3. LAB of Fermented Foods and their Role in Flavor Formation 31619.3.1. Biochemical Processes of Flavor Compound Formation in Food and Potential of LAB 32419.3.2. Flavor Compounds Produced from Carbohydrate Fermentation by LAB 32419.3.3. Flavor Compounds from Amino Acid Conversion by LAB 32619.3.4. Flavor Compounds from Lipids in LAB 32719.3.5. Synthesis of Esters 32819.3.6. Interspecies and Intraspecies Variations of Aroma Compound Production 32819.4. Biotic and Abiotic Factors Modulating the Contribution of LAB to Flavor Formation 33119.4.1. General Scheme of Flavor Formation in Fermented Foods In Situ 33119.4.2. Factors Modulating the Expression of the Flavor-related Activities of LAB 33219.4.3. Factors Determining the Real Contribution of LAB to Food Flavor 33319.5. Conclusions and Research Perspectives 333References 33420. Lactic Acid Bacteria Biofilms: From their Formation to their Health and Biotechnological Potential 341Jean-Christophe Piard and Romain Briandet20.1. Lactic Acid Bacteria Biofilms are Ubiquitous in a Wide Variety of Environments from Nature to Domesticated Settings 34120.2. Biofilm Life Cycle and Bacterial Factors Involved in LAB Biofilm Lifestyle 34620.3. Health and Biotechnological Potential of LAB Biofilms and Underlying Mechanisms 35220.4. Conclusions 354Acknowledgments 355References 355Index 362

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Book SynopsisPlant polyphenols are secondary metabolites that constitute one of the most common and widespread groups of natural products. They express a large and diverse panel of biological activities including beneficial effects on both plants and humans. Many polyphenols, from their structurally simplest representatives to their oligo/polymeric versions (also referred to as vegetable tannins), are notably known as phytoestrogens, plant pigments, potent antioxidants, and protein interacting agents.Sponsored by the scholarly society Groupe Polyphénols, this publication, which is the fifth volume in this highly regarded Recent Advances in Polyphenol Research series, is edited by Kumi Yoshida, Véronique Cheynier and Stéphane Quideau. They have once again, like their predecessors, put together an impressive collection of cutting-edge chapters written by expert scientists, internationally respected in their respective field of polyphenol sciences. This Volume 5 highlights some of tTable of ContentsContributors xv Preface xix 1 The Physical Chemistry of Polyphenols: Insights into the Activity of Polyphenols in Humans at the Molecular Level 1Olivier Dangles, Claire Dufour, Claire Tonnelé and Patrick Trouillas 1.1 Introduction 1 1.2 Molecular complexation of polyphenols 4 1.3 Polyphenols as electron donors 11 1.4 Polyphenols as ligands for metal ions 21 1.5 Conclusions 27 References 28 2 Polyphenols in Bryophytes: Structures, Biological Activities, and Bio- and Total Syntheses 36Yoshinori Asakawa 2.1 Introduction 36 2.1 Distribution of cyclic and acyclic bis-bibenzyls in Marchantiophyta (liverworts) 37 2.3 Biosynthesis of bis-bibenzyls 39 2.4 The structures of bis-bibenzyls and their total synthesis 50 2.5 Biological activity of bis-bibenzyls 58 2.6 Conclusions 60 Acknowledgments 61 References 61 3 Oxidation Mechanism of Polyphenols and Chemistry of Black Tea 67Yosuke Matsuo and Takashi Tanaka 3.1 Introduction 67 3.2 Catechin oxidation and production of theaflavins 71 3.3 Theasinensins 73 3.4 Coupled oxidation mechanism 75 3.5 Bicyclo[3.2.1]octane intermediates 77 3.6 Structures of catechin oxidation products 78 3.7 Oligomeric oxidation products 82 3.8 Conclusions 84 Acknowledgments 85 References 85 4 A Proteomic-Based Quantitative Analysis of the Relationship Between Monolignol Biosynthetic Protein Abundance and Lignin Content Using Transgenic Populus trichocarpa 89Jack P. Wang, Sermsawat Tunlaya-Anukit, Rui Shi, Ting-Feng Yeh, Ling Chuang, Fikret Isik, Chenmin Yang, Jie Liu, Quanzi Li, Philip L. Loziuk, Punith P. Naik, David C. Muddiman, Joel J. Ducoste, Cranos M. Williams, Ronald R. Sederoff and Vincent L. Chiang 4.1 Introduction 90 4.2 Results 94 4.3 Discussion 101 4.4 Materials and methods 102 References 104 5 Monolignol Biosynthesis and Regulation in Grasses 108Peng Xu and Laigeng Li 5.1 Introduction 108 5.2 Unique cell walls in grasses 109 5.3 Lignin deposition in grasses 110 5.4 Monolignol biosynthesis in grasses 111 5.5 Regulation of monolignol biosynthesis in grasses 114 5.6 Remarks 119 Acknowledgments 119 References 120 6 Creation of Flower Color Mutants Using Ion Beams and a Comprehensive Analysis of Anthocyanin Composition and Genetic Background 127Yoshihiro Hase 6.1 Introduction 127 6.2 Induction of flower color mutants by ion beams 129 6.3 Mutagenic effects and the molecular nature of the mutations 131 6.4 Comprehensive analyses of flower color, pigments, and associated genes in fragrant cyclamen 131 6.5 Mutagenesis and screening 133 6.6 Genetic background and the obtained mutants 136 6.7 Carnations with peculiar glittering colors 137 6.8 Conclusion 139 Acknowledgments 140 References 140 7 Flavonols Regulate Plant Growth and Development through Regulation of Auxin Transport and Cellular Redox Status 143Sheena R. Gayomba, Justin M. Watkins and Gloria K. Muday 7.1 Introduction 143 7.2 The flavonoids and their biosynthetic pathway 144 7.3 Flavonoids affect root elongation and gravitropism through alteration of auxin transport 146 7.4 Mechanisms by which flavonols regulate IAA transport 149 7.5 Lateral root formation 151 7.6 Cotyledon, trichome, and root hair development 152 7.7 Inflorescence architecture 154 7.8 Fertility and pollen development 154 7.9 Flavonols modulate ROS signaling in guard cells to regulate stomatal aperture 155 7.10 Transcriptional machinery that controls synthesis of flavonoids 157 7.11 Hormonal controls of flavonoid synthesis 160 7.12 Flavonoid synthesis is regulated by light 161 7.13 Conclusions 162 Acknowledgments 163 References 163 8 Structure of Polyacylated Anthocyanins and Their UV Protective Effect 171Kumi Yoshida, Kin-ichi Oyama and Tadao Kondo 8.1 Introduction 171 8.2 Occurrence and structure of polyacylated anthocyanins in blue flowers 173 8.3 Molecular associations of polyacylated anthocyanins in blue flower petals 178 8.4 UV protection of polyacylated anthocyanins from solar radiation 183 8.5 Conclusion 187 References 188 9 The Involvement of Anthocyanin-Rich Foods in Retinal Damage 193Kenjirou Ogawa and Hideaki Hara 9.1 Introduction 193 9.2 Anthocyanin-rich foods for eye health 195 9.3 Experimental models to mimic eye diseases and the effect of anthocyanin-rich foods 196 9.4 Conclusions 201 References 203 10 Prevention and Treatment of Diabetes Using Polyphenols via Activation of AMP-Activated Protein Kinase and Stimulation of Glucagon-like Peptide-1 Secretion 206Takanori Tsuda 10.1 Introduction 206 10.2 Activation of AMPK and metabolic change 207 10.3 GLP-1 action and diabetes prevention/suppression 212 10.4 Future issues and prospects 220 References 222 11 Beneficial Vascular Responses to Proanthocyanidins: Critical Assessment of Plant-Based Test Materials and Insight into the Signaling Pathways 226Herbert Kolodziej 11.1 Introduction 227 11.2 Appraisal of test materials 228 11.3 Endothelial dysfunction 233 11.4 In vitro test systems 234 11.5 Vasorelaxant mechanisms 235 11.6 Bioavailability and metabolic transformation: the missing link in the evidence to action in the body 249 11.7 Conclusions 250 References 251 12 Polyphenols for Brain and Cognitive Health 259Katherine H. M. Cox and Andrew Scholey 12.1 Introduction 259 12.2 Studies of total polyphenols and cognition 260 12.3 Pine bark 272 12.4 Discussion and conclusions 283 References 283 13 Curcumin and Cancer Metastasis 289Ikuo Saiki 13.1 Introduction 290 13.2 Effects of curcumin on intra-hepatic metastasis of liver cancer 293 13.3 Effects of curcumin on lymp node metastasis of lung cancer 298 13.4 Effects of curcumin on tumor angiogenesis 303 13.5 Conclusions 307 References 307 14 Phytochemical and Pharmacological Overview of Cistanche Species 313Hai-Ning Lv, Ke-Wu Zeng, Yue-Lin Song, Yong Jiang and Peng-Fei Tu 14.1 Introduction 313 14.2 Chemical constituents of Cistanche species 314 14.3 Bioactivities of the extracts and pure compounds from Cistanche species 322 14.4 Conclusions 334 References 334 Index 342

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Book SynopsisAn updated guide to plant pathogens and their management The impact of plant disease is far-reaching. Its effects are felt not only in the spheres of agriculture and horticulture, but also in human health and wellbeing. The challenges of population growth, climate change and global food security all increase the need to protect crops from disease and reduce the losses caused by plant pathogens. This requires ongoing research and novel solutions, making the detailed analysis offered by Plant Pathology and Plant Pathogens more relevant than ever. Striking a balance between laboratory- and field-based aspects of its subject, this revised fourth edition of the text places plant disease in a wide biological context. Its contents cover causal agents and diagnosis, hostpathogen interactions, and disease management, including breeding for resistance, chemical, biological and integrated control. New to this edition are updated sections on molecular epidemiology, bTable of ContentsPreface vii List of Abbreviations ix About the Companion Website xi Part I Plant Disease 1 1 The Diseased Plant 7 2 The Microbial Pathogens 31 3 Pathogen Biology 45 4 Disease Assessment and Forecasting 83 5 Plant Disease Epidemics 109 Part II Host–Pathogen Interactions 137 6 Entry and Colonization of the Host 141 7 The Physiology of Plant Disease 167 8 Microbial Pathogenicity 185 9 Plant Defense 209 10 Host–Pathogen Specificity 241 Part III Disease Management 273 11 Disease Management by Chemicals 279 12 Disease Management by Host Resistance 309 13 Biological Control of Plant Disease 337 14 An Integrated Approach to Disease Management 359 Appendix 1 Annotated List of Pathogens and the Diseases they Cause 375 Appendix 2 Reference Sources for Figures 387 Index 395

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Book SynopsisThe Chernobyl Nuclear Power Plant (NPP) disaster that occurred in Ukraine on April 26, 1986, was one of the most devastating in human history. Using this as a case study, the AGU monograph Groundwater Vulnerability: Chernobyl Nuclear Disaster is devoted to the problem of groundwater vulnerability, where the results of long-term field and modeling investigations of radionuclide transport in soil and groundwater, within the Ukrainian part of the Dnieper River basin (Kyiv region of Ukraine), are discussed. The authors provide a comprehensive review of existing literature on the assessment of groundwater vulnerability and then describe an improved methodology, which is developed based on integration of the methods of hydrogeological zonation and modeling of anomalously fast migration of radioactive contaminants from the land surface toward groundwater. This volume also includes the evaluation of the effect of preferential and episodic flow on transport of radionuclides toward theTable of ContentsAbstract v Introduction: Importance of Lessons Learned from Assessment of Groundwater Vulnerability at Chernobyl vii 1. Methods of Groundwater Vulnerability and Protectability Assessment 1 1.1. Method of hydrogeological zoning 2 1.2. Index methods 3 1.3. Parametric methods 9 1.4. Modeling methods 19 2. Chernobyl-Born Radionuclides in Geological Environment 25 3.Preferential Flow and Migration Zones in Geological Environment 39 3.1. State of problem study 39 3.2. PFMz classification and occurrence 41 3.3. Methodological approaches of PFMZ study 47 3.4. Indicators of PFMZ activity in depressions 53 3.5. Preliminary evaluations of PFMZ influence on upper groundwater 57 3.6. Practical importance of PFMZ 60 4. Methodology of Groundwater Vulnerability and Protectability Assessment 65 4.1. General consideration 65 4.2. Vulnerability and protectability assessment for upper groundwater (Unconfined Aquifer) 70 4.3. Vulnerability and protectability assessment for confined aquifers 73 5. Groundwater Vulnerability and Protectability to Chernobyl-Born Radionuclide 81 5.1. Upper groundwater 81 5.2. Confined aquifers 93 6. Summary 101 References 105 Index 115

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Book SynopsisAnalysis of Food Toxins and Toxicants consists of five sections, providing up-to-date descriptions of the analytical approaches used to detect a range of food toxins. Part I reviews the recent developments in analytical technology including sample pre-treatment and food additives. Part II covers the novel analysis of microbial and plant toxins including plant pyrrolizidine alkaloids. Part III focuses on marine toxins in fish and shellfish. Part IV discusses biogenic amines and common food toxicants, such as pesticides and heavy metals. Part V summarizes quality assurance and the recent developments in regulatory limits for toxins, toxicants and allergens, including discussions on laboratory accreditation and reference materials.Table of ContentsList of Contributors ix Foreword xvii Preface xix Volume 1 Section I: Recent Analytical Technology for Food Pathogens and Toxins 1 1 Omic Analysis of Protein and Peptide Toxins in Food 3Pasquale Ferranti, Chiara Nitride, and Monica Gallo 2 Biotechnology-Based Sensing Platforms for Detecting Foodborne Pathogens 37Akbar S. Khan 3 Review of Sample Treatments and the State-of-the-art of Analytical Techniques for Mycotoxins in Food 51Natalia Arroyo-Manzanares, José F. Huertas-Pérez, Ana M. García-Campaña, and Laura Gámiz-Gracia 4 Isothermal Nucleic Acid Amplification for Food Toxicity Analyses 103Luis A. Tortajada-Genaro, S. Santiago-Felipe, and Angel Maquieira Section II: Microbial and Plant Toxins 137 5 Determination of Mycotoxins in Food 139Muhammad Azhar Hayat Nawaz, Sajid Rauf, Akhtar Hayat, Gaelle Catanante, Rizwan Raza, and Jean-Louis Marty 6 Mycotoxins Detection in Asia 169Chee Wei Lim, Angela Li, and Joanne Sheot Harn Chan 7 Surface Plasmon Resonance Analysis of Food Toxins and Toxicants 195Valerija Vezočnik, Vesna Hodnik, and Gregor Anderluh 8 Food Poisoning Case Studies: Mushroom and Pufferfish Toxin Investigation 217Samuel Tsz-chun Cheung, Winnie Wing-yan Chum, Wai-yan Ha, Pui-kwan Chan, and Tin-yau Law 9 The Analysis of Pyrrolizidine Alkaloids in Honey 237Colin Crews and Till Beuerle 10 Pyrrolizidine Alkaloids in Food: Analytical, Toxicological and Health Considerations 267Caroline T. Griffin, Aisling Sheehan, Martin Danaher, and Ambrose Furey Volume 2 Section III: Marine Toxins 31911 The Determination of Marine Biotoxins in Seafood 321Arjen Gerssen and Mirjam D. Klijnstra 12 Detection of Paralytic Shellfish Poisoning Toxins in Molluscs 363Stephen Burrell and Andrew D. Turner 13 Determination of Saxitoxin and Tetrodotoxin in Fish 403Sara C. McGrath and Jonathan R. Deeds 14 Determination of Saxitoxin, Tetrodotoxin and Common Phycotoxins 431Luis M. Botana, Amparo Alfonso, Mercedes R. Vieytes, M. Carmen Louzao, Ana M. Botana, Carmen Vale, and Natalia Vilariño 15 Ciguatoxin Detection Methods and High-Throughput Assays 469Marco Inserra, Yelena Lavrukhina, Alun Jones, Richard J. Lewis, and Irina Vetter Section IV: Biogenic Amines and Common Food Toxicants 489 16 Detection of Histamine Based on Biosensor System 491Takeshi Ito 17 Flow-based Technology for Analysis of Food Pesticides 505Antonio Ruiz-Medina, Eulogio J. Llorent-Martínez, María Luisa Fernández-de Córdova, and Pilar Ortega-Barrales 18 Residual Pesticides and Heavy Metals Analysis in Food 537Sameeh A. Mansour 19 Microarray Methodologies for Pesticides and Other Toxins in Foods 571Xiaofeng Hu, Suiyan Ouyang, Peiwu Li, Qi Zhang, Xianfeng Ren, Huali Xie, and Zhaowei Zhang Section V: Quality Assurance and Regulatory Development 593 20 Accreditation, a Key Recognition for the Analysis of Food Toxins and Contaminants 595Wang-wah Wong 21 Quality Assurance and Control for Accurate Measurement of Food Toxins 621Alan Richards 22 Analytical Methods and Development of Reference Materials for Toxic Metals and Metal Species in Food and Dietary Supplements 639Stephen E. Long, Michael Ellisor, Frances Nilsen, Laura Wood, Karen Murphy, and Lee Yu 23 Overview of Toxins and Toxicants in Food and Their Regulatory Limits 679Peter A. Brown 24 Food Allergy: Managing Food Allergens 711Michael J. Walker and M. Hazel Gowland Index 743

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Book SynopsisRevised to reflect the most recent developments in food safety, the second edition of Food Safety for the 21st Century offers practitioners an authoritative text that contains the essentials of food safety management in the global supply chain. The authors noted experts in the field reveal how to design, implement and maintain a stellar food safety programme. The book contains industry best-practices that can help businesses to improve their systems and accelerate the application of world-class food safety systems. The authors outline the key food safety considerations for individuals, businesses and organisations involved in today's complex global food supply chains. The text contains the information needed to recognise food safety hazards, design safe products and processes and identify and manage effectively the necessary control mechanisms within the food business. The authors also include a detailed discussion of current issues and key challenges in the global fTable of ContentsAbout the Authors xvii Foreword xix Acknowledgements xxi Glossary of Terms and Acronyms xxiii How to Use This Book xxix Part I Food Safety Challenges in the 21st Century 1 1 Origin and Evolution of theModern Systemof Food Safety Management: HACCP and Prerequisite Programmes 3 1.1 Historical Perspectives 3 1.2 Origin and Evolution of HACCP 5 1.3 The Necessity of Prerequisite Programmes 11 1.4 Recent Regulatory Developments in the United States 11 1.5 The Future of HACCP 12 1.6 Conclusions 13 2 Lessons Learned from Food Safety Successes and Failures 15 2.1 Introduction 15 2.2 Benefits of Using HACCP: Lessons Learned from a Successful Implementation 15 2.3 Misconceptions or ‘Failure to Understand HACCP‘ 18 2.4 Barriers to Effective HACCP Use 20 2.5 Reasons for Failure 22 2.5.1 Lessons Learned from Major Food Safety Events 22 2.5.2 Commonly Observed Mistakes in the Implementation of HACCP and Management of Food Safety Programmes 28 2.6 Difficulties with Applying HACCP through the Entire Food Supply Chain 30 2.7 Roles and Responsibilities: Lessons Learned 32 2.7.1 Industry 33 2.7.2 Government 33 2.7.3 Retailers/Foodservice Establishments 34 2.7.4 Trade and Professional Associations 34 2.7.5 Academia 35 2.7.6 Consumers 35 2.7.7 The Media 36 2.7.8 Advocacy and Pressure Groups 36 2.7.9 Influencers and Experts 37 2.8 Conclusions 37 3 Food Safety Challenges in the Global Supply Chain 39 3.1 Introduction 39 3.2 Increased Complexity of the Global Supply Chain 41 3.2.1 Economic Factors 41 3.2.2 Environmental Factors 43 3.2.3 Social Factors 47 3.3 Food Safety Issues in Global Trade 49 3.3.1 Lack of Uniformity in Regulations and Requirements 52 3.3.2 Lack of Uniformity in Standards and Audit Requirements 54 3.4 Strategic Level Responses 55 3.4.1 Government Communications Systems 55 3.4.2 Global Food Safety Private Audit Standards and Schemes 56 3.4.3 Verification and Auditor Competency 57 3.4.4 Global Food Traceability Systems 57 3.4.5 Public-Private Partnerships 57 3.4.6 FoodWaste Reduction through Labelling Improvements 58 3.5 Tactical Level Responses 58 3.5.1 Supplier Audits and Approvals 59 3.5.2 Business Continuity Planning 60 3.5.3 Sharing Technology 60 3.5.4 Shared Training and Education Resources 61 3.5.5 Increased Awareness of Emerging Issues 61 3.6 Conclusions 61 4 The Future of Food Safety and HACCP in a ChangingWorld 63 4.1 Introduction 63 4.2 Food Safety Issues 64 4.2.1 Emerging Pathogens 64 4.2.2 Changes in Distribution of Pathogens 65 4.2.3 Additional Control Measures 65 4.2.4 Antibiotic-Resistant Pathogens 65 4.2.5 Allergens 65 4.2.6 Other Chemical Hazards 66 4.2.7 Physical Hazards 66 4.2.8 Economically Motivated Contamination 66 4.3 Technology Advancements: Processing and Laboratories 67 4.4 Food Safety Management 68 4.4.1 HACCP Preliminary Steps and Principles 68 4.4.2 Additions to Current Prerequisite Programmes (Codex Principles of Food Hygiene) 70 4.4.3 The Human Factor 70 4.4.4 Global Food Safety Assurance 74 4.5 Changes in Thinking/Policy Making 78 4.5.1 Food Safety Objectives 78 4.5.2 End Product Testing 79 4.5.3 Hazard Analysis versus Risk Assessment 79 4.6 Conclusions 80 Part II Foodborne Hazards and Their Control 81 5 Recognising Food Safety Hazards 83 5.1 Introduction 83 5.1.1 What is a Food Safety Hazard? 83 5.1.2 What is not a Food Safety Hazard? 83 5.2 Biological Hazards 84 5.2.1 Epidemiology and Morbidity Statistics 84 5.2.2 Characteristics of Foodborne Illnesses 86 5.2.3 Bacterial Pathogens: Special Considerations and Features 91 5.2.4 Viral Pathogens 94 5.2.5 Prions 96 5.2.6 Protozoan Parasites 98 5.2.7 ParasiticWorms 98 5.2.8 Biological Hazards, Zoonoses, and Food Chain Biosecurity Issues 98 5.3 Chemical Hazards 99 5.3.1 Allergens 99 5.3.2 Mycotoxins 100 5.3.3 Marine Foodborne Toxins 101 5.3.4 GeneticallyModified (GM) Foods 101 5.3.5 Antibiotics 102 5.3.6 Persistent Organic Pollutants (POP) 102 5.3.7 Heavy Metals 103 5.3.8 Chemicals Used in Food Processing Environments 104 5.3.9 Chemicals Used in Food Packaging Materials 104 5.3.10 Unanticipated Potential Chemical Hazards 104 5.4 Physical Hazards 105 5.4.1 Sources of Foreign Material 105 5.4.2 Injuries Associated with Physical Hazards 106 5.5 Conclusions 106 6 Designing Safety into a Food Product 107 6.1 Introduction 107 6.2 Formulation Intrinsic Control Factors 107 6.2.1 Water Activity 108 6.2.2 pH 110 6.2.3 Chemical Food Preservatives 111 6.2.4 Oxidation-Reduction Potential 115 6.2.5 Interactions between Preservative Factors 116 6.3 Use of Experimental Design and Analysis 118 6.3.1 Challenge Testing 118 6.3.2 Accelerated Shelf Life Testing 121 6.3.3 Predictive Microbiology and Mathematical Modelling 122 6.3.4 Theory versus Reality 123 6.4 Ingredient Considerations 123 6.4.1 High-Risk Ingredients 124 6.4.2 Novel Ingredients 126 6.5 Considering the ‘Unintended’ Use 126 6.6 Conclusions 127 7 Designing a Safe Food Process 129 7.1 Introduction 129 7.2 Process Control of Microbiological Hazards 130 7.2.1 Destruction of Microorganisms 130 7.2.2 Prevention of Microbial Growth 137 7.2.3 Prevention of Contamination 140 7.3 Process Control of Chemical Hazards 143 7.3.1 Allergen Control 143 7.3.2 White Powder Control 144 7.3.3 Cleaning and Maintenance Chemicals 144 7.4 Process Control of Physical Hazards 145 7.4.1 Exclusion Techniques 145 7.4.2 Removal Techniques 146 7.4.3 Detection Techniques 147 7.5 Conclusion 147 Part III Systematic Food Safety Management in Practice 149 8 Overview of aWorld-Class Food Safety Programme 151 8.1 Introduction 151 8.2 Preliminary Concepts and Definitions 152 8.2.1 The EvolvingWorld-Class Food Safety Programme 152 8.2.2 Key Definitions of Relevance toWorld-Class Food Safety Programmes 153 8.3 World-Class Food Safety Programmes: System Elements 155 8.3.1 Safe Product/Process Design 155 8.3.2 Prerequisite Programmes 156 8.3.3 HACCP 156 8.3.4 Food Fraud and Food Defence 156 8.4 World-Class Food Safety Programmes: Fundamental Supporting Elements 157 8.4.1 Essential Management Practices 157 8.4.2 Food Safety Culture 158 8.5 World-Class Food Safety Programmes: Further Supporting Elements 158 8.6 World-Class Food Safety Programmes in the Global Food Supply Chain 159 8.7 Continuous Improvement of theWorld-Class Food Safety Programme 160 8.8 Conclusions 161 9 Building the Foundations of a World-Class Food Safety Management Programme: Essential Steps and Practices 163 9.1 Introduction 163 9.2 Essential Management Practices 165 9.2.1 Management Commitment and its Role in Food Safety Culture 165 9.2.2 Assignment of Roles and Responsibilities 166 9.2.3 Training and Education 166 9.2.4 Resource Management 172 9.2.5 Documentation 173 9.2.6 Supplier/Customer Partnerships 173 9.2.7 Continuous Improvement 173 9.3 Food Safety Culture 174 9.4 Preparation Activities for Food Safety Programmes 175 9.4.1 Preparing a Project Plan 175 9.4.2 Structure the HACCP Programme 176 9.4.3 Carry out a Gap Assessment 176 9.5 Prioritisation of Corrective Actions 183 9.6 Conclusions 185 10 Formalised Prerequisite Programmes in Practice 187 10.1 Introduction 187 10.2 Prerequisite Definitions and Standards 188 10.3 Prerequisite Programmes: The Essentials 189 10.3.1 Primary Production 189 10.3.2 Establishment: Design and Facilities 192 10.3.3 Control of Operation 194 10.3.4 Establishment: Maintenance and Sanitation 198 10.3.5 Establishment: Personal Hygiene 206 10.3.6 Transportation 207 10.3.7 Product Information and Consumer Awareness 207 10.3.8 Training 209 10.4 Prerequisite Programmes and Operational Prerequisites 210 10.5 Validation and Verification of Prerequisite Programmes 212 10.6 Further Reading on Prerequisite Programmes 213 10.7 Conclusions 214 11 Conducting a Product Safety Assessment 215 11.1 Introduction 215 11.1.1 Who Is Involved in Product Safety Assessments? 215 11.1.2 Timing of the Product Safety Assessment Process 217 11.1.3 Product Safety Assessment Process 217 11.2 Training for Research and Development Personnel 218 11.3 Example of a Product Safety Assessment 219 11.3.1 Process Flow Diagram 221 11.4 Conclusions and Principles for Effective Product Safety Assessment 223 12 Developing and Implementing a HACCP Plan 225 12.1 Introduction 225 12.2 Preliminary Concepts 226 12.2.1 HACCP Principles 226 12.2.2 The HACCP Plan and Documentation Approaches 226 12.2.3 HACCP Application Process 228 12.2.4 Codex Logic Sequence 228 12.3 Applying the Codex Logic Sequence to Develop a HACCP Plan 230 12.3.1 HACCP Study Terms of Reference and Scope 230 12.3.2 Codex Logic Sequence Step 1: HACCP Teams 230 12.3.3 Codex Logic Sequence Step 2: Product/Process Descriptions 232 12.3.4 Codex Logic Sequence Step 3: Identify Intended Use 233 12.3.5 Codex Logic Sequence Step 4: Construct Process Flow Diagram(s) 234 12.3.6 Codex Logic Sequence Step 5: On-Site Confirmation of Flow Diagram 237 12.3.7 Codex Logic Sequence Step 6: List All Potential Hazards, Conduct a Hazard Analysis, and Consider Control Measures (Apply HACCP Principle 1) 238 12.3.8 Codex Logic Sequence Step 7: Determine CCPs (HACCP Principle 2) 249 12.3.9 Codex Logic Sequence Step 8: Establish Critical Limits for each CCP (HACCP Principle 3) 252 12.3.10 Codex Logic Sequence Step 9: Establish a Monitoring System for each CCP (HACCP Principle 4) 252 12.3.11 Codex Logic Sequence Step 10: Establish Corrective Actions (HACCP Principle 5) 255 12.3.12 Codex Logic Sequence Step 11: Establish Verification Procedures (HACCP Principle 6) 255 12.3.13 Codex Logic Sequence Step 12: Establish Documentation and RecordKeeping (HACCP Principle 7) 257 12.4 Implementing a HACCP Plan 257 12.4.1 Activities for Implementation of a HACCP Plan 257 12.4.2 The Validated HACCP Plan 258 12.4.3 Implementation Action Planning 259 12.4.4 Training 259 12.4.5 CCP Management Systems 261 12.4.6 HACCP Required Activities 262 12.4.7 Verification of Implementation 263 12.4.8 Handover to Operations Staff 263 12.4.9 Considerations for Implementing Updates and Changes to an Existing HACCP System 263 12.5 Conclusions 264 13 Food Fraud and Food Defence 265 13.1 Introduction 265 13.2 Essential Definitions 265 13.2.1 Food Fraud 266 13.2.2 Food Terrorism 266 13.2.3 Food Defence 267 13.2.4 Food Protection 267 13.3 Food Fraud 268 13.3.1 The Food Fraud Problem 268 13.3.2 Learning from Examples of Food Fraud 269 13.4 Food Terrorism 275 13.4.1 Food Terrorism Examples 275 13.5 Food Defence 276 13.5.1 Food Fraud Prediction 276 13.5.2 Practical Food Defence Strategies 279 13.6 Conclusion 282 14 Maintaining and Improving a Food Safety Programme 283 14.1 Introduction 283 14.2 What Is Food Safety Programme Maintenance? 283 14.3 Responsibility for Food Safety Programme Maintenance 285 14.4 Maintenance of Prerequisite Programme Elements 285 14.5 Maintenance of HACCP System Elements 286 14.5.1 HACCP Verification Activities 286 14.5.2 HACCP Maintenance Activities 287 14.6 Maintenance of Food Fraud and Food Defence Systems 288 14.7 Use of Audit for Successful Food Safety System Maintenance 289 14.7.1 Audit Definitions 289 14.7.2 The Auditor and Audit Skills 290 14.7.3 Audit Checklists 292 14.7.4 Use of External Audit and Certification Schemes as Part of Food Safety Programme Maintenance 293 14.8 Incident Management 294 14.9 Conclusions 294 15 Food Safety Culture: Evaluate, Map, and Mature 297Lone Jespersen, Ph.D. 15.1 Introduction 297 15.1.1 Food Safety Culture: Accepted Assumptions, Not Malicious Intent 297 15.1.2 Essential Definitions 298 15.2 Supply Chain and Critical Food Safety Behaviours 298 15.2.1 Dimensions of Food Safety Culture 300 15.2.2 Follow the Leafy Greens… 300 15.3 Organisational Culture and Food Safety 302 15.4 Evaluate and Map Food Safety Maturity 303 15.4.1 Map to Food Safety Maturity 303 15.4.2 Walking the Food Safety Talk 303 15.4.3 Importance of Using Multiple Methods to Evaluate Food Safety Culture 307 15.5 Tactics to Mature Food Safety Culture 309 15.6 Conclusions 310 Part IV Food Safety Management in Practice: Current Issues and Challenges in Areas of the Global Food Supply Chain 313 16 Food Safety in Agriculture: Determining Farm-Derived Food Safety Risk 315Louise Manning and Pieternel Luning 16.1 Introduction 315 16.2 Notions of Food Quality and Food Safety 315 16.3 Value as a Food Attribute in Primary Agriculture 316 16.3.1 Case Study 1: BSE and the United Kingdom 318 16.4 Uncertainty and Ambiguity Affecting Risk Perceptions and Decisions 319 16.4.1 Case Study 2: Red Tractor Standards 320 16.5 Risks Inherent to Farmers’ Context Characteristics 320 16.5.1 Case Study 3: Quality Egg 325 16.6 Supply Chain Governance and Food Safety 326 16.7 Risk Mitigation at Farm Level 327 16.8 Conclusion 329 17 Helping to Overcome Food Safety Challenges in Developing Markets 331 17.1 Introduction 331 17.2 Sri Lanka Hygiene and Management Systems Development Projects 332 17.2.1 Context 332 17.2.2 Support for the Development and Implementation of Environmental Management Plans 332 17.2.3 A Manufacturer of Dairy-Based Curd and Popsicles 334 17.2.4 A Small Packaging Manufacturer in Sri Lanka 336 17.2.5 A Small Dairy (Ice-Cream) Processor 337 17.2.6 A Coconut Processor in Sri Lanka 339 17.2.7 Quality and GMP Training in Sri Lanka 340 17.3 Rwanda Dairy Development Projects 342 17.3.1 Context 342 17.3.2 A Growing Dairy Company in Northern Rwanda 342 17.3.3 Yogurt and Fermented Milk Processor 343 17.4 Bangladesh Milk Supply Chain Development Project 346 17.4.1 Context 346 17.4.2 Project 347 17.4.3 Insights and Lessons Learned 347 17.5 Key Points Learned as Assignees to a Less-Developed Country 348 17.6 Kenya Development Project: InternationalWater and Health Alliance (IWHA) 349 17.6.1 Context 349 17.6.2 Challenges in Low-Income Countries 350 17.6.3 Addressing theWater-Testing Challenge in Low-Income Countries 351 17.6.4 Accomplishments 352 17.7 Conclusions 353 18 Consumer Food Safety 355 18.1 Introduction 355 18.2 Potential Hazards 356 18.3 Potential Control Measures 357 18.3.1 SafeWater and Raw Materials 357 18.3.2 Refrigeration 358 18.3.3 Heating (Cooking) 358 18.3.4 Separation, Cleaning, Sanitation, and Personal Hygiene 359 18.4 Potential CCPs and Preventive Controls (PCs) in the Home 360 18.5 Consumer Education 360 18.6 Good Consumer Practices (GCPs) 361 18.7 Case Studies 364 18.7.1 Fictional Case Study: Microbiological Food Safety 364 18.7.2 Real Life Case Study: Allergen Food Safety 366 18.8 Conclusion 369 19 Food Safety in Foodservice Operations 371 19.1 Introduction 371 19.2 Mapping the Foodservice Landscape 372 19.3 Quick-Service Restaurants 376 19.3.1 Challenges in Quick-Service Chain Restaurants 376 19.3.2 Ongoing Control of Food Safety in Quick-Serve Restaurants 378 19.4 Institutional Catering 380 19.5 Foodservice SMEs: Owner-led Restaurants, Cafés, and Snack Bars 381 19.6 Fine Dining, Star Ratings, and Celebrity Chefs 383 19.7 Mobile Foodservice: Market Stalls, Food Vans/Trucks, Festivals, and Pop-Up Facilities 385 19.8 Conclusions 386 Epilogue 387 References 391 Appendix 1 Manufacturing HACCP Case Study 417 Appendix 2 Global Food Safety Resources 439 Index 443

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Book SynopsisScience is built on trust. The assumption is that scientists will conduct their work with integrity, honesty, and a strict adherence to scientific protocols. Written by geoscientists for geoscientists, Scientific Integrity and Ethics in the Geosciencesacquaints readers with the fundamental principles of scientific ethics and shows how they apply to everyday work in the classroom, laboratory, and field. Resources are provided throughout to help discuss and implement principles of scientific integrity and ethics. Volume highlights include: Examples of international and national codes and policiesExploration of the role of professional societies in scientific integrity and ethicsReferences to scientific integrity and ethics in publications and research dataDiscussion of science integrity, ethics, and geoethics in educationExtensive coverage of data applications Scientific Integrity and Ethics in the Geosciencesis a valuable resource for students, faculty, instructors, and scientists inTable of ContentsTable of Contents Contributors Preface Acknowledgements Section I. Examples of Recently Developed International and National Codes and Policies Chapter 1. The Origin, Objectives and Evolution of the World Conferences on Research IntegrityNicholas H. Steneck, Tony Mayer, Melissa S. Anderson, Sabine Kleinert Chapter 2. Fostering Integrity in Research: Overview of the National Academies of Sciences, Engineering, and Medicine ReportThomas Arrison and Robert Nerem Chapter 3. Scientific Integrity – Recent Department of Interior Policies, Codes, and their ImplementationAlan Thornhill and Rick Coleman Section II. The Role of Geoscience Professional Societies in Scientific Integrity and Ethics Chapter 4. The American Geosciences Institute Guidelines for Ethical Professional ConductMaeve A. Boland and David W. Mogk Chapter 5. American Geophysical Union Adopts and Implements A New Scientific Integrity and Professional Ethics PolicyMichael McPhaden Chapter 6. The National Association of State Boards of Geology (ASBOG®) Involvement in Geoscience Professional EthicsJohn Williams Chapter 7. Brief History and Application of Enforceable Professional Geoscience Ethics CodesDavid M. Abbott, Jr. Section III. Scientific Integrity and Ethics in Publications and Data Chapter 8. The New Landscape of Ethics and Integrity in Scholarly Publishing, Brooks Hanson Chapter 9. Scientific Integrity and Ethical Considerations for the Research Data Life CycleLinda C. Gundersen Section IV. Ethical Values and Geoethics Chapter 10. Understanding Coupled Ethical-Epistemic Issues Relevant to Climate Modeling and Decision Support ScienceNancy Tuana Chapter 11. The Emerging Field of GeoethicsPeter Bobrowsky, Vincent S. Cronin, Giuseppe Di Capua, Susan W. Kieffer, Silvia Peppoloni Section V. Scientific Integrity, Ethics, and Geoethics in Education Chapter 12. Experiential Ethics Education Vance S. Martin and Donna C. Tonini Chapter 13. Teaching Geoethics Across the Geoscience Curriculum: Why, When, What, How, and Where? David W. Mogk, John W. Geissman, and Monica Z. Bruckner Chapter 14. Facilitating a Geoscience Student's Ethical DevelopmentVincent S. Cronin Appendix A. Case Studies for Science Integrity and Geoethics Practice Appendix B. Resources and References for Scientific Integrity, Ethics, and Geoethics

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Book SynopsisTable of ContentsPreface xiii List of Contributors xvii 1 The Multiple Roles of Various Reactive Oxygen Species (ROS) in Photosynthetic Organisms 1 Franz-Josef Schmitt, Vladimir D. Kreslavski, Sergey K. Zharmukhamedov, Th omas Friedrich, Gernot Renger, Dmitry A. Los, Vladimir V. Kuznetsov and Suleyman I. Allakhverdiev 1.1 Introduction 2 1.2 Generation, Decay and Deleterious Action of ROS 7 1.3 Non-photochemical Quenching in Plants and Cyanobacteria 15 1.4 Monitoring of ROS 19 1.4.1 Exogenous ROS Sensors 20 1.4.2 Genetically Encoded ROS Sensors 25 1.4.3 Chromophore-Assisted Laser Inactivation (CALI) 28 1.5 Signaling Role of ROS 30 1.5.1 Signaling by Superoxide and Hydrogen Peroxide in Cyanobacteria 37 1.5.2 Signaling by 1ΔgO2 and Hydrogen Peroxide in Eukaryotic Cells and Plants 41 1.6 Light-Induced ROS and Cell Redox Control and Interaction with the Nuclear Gene Expression 45 1.7 Second Messengers and Signaling Molecules in H2O2 Signaling Chains and (Nonlinear) Networking 49 1.8 Concluding Remarks and Future Perspectives 55 Acknowledgments 56 Abbreviations 57 References 58 2 Photooxidation of Mn-bicarbonate Complexes by Reaction Centers of Purple Bacteria as a Possible Stage in the Evolutionary Origin of the Water-Oxidizing Complex of Photosystem II 85 Vasily V. Terentyev, Andrey A. Khorobrykh and Vyacheslav V. Klimov 2.1 Introduction 86 2.2 Appearance of Photosynthesis 87 2.3 Classification of Photosynthetic Bacteria 88 2.4 Mechanism of Light Energy Transformation during Photosynthesis 90 2.5 The Water-oxidizing Complex of Photosystem II 92 2.6 Localization and Function of Bicarbonate in Photosystem II 95 2.7 Composition and Electrochemical Properties of Mn2+-bicarbonate Complexes 100 2.8 A Possible Role of Mn2+-bicarbonate Complexes for the Origin and Evolution of the Inorganic Core of the Water-oxidizing Complex of Photosystem II 104 2.9 Investigation of Redox Interaction Between Mn2+ and Type II Reaction Centers of Anoxygenic Photosynthetic Bacteria in the Presence of Bicarbonate 107 2.10 Influence of the Redox Potential of the Р+/Р Pair and Steric Accessibility of P+ on Electron Donation from Mn2+ to Type II Reaction Centers from Anoxygenic Photosynthetic Bacteria in the Presence of Bicarbonate 113 2.11 Conclusions 121 Acknowledgments 122 Abbreviations 122 References 123 3 Hydrogen Metabolism in Microalgae 133 Anatoly A. Tsygankov, Azat Abdullatypov 3.1 Introduction 133 3.2 Physiology of Hydrogen Metabolism 134 3.3 Hydrogenases 136 3.4 Ferredoxin 139 Contents ix 3.5 Nutrient Deprivation 140 3.6 Physiological Significance of Light-Dependent Hydrogen Production 146 3.7 Practical Importance of Hydrogen Photoproduction 147 3.8 Towards Practical Application of Microalgal Hydrogen Production 151 3.8.1 Hydrogenase Modifications 151 3.8.2 Elimination of Routes Competitive to H2 production 152 3.8.3 The Role of Transmembrane Gradient of the Potential 153 3.9 Conclusion 154 Acknowledgements 154 Abbreviations 154 References 155 4 The Structure and Regulation of Chloroplast ATP Synthase 163 Alexander N. Malyan 4.1 Introduction 163 4.2 The Structure and Functional Basics of Chloroplast ATP Synthase 164 4.3 The Thiol-Dependent Mechanism of Chloroplast ATP Synthase Regulation 166 4.4 The Nucleotide-Dependent Mechanism of Chloroplast ATP Synthase Regulation 167 4.5 The Properties and the Role of Chloroplast ATPase Noncatalytic Sites 168 4.6 Conclusion 173 Abbreviations 173 References 173 5 Structural and Functional Organization of the Pigment-Protein Complexes of the Photosystems in Mutant Cells of Green Algae and Higher Plants 179 Vladimir G. Ladygin 5.1 Introduction 180 5.2 The Mutants as Model Objects 182 5.2.1 Effects of Mutagenic Agents 182 5.2.2 Obtaining Mutants 182 5.3 The Chlorophyll-Protein Complexes 185 5.3.1 Pigment Content of Individual Complexes 185 5.3.2 Identification of Chlorophyll-Protein Complexes 188 5.3.3 Polypeptide Composition of Individual Complexes 188 5.4 Spectral Properties of Native Chlorophyll-Protein Complexes 189 5.4.1 Spectral Forms of Chlorophyll in Native Complexes 189 5.4.2 Fluorescence Spectra of the Chlorophyll in Native Complexes 190 5.5 Functional Organization of the Photosystems 195 5.5.1 Photosynthetic Activity 195 5.5.2 The Value of Photosynthetic Unit 197 5.5.3 The Number of the Reaction Centers of Photosystems 197 5.6 Structural Localization of the Photosystem in Chloroplast Thylakoids 201 5.6.1 Spatial Localization of the Photosystem in Thylakoid Membranes 201 5.6.2 Localization of Carotenoids in Pigment-Protein Complexes of the Photosystems 210 5.7 Molecular Organization of the Complexes of Photosystem I and II 213 5.7.1 Structure of the Complex of Photosystem I 213 5.7.2 Structure of the Complex of Photosystem II 217 5.7.3 The Core Complex of Photosystem II 220 Abbreviations 222 References 222 6 Photosynthetic Carbon Metabolism: Strategy of Adaptation over Evolutionary History 233 Irina R. Fomina and Karl Y. Biel 6.1 Introduction 234 6.2 Photosynthesis in Prokaryotes 235 6.2.1 What Was the First Autotroph on Our Planet? 235 6.2.2 Green Non-Sulfur Bacteria, Green Sulfur Bacteria, Heliobacteria: from the Archaic Way of Carbon Reduction to the Arnon-Buchanan Cycle 240 6.2.3 Purple Bacteria: The Emergence of the Reductive Pentose Phosphate Cycle – Biochemical “Add-ons” to the Arnon-Buchanan Cycle 245 6.2.4 Cyanobacteria: The Reductive Pentose Phosphate Cycle Becomes the Main Path of Carbon in Photosynthesis 247 6.2.5 The Main Stages of Development of Photosynthetic Carbon Metabolism in Prokaryotes 249 6.3 Photosynthesis in Eukaryotes 250 6.3.1 C3 plants: Photosynthesis via the Reductive Pentose Phosphate or Benson-Bassham-Calvin cycle 250 6.3.2 C4 plants: Cooperative Photosynthesis 254 6.3.3 CAM-plants: Crassulacean Acid Metabolism 259 6.3.4 C4-CAM plants: Cooperation of the Second Order 262 6.4 About Compartmentalization and Cooperation between the Reduction and Oxidation Reactions in Photosynthetic Cells 264 6.5 Examples of Physiological Adaptation of Photosynthetic Carbon Metabolism to Environmental Factors at the Cellular, Tissue, and Organism Levels 266 6.5.1 Cooperative Relationship of Phototrophic Endosymbionts and Heterotrophic Host Cells with Carbon Assimilation 266 6.5.2 The Protective Role of Leaf Tissues in Illuminated Plants 283 6.6 General Conclusion 293 Acknowledgements 297 Abbreviations 297 References 298 7 Adaptive Changes of Photosynthetic Apparatus to Higher CO2 Concentration 327 Anatoly A. Kosobryukhov 7.1 Introduction 327 7.2 Higher Concentration of CO2 and Its Effect on the Plants: History of the Question 328 7.3 Influence of the Higher CO2 Concentration on the Growth and Productivity of the Plants 329 7.4 Photosynthesis at Short-Term Increase of CO2 Concentration 331 7.5 Adaptive Changes of Photosynthetic Apparatus at Long-Term Effect of the Higher CO2 Concentration 332 7.6 The Role of Carbohydrate Metabolism in Regulation of the Photosynthetic Apparatus Activity at Increased CO2 Concentration 334 7.7 Soluble Sugars in Leaves and Other Plant Organs 337 7.8 Dependence of Photosynthetic Rate on Environmental Factors and its Regulation 338 Abbreviations 344 References 344 8 Photosynthetic Machinery Response to Low Temperature Stress 355 Evgenia F. Markovskaya, Anatoly A. Kosobryukhov and Vladimir D. Kreslavski 8.1 Mechanisms of Plant Adaptation to Low Temperature 355 8.2 Role of Reactive Oxygen Species 357 8.3 Plant Cell Membranes and Their Role in Response to Low Temperature 358 8.4 Hormonal Response to the Temperature 362 8.5 Phytochrome as a Receptor of Low Temperature 362 8.6 Carbohydrate Function under Low Temperature 364 8.7 Protein Changes 365 8.8 Cold Stress and Photoinhibition 367 8.9 Molecular Mechanisms of Plants’ Response to Low Temperatures 368 8.10 Concluding Remarks and Future Perspectives 370 Acknowledgments 370 References 370 Index 383

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Book SynopsisWhat do we mean by the tropics? The weather and the climates it produces across the tropical zone are significantly different from those experienced by the people living in higher latitudes, so forecasters across Europe and much of North America are unfamiliar with its effects.Table of ContentsAbout the Author xi Preface xii Acknowledgements xiii 1 Setting the Scene 1 1.1 Introduction 1 1.2 What do we mean by ‘the tropics’? 2 1.3 The geography of the tropics 5 1.4 The tropical troposphere 5 1.5 Climate and population in the tropics 7 1.6 Question 8 2 The Energy Balance and the Dynamics of Weather in the Tropics 9 2.1 The tropical ‘heat engine’ 9 2.2 Absorption, reflection and apparent solar elevation 9 2.3 Emission from the surface 11 2.4 The radiation balance and the tropical zone 12 2.5 The dynamics of weather systems in the tropics 14 2.6 Questions 15 3 Winds, Temperature and Weather in the Tropical Zone 16 3.1 Winds 16 3.2 Temperature 20 3.3 The weather patterns and climates of the tropics 21 3.4 Clouds and fog in the tropics 23 3.5 Questions 28 4 The Subtropical Jet Streams 29 4.1 The formation of jet streams at the margins of the tropics 29 4.2 Weather associated with the subtropical jet stream 31 4.3 Folds and bifurcations in the flow 33 4.4 Clear‐air turbulence 34 4.5 Questions 36 5 Synoptic‐scale Weather Systems 38 5.1 Introduction 38 5.2 Convection in the tropics 38 5.3 The inter‐tropical convergence zone 42 5.4 The depth of convective clouds 47 5.5 Layer clouds and shallow convection 48 5.6 The effects of heavy rainfall in the tropics 48 5.7 Atmospheric teleconnections 49 5.8 Questions 49 6 Climate, Flora and Fauna 51 6.1 The relationship of climate to plants and animals 51 6.2 Tropical rainforest 51 6.3 Seasonal tropical forest 57 6.4 The savannas 58 6.5 Tropical deserts and scrublands 60 6.6 Mountain climates 61 6.7 Tropical oceans and coasts 65 6.8 Climatic variability 67 6.9 Questions 68 7 Dry Environments 69 7.1 Background 69 7.2 Wind and weather in the deserts 70 7.3 Fog and low cloud 78 7.4 Severe weather in the dry tropics 79 7.5 The effects of desert weather 82 7.6 Settlement and the over‐use of scarce water supplies 84 7.7 Questions 85 8 Monsoons 86 8.1 Introduction 86 8.2 The summer monsoon over southern Asia 86 8.3 The summer monsoon over East Asia 89 8.4 Variations of rainfall in the Asian summer monsoon 93 8.5 The Asian winter monsoon 94 8.6 The West African summer monsoon 96 8.7 The West African winter monsoon 103 8.8 Rainfall and the monsoons in East Africa 104 8.9 The South American–Caribbean ‘monsoons’ 106 8.10 The Australian summer monsoon 107 8.11 Variable broad‐scale factors affecting the monsoons 111 8.12 Questions 112 9 Tropical Revolving Storms 114 9.1 Broad‐scale convection and the development of tropical storms 114 9.2 Tropical storm development and decline 114 9.3 The effects of tropical revolving storms 120 9.4 Storm tracks in the Pacific Ocean 124 9.5 The formation and tracks of hurricanes in the North Atlantic–Caribbean 125 9.6 Tropical cyclones in the Indian Ocean 126 9.7 Tropical revolving storms in the south‐west Pacific 127 9.8 Variability in the development of tropical storms 128 9.9 Extra‐tropical transition 132 9.10 Conclusion 132 9.11 Questions 132 10 Mesoscale Weather Systems 134 10.1 Introduction 134 10.2 Mesoscale convective complexes 134 10.3 Sea‐ and land‐breeze convergence zones 135 10.4 Easterly waves and squall lines 139 10.5 Mesoscale convective systems in northern India 143 10.6 Depressions in north‐west India, north Pakistan and Afghanistan 144 10.7 Cross‐equatorial flows 144 10.8 Mesoscale convective systems in the Gulf of Guinea 145 10.9 Local convection 145 10.10 Extra‐tropical interaction with moist tropical air masses 148 10.11 Conclusion 148 10.12 Questions 149 11 Forecasting Clouds and Weather 150 11.1 Background 150 11.2 Distribution of significant cloud 150 11.3 The effect of high ground as an elevated heat source 155 11.4 Tropical upper‐tropospheric troughs 157 11.5 Effects of severe convection on aviation 159 11.6 Questions 162 12 The Variability of Weather and Climate Change in the Tropics 164 12.1 Introduction 164 12.2 El Niño–La Niña 164 12.3 The Madden–Julian Oscillation 166 12.4 The quasi‐biennial oscillation 168 12.5 A discussion of anthropogenic climate change 171 12.6 How is climate likely to change in the tropical zone? 172 12.7 Modelling climate change 175 12.8 Conclusion 176 12.9 Questions 176 13 Tropical Agriculture 177 13.1 Agricultural productivity and tropical environments 177 13.2 Agriculture in the humid tropics and the effects of forest clearance 178 13.3 Agriculture in the savannas 180 13.4 Dry‐land agriculture 180 13.5 Weather and locust swarms 182 13.6 The effects of agriculture in the tropics 183 13.7 Agriculture and climate change 185 13.8 Question 186 14 The Importance of the Tropical Ozone Layer 187 14.1 Background 187 14.2 The role of the tropics in replenishing the extra‐tropical stratospheric ozone 191 14.3 The effect of ‘global warming’ on stratospheric ozone destruction in the tropics 193 14.4 The effects of exposure to short‐wave radiation 194 14.5 Current state of the stratospheric ozone layer 195 14.6 Question 195 15 Remote Sensing of Tropical Weather 196 15.1 Background 196 15.2 Satellite remote sensing 196 15.3 Precipitation 197 15.4 Wind profilers 199 15.5 Thunderstorm observation 199 15.6 Monitoring surface cover, fires and volcanic eruptions 199 15.7 Question 202 16 Tropical Weather and Health 203 16.1 Introduction 203 16.2 The effects of tropical sunshine and warmth 203 16.3 Lifted dust and its effects on health 203 16.4 Industrial and smoke pollution 204 16.5 Parasitic and infectious diseases 204 16.6 Response of the meteorological community 206 16.7 Questions 206 17 Conclusions and a Look to the Future 207 17.1 A summary 207 17.2 Forecasting the weather 208 17.3 Questions 208 Appendix 1 Observations from the Tropics 209 Appendix 2 Named Winds of the Tropics 213 Appendix 3 An Introduction to Cloud Types, Cloud Species and Precipitation 234 A3.1 Introduction 234 A3.2 The high clouds 235 A3.3 The medium‐level clouds 235 A3.4 The low clouds 236 A3.5 Cloud species and varieties 239 Appendix 4 An Introduction to Meteorological Diagrams, Stability, Instability and Aviation Weather Charts 246 A4.1 Temperature–pressure graphs 246 A4.2 Stability and instability 248 A4.3 Aviation‐significant weather charts 248 Appendix 5 Snow in the Desert: A Case Study 250 A5.1 Introduction 250 A5.2 Development of a depression over the desert 250 A5.3 The weather features associated with the upper low 253 A5.4 Summary 256 Appendix 6 A Climatic Summary for Tropical Countries and States 257 Appendix 7 Two Easterly Waves in West Africa in Summer 2009: A Case Study 265 A7.1 Introduction 265 A7.2 The wave of 28 August to 5 September 2009 266 A7.3 The wave of 2–11 September 2009 and the development of Hurricane Fred 270 A7.4 A model for the development of squall lines in the Sahel 272 A7.5 Conclusion 277 References 280 Glossary 293 Index 303

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Book SynopsisIn the 21st Century, the world will see an unprecedented migration of people moving from rural to urban areas. With global demand for water projected to outstrip supply in the coming decades, cities will likely face water insecurity as a result of climate change and the various impacts of urbanisation. Traditionally, urban water managers have relied on large-scale, supply-side infrastructural projects to meet increased demands for water; however, these projects are environmentally, economically and politically costly. Urban Water Security argues that cities need to transition from supply-side to demand-side management to achieve urban water security. This book provides readers with a series of in-depth case studies of leading developed cities, of differing climates, incomes and lifestyles from around the world, that have used demand management tools to modify the attitudes and behaviour of water users in an attempt to achieve urban water security. Urban Water Security will be of parTable of ContentsSeries Editor Foreword – Challenges in Water Management xvii Acknowledgements xix Introduction 1 1 Water 101 5 Introduction 5 1.1 What is water? 5 1.2 Hydrological cycle 6 1.3 Natural variations to water quantity 11 1.4 Natural variations to water quality 14 1.5 Impacts of urbanisation on water resources 17 1.6 Water and wastewater treatment processes 20 Notes 22 2 What is urban water security? 25 Introduction 25 2.1 Non]climatic challenges to achieving urban water security 26 2.2 Climatic challenges to achieving urban water security 30 2.3 Reducing non]climatic and climatic risks to urban water security 32 Notes 34 3 Managing water sustainably to achieve urban water security 37 Introduction 37 3.1 What is sustainability? 37 3.2 What does sustainability mean in urban water management? 42 3.3 Sustainable water resources management frameworks 45 3.4 Framework for managing urban water sustainably: Integrated urban water management 49 3.5 Other frameworks for managing urban water sustainably 52 Notes 53 4 Demand management to achieve urban water security 60 Introduction 60 4.1 Purpose of demand management 60 4.2 Regulatory and technological demand management instruments 62 4.3 Communication and information demand management instruments 75 4.4. Portfolio of demand management tools 78 Notes 79 5 Transitions 86 Introduction 86 5.1 What is a transition? 86 5.2 Operationalisation of transitions 91 5.3 Diffusion mechanisms 93 5.4 Transition management 95 Notes 97 6 Transitions towards managing natural resources and water 105 Introduction 105 6.1 Transitions in natural resource management 106 6.2 What is a transition in urban water management? 109 6.3 Operationalising transitions in third]order scarcity 112 6.4 Barriers to transitions towards urban water security 115 Notes 121 7 Amsterdam transitioning towards urban water security 136 Introduction 136 7.1 Brief company background 136 7.2 Water supply and water consumption 137 7.3 Strategic vision: Amsterdam’s Definitely Sustainable 2011–2014 138 7.4 Drivers of water security 138 7.5 Regulatory and technological demand management tools to achieve urban water security 141 7.6 Communication and information demand management tools to achieve urban water security 144 7.7 Case study SWOT analysis 146 7.8 Transitioning towards urban water security summary 149 Notes 150 8 Berlin transitioning towards urban water security 151 Introduction 151 8.1 Brief company background 151 8.2 Water supply and water consumption 152 8.3 Strategic vision: Using water wisely 153 8.4 Drivers of water security 153 8.5 Regulatory and technological demand management tools to achieve urban water security 155 8.6 Communication and information demand management tools to achieve urban water security 159 8.7 Case study SWOT analysis 160 8.8 Transitioning towards urban water security summary 163 Notes 164 9 Copenhagen transitioning towards urban water security 165 Introduction 165 9.1 Brief company background 165 9.2 Water supply and water consumption 166 9.3 Strategic vision: Water supply plan (2012–2016) 166 9.4 Drivers of water security 167 9.5 Regulatory and technological demand management tools to achieve urban water security 169 9.6 Communication and information demand management tools to achieve urban water security 174 9.7 Case study SWOT analysis 175 9.8 Transitioning towards urban water security summary 178 Notes 179 10 Denver transitioning towards urban water security 180 Introduction 180 10.1 Brief company background 180 10.2 Water supply and water consumption 181 10.3 Strategic vision: Denver Water’s 22 percent water target 183 10.4 Drivers of water security 183 10.5 Regulatory and technological demand management tools to achieve urban water security 185 10.6 Communication and information demand management tools to achieve urban water security 191 10.7 Case study SWOT analysis 194 10.8 Transitioning towards urban water security summary 196 Notes 198 11 Hamburg transitioning towards urban water security 199 Introduction 199 11.1 Brief company background 199 11.2 Water supply and water consumption 200 11.3 Strategic vision: The HAMBURG WATER Cycle 200 11.4 Drivers of water security 200 11.5 Regulatory and technological demand management tools to achieve urban water security 202 11.6 Communication and information demand management tools to achieve urban water security 206 11.7 Case study SWOT analysis 207 11.8 Transitioning towards urban water security summary 210 Note 210 12 London transitioning towards urban water security 211 Introduction 211 12.1 Brief company background 211 12.2 Water supply and water consumption 212 12.3 Strategic vision: Reducing consumption 212 12.4 Drivers of water security 212 12.5 Regulatory and technological demand management tools to achieve urban water security 213 12.6 Communication and information demand management tools to achieve urban water security 216 12.7 Case study SWOT analysis 220 12.8 Transitioning towards urban water security summary 224 Notes 224 13 Singapore transitioning towards urban water security 225 Introduction 225 13.1 Brief company background 225 13.2 Water supply and water consumption 226 13.3 Strategic vision: Balancing supply with rising demand 227 13.4 Drivers of water security 227 13.5 Regulatory and technological demand management tools to achieve urban water security 229 13.6 Communication and information demand management tools to achieve urban water security 235 13.7 Case study SWOT analysis 237 13.8 Transitioning towards urban water security summary 241 Notes 241 14 Toronto transitioning towards urban water security 242 Introduction 242 14.1 Brief company background 242 14.2 Water supply and water consumption 243 14.3 Strategic vision: Toronto’s Water Efficiency Plan 244 14.4 Drivers of water security 244 14.5 Regulatory and technological demand management tools to achieve urban water security 245 14.6 Communication and information demand management tools to achieve urban water security 250 14.7 Case study SWOT analysis 252 14.8 Transitioning towards urban water security summary 256 Notes 256 15 Vancouver transitioning towards urban water security 257 Introduction 257 15.1 Brief company background 257 15.2 Water supply and water consumption 258 15.3 Strategic vision: Clean water and lower consumption 259 15.4 Drivers of water security 260 15.5 Regulatory and technological demand management tools to achieve urban water security 261 15.6 Communication and information demand management tools to achieve urban water security 266 15.7 Case study SWOT analysis 267 15.8 Transitioning towards urban water security summary 271 Notes 271 16 Sharing the journey: Best practices and lessons learnt 272 Introduction 272 16.1 Best practices 272 16.2 Lessons learnt 276 16.3 Moving forwards 280 Conclusions 284 Index 292

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Book SynopsisThe essential guide to the history, current trends, and the future of meteorology This comprehensive review explores the evolution of the field of meteorology, from its infancy in 3000 bc, through the birth of fresh ideas and the naming of the field as a science, to the technology boom, to today. The Evolution of Meteorology reveals the full story of where meteorology was then to where it is now, where the field is heading, and what needs to be done to get the field to levels never before imagined. Authored by experts of the topic, this book includes information on forecasting technologies, organizations, governmental agencies, and world cooperative projects. The authors explore the ancient history of the first attempts to understand and predict weather and examine the influence of the very early birth of television, computers, and technologies that are useful to meteorology. This modern-day examination of meteorology is filled with compelling research, sTable of ContentsAbout the Authors xiii Preface xv Acknowledgments xvii Section I Building Blocks of Meteorology (3000 bc–ad 1950) 1 1 Ancient Civilizations, Philosophical Theories, and Folklore (3000 bc–ad 1400) 3Kevin Anthony Teague 1.1 Ancient Babylonians 3 1.2 Ancient Chinese 4 1.3 Aristotle and Meteorologica 4 1.4 Theophrastus and the Book of Signs 5 1.5 Ibn Wahshiyya and Nabataean Agriculture 6 1.6 William of Ockham and Nominalism 6 1.7 Religion, Folklore, and Animals 7 2 Inventions of Weather Instruments (1400–1800) 11Nicole Gallicchio 2.1 Rain Gauge 11 2.2 Hygrometer 12 2.3 Thermometer 13 2.4 Barometer 15 2.5 Anemometer 16 3 The Birth of Modern Meteorology (1800–1950) 19Kevin Anthony Teague and Nicole Gallicchio 3.1 Telegraph 19 3.2 Fitzroy 20 3.3 Hugo Hildebrand Hildebrandsson 20 3.4 Weather Balloons/Radiosondes 20 3.5 Birth of Governmental Weather Departments 22 3.6 Numerical Weather Prediction 25 3.7 Weather Broadcasting 26 3.8 Forecasting for WWII 26 3.9 Extreme Weather Forecasting: ‘Nowcasting’ 27 Section II The Early Television, Computer, Satellite, and Radar Era (1950–1980) 31 4 Television and the First Computerized Advancements 33Kevin Anthony Teague 4.1 Television in the Household 33 4.2 Television Weather Forecasting of the 1950s 33 4.3 Television Weather Forecasting of the 1960s and 1970s 34 4.4 The Beginning of Computers and Numerical Weather Prediction (NWP) 35 4.5 Computers and NWP in the Met Office 37 4.6 Computers and NWP Worldwide 37 4.7 The 1970s and Its Lasting Influences on Forecasting 39 5 Radar and Satellite History 43Nicole Gallicchio 5.1 Invention of the Radar 43 5.2 Development of Weather Radar 44 5.3 Invention of the Satellite 46 5.4 Remote Sensing 46 5.5 Development of Weather Satellites 47 Section III Modern]Day Technologies, Advancements, and Social Media Impacts (1980–2013) 51 6 Personal Technology Boom 53Nicole Gallicchio 6.1 Television Networks 53 6.2 Personal Computers 55 6.3 The Internet and Meteorology 56 6.4 Cellphones and Social Media 56 6.5 Movies 58 7 Covering Major Storms 61Nicole Gallicchio 7.1 The Great Storm of 1987 61 7.2 Hurricanes and Tropical Cyclones 63 7.3 Tornadoes 66 7.4 Floods, Droughts, and Wildfires 68 7.5 Storm Chasing 70 7.6 Media 8 The Rise of Modern Computer Models 75Kevin Anthony Teague 8.1 European Center for Medium]Range Weather Forecasting (ECMWF) 75 8.2 Main US Models 78 8.3 Specific Use Forecasting Models 79 8.4 Weather Research and Forecasting Model (WRF) 79 8.5 Global Data]Processing and Forecasting System (GDPFS) 80 8.6 Main Model Biases and Various Characteristics 80 9 Advancements within the Nationalized Governmental Weather Departments 87Kevin Anthony Teague 9.1 The National Weather Service 87 9.2 The Met Office 91 9.3 Advancements across the World 93 9.4 Radar Development 96 9.5 New Satellite Developments 100 10 Meteorological Agencies at the Global and Private Level 107Kevin Anthony Teague 10.1 World Government Agencies 107 10.2 Operations of World Organizations 110 10.3 Global Discussions 110 10.4 What a Private]Sector Weather Business Entails 111 10.5 Government vs. Private Sector 112 10.6 The Lesser]Known Services of the Private Sector 115 Section IV Current and Future Ideologies of Climate Change and Meteorological Processes 121 11 Climate Change 123Nicole Gallicchio 11.1 Climate Discussions 123 11.2 Earth’s Lifetime Fluctuations 125 11.3 Past Climate Data 127 11.4 Permafrost and Climate Change 130 11.5 Greenhouse Gases 132 11.6 The Intergovernmental Panel on Climate Change 133 12 Extreme Weather 141Nicole Gallicchio 12.1 Current Climate and Weather Trends 141 12.2 Classifying Extreme Weather 144 12.3 Extreme Weather Influences 147 12.4 Is Extreme Weather on the Rise? 150 12.5 Weather Pattern Predictions 153 13 Additional Meteorological Impacts 169Nicole Gallicchio 13.1 Space Weather 169 13.2 Earthquakes and the Effect on Climate Change 171 13.3 Weather and the Effects on the Human Body 172 14 Weather Technology 179Kevin Anthony Teague 14.1 Tropical Cyclone Technology 179 14.2 Coastal Flooding 186 14.3 Extreme Weather 190 14.4 Enhancements to Radar, Satellite, and Model Output of Supercomputers 198 14.5 Long]Range Forecasting 203 14.6 Various Planned Advancements 203 15 Global Cooperation 211Kevin Anthony Teague 15.1 Overall Global Forecasting 211 15.2 Global Networking in Meteorology 213 15.3 Disaster Management 215 15.4 Global Radar and Satellite Cooperation 220 15.5 Global Data]Processing and Forecasting Systems 221 15.6 Global Response to Climate Change 223 Appendix Figures A–H 231 Index 245

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Book SynopsisWater is the Earth''s most precious resource. Until recent years, water was often overlooked as being overly abundant or available, but much has changed all over the world. As climate change, human encroachment on environmental areas, and deforestation become greater dangers, the study of groundwater has become more important than ever and is growing as one of the most important areas of science for the future of life on Earth. This three-volume set is the most comprehensive and up-to-date treatment of hydrogeochemistry that is available. The first volume lays the foundation of the composition, chemistry, and testing of groundwater, while volume two covers practical applications such as mass transfer and transport. Volume three, which completes the set, is an advanced study of the environmental analysis of groundwater and its implications for the future. This first volume in the set is an important milestone in hydrogeochemistry, covering the fundamentals of groundwateTable of ContentsPreface xv Introduction 1 1 Analytical Composition and Properties of Ground Water 19 1.1 Moisture 21 1.2 Mineral Components 29 1.2.1 Testing and Preparation 30 1.2.2 Chemical Analysis 34 1.2.3 Processing of Analysis Results 35 1.3 Gas Components 41 1.3.1 Testing and Preparation 43 1.3.2 Analysis of the Natural Gas Composition 49 1.3.3 Conversions of Gas Analysis Results 52 1.4 Organic Components 56 1.4.1 Testing and Preparation 60 1.4.2 Analysis of Organic Substance 68 1.4.2.1 General Content of Organic Matter 68 1.4.2.2 Content of Organic Component Groups 70 1.4.2.3 Content of Individual Organic Components 74 1.4.3 Conversion of Analysis Results 74 1.5 Substances in the Dispersed State 76 1.5.1 Inert Suspended Particles 78 1.5.1.1 Methods of Study 79 1.5.2 Living Organisms 80 1.5.2.1 Pathogen Microorganisms 81 1.5.2.2 Biochemical Microorganisms 86 1.5.2.3 Methods of Study 86 1.6 Properties of Ground Water 89 1.6.1 Organoleptic and Balneological Properties 90 1.6.2 Chemical Properties 96 1.6.3 Physical Properties 113 2 Hydrogeochemical Testing 125 2.1 Assignment and Purpose of Hydrogeochemical Testing 126 2.1.1 Regime and Scope of Testing 127 2.1.2 Measured Parameters and Their Errors 128 2.2 Logistics of Field Testing 131 2.2.1 Natural Conditions and Previous Studies of the Area 132 2.2.2 Planning the Testing Regime and Points 133 2.2.3 Preparation of Wells and Equipment 138 2.2.4 Preparation of Analytical Base 148 2.2.4.1 Selection of Property and Composition Parameters 150 2.2.4.2 Substantiation of Margin of Error Measurements 151 2.2.4.3 Selection of Chemical Analysis Technique 164 2.2.4.4 Selection of a Laboratory and Executants 197 2.2.5 Field Testing Protocol 202 2.2.6 Sample Safekeeping and Delivery to the Laboratory 212 3 Processing of Testing Results 215 3.1 Processing and Systematization of Observed Values 216 3.1.1 Checking the Observed Values 216 3.1.2 Systematizing the Observed Values 219 3.1.3 Control of Measurement Quality 222 3.1.3.1 Sensitivity of Testing Techniques 224 3.1.3.2 Precision of Testing Results 225 3.1.3.3 Testing Correctness of the Results 228 3.1.3.4 Systematic Error of the Testing Results 229 3.1.3.5 Testing Results’ Accuracy 231 3.1.4 Measurements Results and Their Reliability 232 3.1.4.1 Mathematical Expectation 232 3.1.4.2 Confidence Interval 233 3.2 Modeling of the Hydrogeochemical Condition 237 3.2.1 Empirical–statistical Modeling 238 3.2.1.1 Anomalies and Background 238 3.2.1.2 Water Distinction in Quality Parameters 240 3.2.1.3 Search for the Factors 244 3.2.2 Space–time Modeling 247 3.2.2.1 Autocorrelation Metamodels 249 3.2.2.2 Semivariance Metamodels 254 3.3 Classification and Visualization of Hydrogeochemical Parameters 261 3.3.1 Chemical Classification of Ground Waters 262 3.3.2 Graphic Imaging of the Water Composition 269 3.3.3 Graphic Comparison of Different Composition Waters 272 3.3.4 Hydrogeochemical Maps and Cross–sections 276 3.3.4.1 Making Hydrogeochemical Maps 278 3.3.4.2 Generating Hydrogeochemical Cross–sections 288 Symbols 291 References 297 Index 301

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

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Book SynopsisThe FDA''s (Food and Drug Administration) FSMA (Food Safety Modernization Act) is the most sweeping reform of United States food safety laws in more than 70 years. The key to successful implementation of FSMA rules depends on building a comprehensive Food Safety System with effective prerequisite programs in place and a well-designed Food Safety Plan that incorporates risk-based preventive controls to mitigate hazards. This book provides essential guidance for small to mid-sized businesses on how to design, implement, and maintain a world-class Food Safety Plan that conforms to FSMA regulations. With practical and up-to-date advice, the author offers a straight forward approach for readers to successfully migrate into FSMA. The inclusion of fully developed Food Safety Plans as well as examples of hazards and preventative controls make this a must-read not only for those that are new to the regulations, but also those with a plan already in place. FSMA and Food SafetTable of ContentsPreface xi About the Author xiii 1 What is Modern Food Safety, and How is that Different from HACCP? 1 1.1 Introduction 1 1.2 FSMA Sanitation and cGMPs 3 1.3 FSMA Preventive Controls 4 1.4 Process Controls 5 1.5 Sanitation Controls 6 1.6 Supplier Controls 8 References 10 2 Why is a Food Safety System the Best Path to Food Safety? 11 2.1 What are Biological Hazards and Their Controls? 11 2.2 What are Chemical Hazards, Including Allergens and Radioactivity, and Their Controls? 15 2.3 What are Physical Hazards and Their Controls? 17 References 19 3 What are the Essential Elements of a Food Safety System? 21 3.1 What are Prerequisite Programs, and What Do They Do? 22 3.2 What is a Hazard Analysis, and Why is it Performed? 23 3.3 What are Risk-Based Preventive Controls, and How are they Assigned? 25 3.3.1 What Controls are used to Control Allergen-Related Hazards? 26 3.3.2 What Controls are used to Control Sanitation-Related Hazards? 27 3.3.3 What Controls are used to Control Process Hazards? 29 3.3.4 What Controls are used to Control Supplier-Related Hazards? 30 3.4 What is a Food Safety Plan, and Who Develops It? 32 4 How is a Food Safety System Managed? 35 4.1 What is the Role of Management and Plant Operations in a Food Safety System? 35 4.2 How are SOPs Developed and Managed? 36 4.3 How are Preventive Controls Managed? 39 4.3.1 What are Performance Criteria for Controls, Including Critical Limits? 39 4.3.2 How are Preventive Controls Monitored? 40 4.3.3 If Preventive Controls Fail, What Corrective Actions are Needed? 41 4.3.4 How is the System and its Parts Verified as Being Compliant? 43 4.3.5 How are Process Preventive Controls Validated? 44 4.4 How are Records Established and Maintained? 46 4.5 Why and How is a Recall Plan Developed and Managed? 48 References 51 Supplemental References for Recalls 51 5 How is a Food Safety System Developed and Implemented? 53 5.1 Developing a Food Safety Plan 54 5.2 Assemble the Food Safety Team 55 5.3 Describe the Food and its Distribution 55 5.4 Describe the Intended Use and Consumers of the Food 55 5.5 Develop a Flow Diagram that Describes the Process 56 5.6 Verify the Flow Diagram 56 5.7 Conduct a Hazard Analysis 56 5.8 Essential Elements of the Food Safety Plan 58 6 What Triggers a Reanalysis of the Food Safety Plan? 61 7 Resources for Preparing Food Safety Preventive Controls Plans 63 7.1 Examples of Prerequisite Programs 63 7.2 Examples of Allergen Preventive Controls 65 7.3 Examples of Sanitation Preventive Controls 65 7.4 Examples of Process Preventive Controls 66 7.5 Examples of Supplier Controls 68 7.6 Useful Forms 68 7.7 FSMA Training and the Food Safety Preventive Controls Alliance 75 8 Example Food Safety Plans 77 Barbeque Sauce – Example Food Safety Plan 78 Company Overview 78 Process Narrative 79 Chocolate Chip Walnut Cookies – Example Food Safety Plan 88 Company Overview 88 Process Narrative 89 Deli Potato Salad – Example Food Safety Plan 102 Company Overview 102 Process Narrative 103 Macaroni & Cheese Frozen Meal – Example Food Safety Plan 118 Company Overview 118 Process Narrative 119 9 FSMA Regulations: cGMPs, Hazard Analysis, and Risk-Based Preventive Controls for Human Foods 131 FDA Regulations on cGMP’s, Hazard Analysis and Risk-based Preventive Controls for Human Foods 132 Part 117—Current Good Manufacturing Practice, Hazard Analysis, and Risk–Based Preventive Controls for Human Food 132 Subpart A—General Provisions 132 Subpart B—Current Good Manufacturing Practice 132 Subpart C—Hazard Analysis and Risk‐Based Preventive Controls 132 Subpart D—Modified Requirements 133 Subpart E—Withdrawal of a Qualified Facility Exemption 133 Subpart F—Requirements Applying to Records That Must Be Established and Maintained 133 Subpart G—Supply-Chain Program 134 Subpart A—General Provisions 134 § 117.1 Applicability and status 134 § 117.3 Definitions 135 § 117.4 Qualifications of individuals who manufacture, process, pack, or hold food 141 § 117.5 Exemptions 141 § 117.7 Applicability of subparts C, D, and G of this part to a facility solely engaged in the storage of unexposed packaged food 149 § 117.8 Applicability of subpart B of this part to the off‐farm packing and holding of raw agricultural commodities 150 § 117.9 Records required for this subpart 150 Subpart B—Current Good Manufacturing Practice 150 § 117.10 Personnel 150 § 117.20 Plant and grounds 151 § 117.35 Sanitary operations 153 § 117.37 Sanitary facilities and controls 154 § 117.40 Equipment and utensils 155 § 117.80 Processes and controls 156 § 117.93 Warehousing and distribution 159 § 117.110 Defect action levels 160 Subpart C—Hazard Analysis and Risk-Based Preventive Controls 160 § 117.126 Food safety plan 160 § 117.130 Hazard analysis 160 § 117.135 Preventive controls 161 § 117.136 Circumstances in which the owner, operator, or agent in charge of a manufacturing/processing facility is not required to implement a preventive control 163 § 117.137 Provision of assurances required under § 117.136(a) (2), (3), and (4) 164 § 117.139 Recall plan 164 § 117.140 Preventive control management components 165 § 117.145 Monitoring 165 § 117.150 Corrective actions and corrections 166 § 117.155 Verification 167 § 117.160 Validation 167 § 117.165 Verification of implementation and effectiveness 168 § 117.170 Reanalysis 170 § 117.180 Requirements applicable to a preventive controls qualified individual and a qualified auditor 171 § 117.190 Implementation records required for this subpart 172 Subpart D—Modified Requirements 172 § 117.201 Modified requirements that apply to a qualified facility 172 § 117.206 Modified requirements that apply to a facility solely engaged in the storage of unexposed packaged food 174 Subpart E—Withdrawal of a Qualified Facility Exemption 175 § 117.251 Circumstances that may lead FDA to withdraw a qualified facility exemption 175 § 117.254 Issuance of an order to withdraw a qualified facility exemption 176 § 117.257 Contents of an order to withdraw a qualified facility exemption 176 § 117.260 Compliance with, or appeal of, an order to withdraw a qualified facility exemption 177 § 117.264 Procedure for submitting an appeal 177 § 117.267 Procedure for requesting an informal hearing 178 § 117.270 Requirements applicable to an informal hearing 178 § 117.274 Presiding officer for an appeal and for an informal hearing 179 § 117.277 Timeframe for issuing a decision on an appeal 179 § 117.280 Revocation of an order to withdraw a qualified facility exemption 179 § 117.284 Final agency action 180 § 117.287 Reinstatement of a qualified facility exemption that was withdrawn 180 Subpart F—Requirements Applying to Records That Must Be Established and Maintained 181 § 117.301 Records subject to the requirements of this subpart 181 § 117.305 General requirements applying to records 181 § 117.310 Additional requirements applying to the food safety plan 181 § 117.315 Requirements for record retention 182 § 117.320 Requirements for official review 182 § 117.325 Public disclosure 182 § 117.330 Use of existing records 182 § 117.335 Special requirements applicable to a written assurance 183 Subpart G—Supply‐Chain Program 183 § 117.405 Requirement to establish and implement a supply‐chain program 183 § 117.410 General requirements applicable to a supply‐chain program 184 § 117.415 Responsibilities of the receiving facility 186 § 117.420 Using approved suppliers 186 § 117.425 Determining appropriate supplier verification activities (including determining the frequency of conducting the activity) 187 § 117.430 Conducting supplier verification activities for raw materials and other ingredients 187 § 117.435 Onsite audit 189 § 117.475 Records documenting the supply‐chain program 190 Appendix A Food Safety Plan Checklist 193 Food Safety Plan Checklist 193 Introduction 193 Purpose 194 References 198 Appendix B HACCP Principles and Application Guidelines 199 National Advisory Committee on Microbiological Criteria for Foods 199 Executive Summary 199 Definitions 200 HACCP Principles 202 Guidelines for Application of HACCP Principles 203 Introduction 203 Prerequisite Programs 203 Education and Training 204 Developing a HACCP Plan 204 Implementation and Maintenance of the HACCP Plan 215 References 216 Glossary 217

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Book SynopsisAn introduction to the urgent global question of how to feed the hungry Global food production has never been more abundant, yet nearly a billion people worldwide suffer from malnutrition, virtually all of them in the developing world. Food security in these countries is a global humanitarian issue which becomes more urgent with every passing year. There is a vital need to understand the nature and causes of food scarcity in developing countries in order to see to it that our global bounty reaches the hungry people who need it. Food Security in the Developing World offers a comprehensive single-volume introduction to the subject. It focuses on three core issuesfood availability, food accessibility, and food utilizationin order to produce a rounded picture of the causes and possible solutions for food scarcity. Thorough and accessible, it promises to help researchers and policymakers address this growing humanitarian crisis in a reasoned and targeted way. Food Security in the Developing

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Book SynopsisPlant Breeding Reviews presents state-of-the-art reviews on plant genetics and the breeding of all types of crops by both traditional means and molecular methods. Many of the crops widely grown today stem from a very narrow genetic base; understanding and preserving crop genetic resources is vital to the security of food systems worldwide.Table of ContentsContributors ix 1. James L. Brewbaker: Distinguished Geneticist, Tropical Plant Breeder, Inspiring Teacher 1Ganesan Srinivasan and Jules Janick I. Early Years 2 II. Research 5 III. Educator 17 IV. The Man 24 Releases and Publications of James L. Brewbaker 27 2. Breeding Leucaena: Tropical Multipurpose Leguminous Tree 43James L. Brewbaker I. Introduction 45 II. Genetic Resources 58 III. Genetics in Relation to Breeding 70 IV. Cultivar Development 75 V. Breeding Challenges 88 VI. The Future 108 Acknowledgments 111 Literature Cited 111 3. Maize Doubled Haploids 123Zhixin Liu, Yanbo Wang, Jiaojiao Ren, Mei Mei, Ursula K. Frei, Benjamin Trampe, and Thomas Lübberstedt I. Introduction 125 II. History of Haploid Research in Maize 126 III. Milestones for Establishing DH Technology in Maize Breeding 131 IV. Application of DH Technology in Maize Breeding and Genetic Studies 148 V. Application of DH Technology in Maize-Breeding Programs 152 VI. Future Perspectives in Using DH Technology in Maize 157 Acknowledgments 159 Literature Cited 160 4. Nitrogen and Phosphorus Use Efficiencies in Wheat: Physiology, Phenotyping, Genetics, and Breeding 167Harindra S. Balyan, Vijay Gahlaut, Anuj Kumar, Vandana Jaiswal, Raman Dhariwal, Sandhya Tyagi, Priyanka Agarwal, Supriya Kumari, and Pushpendra K. Gupta I. Introduction 170 II. Physiology of N Uptake and Assimilation 173 III. Physiology of P Uptake and Assimilation 177 IV. Crop Phenotyping for NUE/PUE 180 V. Genes Involved in N Uptake and Metabolism 184 VI. QTL for NUE/PUE 188 VII. MicroRNA, Long Non-Coding RNA, Target Mimics for N/P Homeostasis 195 VIII. Approaches for the Genetic Improvement of NUE/PUE 200 IX. Outlook 212 Acknowledgments 214 Literature Cited 214 5. Interspecific Periclinal Chimeras as a Strategy for Cultivar Development 235Nagib A. Nassar, Nayra N. Bomfim Fernandes, Danielle Y. Hashimoto Freitas, and Thomas M. Gradziel I. Introduction 236 II. Chimera Form and Function 239 III. Interspecies Chimeras 241 IV. Case Studies 252 V. Prospects 262 Acknowledgments 262 Literature Cited 263 6. Open Source Plant Breeding and the Open Source Seed Initiative 271Claire H. Luby, Jack R. Kloppenburg, and Irwin L. Goldman I. Introduction 273 II. Restrictions on Freedom to Operate in Plant Breeding 275 III. The Open Source Seed Initiative 280 IV. Social and Political Context of Open Source Plant Breeding 283 V. Breeding Context: Working with OSSI Germplasm 288 VI. Outlook 296 Literature Cited 297 7. Rapid Cycle Breeding: Application of Transgenic Early Flowering for Perennial Trees 299Ann M. Callahan, Chinnathambi Srinivasan, Chris Dardick, and Ralph Scorza I. Introduction 300 II. Generation of Early Flowering Trees 302 III. Utilizing Early Flowering for Rapid Cycle Breeding 317 IV. Outlook 325 Literature Cited 327 Subject Index 335 Cumulative Subject Index 337 Cumulative Contributor Index 365

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Book SynopsisHorticultural Reviews presents state-of-the-art reviews on topics in horticultural science and technology covering both basic and applied research. Topics covered include the horticulture of fruits, vegetables, nut crops, and ornamentals. These review articles, written by world authorities, bridge the gap between the specialized researcher and the broader community of horticultural scientists and teachers.Table of ContentsContributors ix Dedication: Cary A. Mitchell xiiiRobert J. Joly 1. Identification of Phytomorphs in the Voynich Codex 1Arthur O. Tucker and Jules Janick I. Introduction and Historical Context 4 II. Phytomorph Identification 5 III. Sources and Techniques 58 Acknowledgments 60 Literature Cited 60 2. Urban Agriculture: Environmental, Economic, and Social Perspectives 65Steve Hallett, Lori Hoagland, and Emily Toner I. Introduction 66 II. Historical Perspectives 68 III. Global Perspectives 72 IV. The Three Pillars of Sustainability 82 V. New Technologies 98 VI. Urban Agriculture and Food Systems 104 VII. Conclusions 107 Literature Cited 109 3. The Floriculture Vegetative Cutting Industry 121James E. Faust, John M. Dole, and Roberto G. Lopez I. Scope of the Industry 123 II. Stock-Plant Production 126 III. Postharvest Handling and Physiology 137 IV. Cutting Management and Propagation 148 V. Case Studies 155 VI. Future Directions 162 Literature Cited 165 4. Orchid Biotechnology 173Wagner A. Vendrame and Amir A. Khoddamzadeh I. Introduction 175 II. In Vitro Propagation Technology 178 III. Bioreactor Technology 193 IV. Synthetic Seed Technology (Synseed) 195 V. Cryopreservation Technology 198 VI. Summary and Conclusions 210 Literature Cited 211 5. Chilling Injury in Tomato Fruit 229Palash Biswas, Andrew R. East, Errol W. Hewett, and Julian A. Heyes I. Introduction 231 II. Chilling Injury in Fruit 232 III. Chilling Injury Symptoms in Tomato 241 IV. Time–Temperature Thresholds for CI Symptoms 259 V. Concluding Remarks 264 Acknowledgment 265 Literature Cited 265 6. Oomycete Diseases of Cucurbits: History, Significance, and Management 279Mohammad Babadoost I. Introduction 281 II. Oomycetes 282 III. Oomycete Diseases of Cucurbits and their Management 288 IV. Concluding Remarks 304 Literature Cited 306 7. Huanglongbing: Devastating Disease of Citrus 315Greg McCollum and Elizabeth Baldwin I. Introduction to Citrus 317 II. Huanglongbing Disease 319 III. Changes Induced by CLas Infection 328 IV. Management Strategies to Minimize or Prevent HLB Disease 336 V. HLB Effects on Flavor and Postharvest Quality 345 VI. Conclusions 350 Literature Cited 352 8. Scab and Fire Blight of Apple: Issues in Integrated Pest Management 363Janna L. Beckerman and George W. Sundin I. Introduction 364 II. IPM and Apple Scab 366 III. IPM and Fire Blight 375 IV. Conclusions and Future Trends 383 Acknowledgments 384 Literature Cited 385 Subject Index 391 Cumulative Subject Index 393 Cumulative Contributor Index 429

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Book SynopsisRiver Restoration River restoration initiatives are now widespread across the world. The research efforts undertaken to support them are increasingly interdisciplinary, focusing on ecological, chemical, physical as well as societal issues. River Restoration: Political, Social, and Economic Perspectives provides a comprehensive overview of research in the field of river restoration in humanities and the social sciences. It illustrates how, in the last thirty years or so, such approaches have evolved and strengthened within the restoration sciences. The scientific community working in this domain has structured itself, often regionally and circumstantially, to critically assess and improve restoration policies and practices. As a research field, river restoration tackles three thematic axes: Human-river interactions especially perceptions and practices of rivers, and how these interactions can be changed by restoration projects Political processes, Table of ContentsSeries Foreword vii Acknowledgments viii List of Contributors ix Part I Introduction 1 1 What are the Political, Social, and Economic Issues in River Restoration? Genealogy and Current Research Issues 3 Marylise Cottet, Bertrand Morandi, and Hervé Piégay Part II People–River Relationships: From Ethics to Politics 49 2 Ethics of River Restoration: The Imitationist Paradigm 51 Henry Dicks 3 Restoring Sociocultural Relationships with Rivers: Experiments in Fluvial Pluralism 66 Dan Hikuroa, Gary Brierley, Marc Tadaki, Brendon Blue, and Anne Salmond 4 Political Ecology and River Restoration 89 Jamie Linton Part III Governance and Power Relationships Between Stakeholders 107 5 The Policy and Social Dimension of Restoration Thinking: Paying Greater Attention to “Interdependency” in Restoration Governing Practice 109 Caitriona Carter , Gabrielle Bouleau, and Sophie Le Floch 6 From Public Policies to Projects: Factors of Success and Diversity Through a Comparative Approach 128 Catherine Carré, Jean-Paul Haghe, and Pere Vall-Casas 7 How to Better Involve Stakeholders in River Restoration Projects: The Case of Small Dam Removals 147 Marie-Anne Germaine, Ludovic Drapier, Laurent Lespez, and Beth Styler-Barry 8 Letting the Political Dimension of Participation in River Restoration have its Space 169 Nora S. Buletti, Franziska E. Ruef, and Olivier Ejderyan Part IV Evaluation of Socioeconomic Effects 189 9 What is the Total Economic Value of River Restoration and Why is it Important? 191 John C. Bergstrom and John B. Loomis 10 Valuation of Ecosystem Services to Assess River Restoration Projects 210 Xavier Garcia, Stefanie Müller, and Matthias Buchecker 11 Public Perspectives of River Restoration Projects 233 Riyan van den Born, Bernadette van Heel, Kerstin Böck, Arjen Buijs, and Matthias Buchecker Part V Diversity of Methods, Diversity of Knowledge 253 12 Social Surveys: Methods for Taking into Account Actors’ Practices and Perceptions in River Restoration 255 Caroline Le Calvez, Silvia Flaminio, Marylise Cottet, and Bertrand Morandi 13 Documents on River Restoration: Temporal and Spatial Analyses of Written Discourses 273 Emeline Comby, Bertrand Morandi, Yves-François Le Lay, Silvia Flaminio, and Helena Zemp 14 Participatory Approaches: Principles and Practices for River Restoration Projects 294 Alba Juárez-Bourke and Kirsty L. Blackstock 15 Economic Benefits: Operationalizing their Valuation in River Restoration Projects 308 Sylvie Morardet Part VI Conclusions 333 16 Social, Economic, and Political Stakes of River Restoration: A Dynamic Research Field Facing Several Challenges to Strengthen Links with Practitioners 335 Marylise Cottet, Bertrand Morandi, and Hervé Piégay Index 351

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Book SynopsisAn updated treatment of management and geomorphology of large rivers around the world The newly revised Second Edition of Large Rivers: Geomorphology and Management delivers a thoroughly updated exploration of the form and function of major rivers. The book brings together a set of papers on the large rivers of the world, offering readers an insightful examination of a demanding subject. The new Second Edition of the book includes fully updated and revised chapters, as well as two entirely new chapters on the Ayeyarwady and the Arctic rivers. This fascinating volume describes the environmental requirements for creating and maintaining a major river system, case studies on over a dozen large rivers from different continents in a variety of physical environments, and the measurement and management of large rivers. Unmatched in scope, Large Rivers sheds light on a subject lacking in comprehensive study. Readers will benefit from the inclusion of: A thorough introduction to the geology of large river systems, hydrology and discharge, transcontinental moving and storage of sediment, and the greatest floods and largest riversAn exploration of the classification, architecture, and evolution of large-river deltasDiscussions of sedimentology and stratigraphy of large river deposits, including their recognition in the ancient record and the distinction from incised valley fillsAn examination of the effects of tectonism, climate change, and sea-level change on the form and behavior of the modern Amazon river and its floodplainMeasurement and management of large riversThe effect of climatic change on large riversPerfect for postgraduate students and researchers in fluvial geomorphology, hydrology, sedimentary geology, and river management, Large Rivers: Geomorphology and Management will also earn a place in the libraries of engineers and environmental consultants in the private and public sectors working on major rivers around the world.Table of ContentsAbout the Editor xxiii List of Contributors xxv Preface xxxiii 1 Introduction 1Avijit Gupta 1.1 Large Rivers and People 1 1.2 What Is a Large River? 1 1.3 The Book and its Content 4 References 6 Part I Background 2 Geology of Large River Systems 7Sampat K. Tandon and Rajiv Sinha 2.1 Introduction 7 2.2 Tectonic Settings of Large River Systems 9 2.3 Complexity of Drainage Types and Channel Morphology 12 2.4 Large Rivers – Climatic Settings and Climatic Variability 17 2.5 Modern Large Rivers – Hydrology and Sediment Dispersal 19 2.6 Landforms and Alluvial Architecture of Large River Systems 23 2.7 Growth and Development of Large River Systems 28 2.8 Duration of Large River Systems and the Rock Record 30 2.9 Sea Level, Tectonic, and Climatic Controls on the Large River Systems 31 2.10 Concluding Remarks 33 Acknowledgments 34 References 34 3 Hydrology and Discharge 42Ellen Wohl and Katherine B. Lininger 3.1 Introduction 42 3.2 Large Rivers of the Equatorial Regions 51 3.3 Large Rivers of the Drylands 54 3.4 Rivers of the Mid-Latitudes 57 3.5 Rivers Draining South from the Himalaya 59 3.6 Rivers of East and Southeast Asia 61 3.7 High-Latitude Rivers 63 3.8 Conclusion 64 Acknowledgment 66 References 67 4 Transcontinental Moving and Storage: The Orinoco and Amazon Rivers Transfer the Andes to the Atlantic 76Robert H. Meade 4.1 Introduction 76 4.2 Andean Sources and Alluvial Storage 76 4.3 Orinoco 78 4.4 Amazon 82 4.5 The Amazon Goes to Sea 92 4.6 Coda 94 Acknowledgements 94 References 95 5 Megafloods and Large Rivers 100Victor R. Baker 5.1 Introduction 100 5.2 Historical Background 100 5.3 Terrestrial Glacial Megafloods 101 5.4 Extraterrestrial Megafloods and Megarivers 108 5.5 Conclusion 109 References 110 6 Classification, Architecture, and Evolution of Large River Deltas 114Kazuaki Hori and Yoshiki Saito 6.1 Introduction 114 6.2 Definition of a Delta and Delta Components 116 6.3 Classification of Deltas 122 6.4 Morphology and Sediment 124 6.5 Delta Evolution 130 6.6 Problems of Sediment Supply 134 6.7 Concluding Remarks 135 Acknowledgements 136 References 136 7 Sedimentology and Stratigraphy of Large River Deposits: Recognition and Preservation Potential in the Rock Record 146Christopher R. Fielding 7.1 Introduction 146 7.2 Geomorphology of Modern Big Rivers 150 7.3 Sedimentology and Stratigraphy of Modern Big Rivers 150 7.4 Sedimentology and Stratigraphy of Ancient Big Rivers 156 7.5 Discussion: Preservation Potential of Big River Deposits 159 7.6 Conclusion 160 Acknowledgments 161 References 161 Part II Case Studies 8 Effects of Tectonism and Sea-Level Change on the Form and Behaviour of the Modern Amazon River and Its Floodplain 171Leal A.K. Mertes and Thomas Dunne 8.1 Background 171 8.2 Amazon Basin Characteristics 172 8.3 Tectonic Influences on the Modern Amazon 177 8.4 Structural Influences on Amazon River Geomorphology 183 8.5 Influences of Sea-Level Changes on the Amazon River and Floodplain 193 8.6 Conclusion 197 Acknowledgements 198 References 199 9 The Mississippi River System 205James C. Knox 9.1 Introduction 205 9.2 Cenozoic Drainage Evolution 206 9.3 Influence of Quaternary Glaciations 209 9.4 Proglacial Lakes and Extreme Floods 211 9.5 Response of the Lower Mississippi Valley to Upper Valley Glaciation and Flooding 213 9.6 The Mississippi River System During the Holocene 215 9.7 Morphology of the Mississippi River 227 9.8 Modern Hydrology 233 9.9 The Mississippi River System: Summary and Outlook 242 Acknowledgements 244 References 245 10 The Colorado River 253John C. Schmidt, Lindsey Bruckerhoff, Homa Salehabadi, and Jian Wang 10.1 Introduction 253 10.2 Physiography 255 10.3 Gradient, Valley Width, and Channel Form in the Colorado Plateau 257 10.4 Hydrology 260 10.5 The Colorado River in the Millennium Drought 265 10.6 Hydrology: Past and Future 281 10.7 Pre-dam and Post-dam Sediment Yield and Sediment Transport 285 10.8 Channel Adjustment and Ecological Change During the Twentieth Century 289 10.9 Modern Fish Community 299 10.10 Environmental Management of the Modern River 302 10.11 The Future 306 10.12 Conclusion 307 References 308 11 The Lena: A Large River in a Deep Permafrost Zone 320Emmanuèle Gautier, François Costard, and Alexander Fedorov 11.1 Introduction 320 11.2 Description of the Lena Drainage Basin 321 11.3 A Periglacial Environment 323 11.4 Floodplain, Delta, and Periglacial Land Forms 323 11.5 Impact of Climatic Change on the Hydrosystem 330 11.6 Conclusion 331 References 332 12 The Danube: Morphology, Evolution, and Environmental Issues 335Dénes Lóczy 12.1 Introduction 335 12.2 Water and Sediment 337 12.3 Headwaters of the Danube 339 12.4 Hydromorphology of the Danube Sections 341 12.5 The Danube Delta 345 12.6 The Evolution of the Valley of the Danube 347 12.7 Human Impacts 354 References 360 13 The Yukon and the Mackenzie: Large Arctic Rivers of North America 368Ellen Wohl, Natalie Kramer, and Katherine B. Lininger 13.1 Introduction 368 13.2 Large Arctic Rivers of North America 369 13.3 The Yukon and the Mackenzie: A Study in Contrasts 374 13.4 The Future of Large Arctic Rivers in North America 378 13.5 Conclusion 381 References 381 14 The River Nile: Evolution and Environment 388Jamie C. Woodward, Mark G. Macklin, Michael D. Krom, and Martin A.J. Williams 14.1 Introduction 388 14.2 Nile Basin River Environments 390 14.3 Early Origins and the Neogene Nile 391 14.4 The Late Pleistocene and Holocene Nile 394 14.5 Records of Nile River Behaviour in the Eastern Mediterranean Sea 402 14.6 The Modern Nile: Hydrology and Geomorphology 406 14.7 The Suspended Sediment Budget 415 14.8 The Nile Delta and The Eastern Mediterranean 417 14.9 River Basin Management and Global Change 421 Acknowledgements 425 References 425 15 The Congo River, Central Africa 433Jürgen Runge 15.1 Introduction 433 15.2 The Course of the Congo River 434 15.3 Geology and Geomorphology of the Congo Basin 440 15.4 Evolution of the Congo River 444 15.5 The Flow Regime of the Congo 445 15.6 Solid, Suspended, and Dissolved Load 448 15.7 The Congo Mouth and the Submarine Canyon 449 15.8 The Congo River and Its Economic Importance 450 15.9 Conclusion 451 Acknowledgements 452 References 452 16 The Zambezi: Origins and Legacies of Earth’s Oldest River System 457Andy E. Moore, Fenton P.D. Cotterill, Mike P.L. Main, and Hugh B. Williams 16.1 Introduction 457 16.2 The Zambezi River System 459 16.3 Hydrology 464 16.4 Ecological Impact of Major Dams 467 16.5 Evolution of the Zambezi River System 469 16.6 Drainage Evolution and Speciation 478 16.7 Cultural and Economic Aspects 481 16.8 Conclusion 482 Acknowledgements 483 References 483 17 The Geographic, Geological, and Oceanographic Setting of the Indus River – An Update 488Asif Inam, Peter D. Clift, Liviu Giosan, Anwar Alizai, Samina Kidwai, Muhammad I. Shahzad, Ibrahim Zia, Majid Nazeer, Muhammad J. Khan, Syed S. Ali, Aneela Shaheen, Rashida Qari, and Sanober Kehkashan 17.1 Introduction 488 17.2 The Drainage Basin 491 17.3 Evolution of the Indus River 492 17.4 Indus Water and Sediment Discharge 493 17.5 The Indus Delta 495 17.6 Submarine Indus System 499 17.7 Water Management 503 17.8 The Indus Dolphins 505 17.9 Environmental Changes 506 17.10 Conclusion 510 References 513 18 The Ganga River 521Indra B. Singh 18.1 Introduction 521 18.2 Hydrology 522 18.3 Water Quality 526 18.4 Material Transfer in the Ganga 527 18.5 Mineralogy and Geochemistry of Sediments 530 18.6 Heavy Metals and Pollutants in the Sediment 531 18.7 The Plain and the River 531 18.8 The Delta 533 18.9 A Summary of Current Geomorphic Processes 538 18.10 Quaternary Evolution of the Ganga 538 18.11 Utilization of the River and Associated Problems 542 Acknowledgements 546 References 546 19 Erosion and Weathering in the Brahmaputra River System 551Sunil K. Singh 19.1 Introduction 551 19.2 The Brahmaputra River System 552 19.3 Geology of the Basin 554 19.4 Hydrology 556 19.5 Floods in the Brahmaputra 557 19.6 Characteristics of the Brahmaputra Channel 562 19.7 Erosion and Weathering 562 19.8 Sediment Yield or Erosion Rates in the Various Zones 567 19.9 Chemical Weathering and Erosion 568 19.10 Bed Load and Weathering Intensity 572 19.11 Control of Physical and Chemical Erosion in the Brahmaputra Basin 572 19.12 Conclusion 574 References 574 20 The Jamuna–Brahmaputra River, Bangladesh 579James L. Best, Philip J. Ashworth, Erik Mosselman, Maminul H. Sarker, and Julie E. Roden 20.1 Background 579 20.2 Channel Scale Morphology and Recent Historical Changes in the Course of the Brahmaputra–Jamuna River 588 20.3 Bedform Types and Dynamics 595 20.4 Bifurcations, Offtakes, and Confluences 603 20.5 Floodplain Sedimentation 607 20.6 Sedimentology of the Jamuna River 611 20.7 Applied Geomorphology and Engineering in the Jamuna River 617 20.8 Summary: What Does the Future Hold? 628 Acknowledgements 630 References 631 21 The Ayeyarwady River 641Alexis Licht and Liviu Giosan 21.1 Introduction 641 21.2 The Ayeyarwady Drainage Basin 641 21.3 History of the Ayeyarwady 653 21.4 Looking Ahead 655 References 655 22 The Mekong River: Morphology, Evolution, and Management 661Avijit Gupta 22.1 Introduction 661 22.2 The Mekong Basin: Physical Characteristics 663 22.3 The River 669 22.4 The Mekong Over Time: The Geomorphic History 676 22.5 Erosion and Sediment Transfer 678 22.6 The Mekong and Its Basin: Resource and Management 679 22.7 Conclusion 684 Acknowledgements 684 References 684 23 Dynamic Hydrology and Geomorphology of the Yangtze River 687Zhongyuan Chen, Kaiqin Xu, and Masataka Watanabe 23.1 Basin Geology and Landforms 687 23.2 River Morphology 689 23.3 Storage and Transfer of Water and Sediment 691 23.4 Large-Scale River Management – Three Gorges Damand the Planned Water Transfer 700 Acknowledgements 702 References 702 Part III Measurement and Management 24 The Nile River: Geology, Hydrology, Hydraulic Society 704M. Gordon Wolman, Capucine Le Meur, and Robert F. Giegengack 24.1 Introduction 704 24.2 Physiography 705 24.3 Geologic History 709 24.4 Climate and Climate Change 712 24.5 Hydrology 715 24.6 A Unique Record 719 24.7 The Nile and Hydraulic Civilizations 721 24.8 A Recent History of Nile Water Management 725 Acknowledgements 732 References 732 25 Patterns and Controls on Historical Channel Change in the Willamette River, Oregon USA 737Jennifer R. Wallick, Gordon Grant, Stephen Lancaster, John P. Bolte, and Roger Denlinger 25.1 Introduction 737 25.2 An Approach for Interpreting Multiple Impacts on Large Rivers 739 25.3 Geologic Setting, Human, and Flood History of the Willamette 742 25.4 Data and Methods for Measuring Historical Channel Change 750 25.5 Results: Patterns and Controls on Historical Channel Changes 753 25.6 Discussion, Narrative of Historical Channel Change 759 25.7 Conclusion 770 Acknowledgements 771 References 771 26 Rivers and Humans – Unintended Consequences 776Stanley A. Schumm 26.1 Introduction 776 26.2 Armour 776 26.3 Hydrology 783 26.4 Conclusion 793 References 793 27 Large Rivers from Space 796Leal A. K. Mertes and Tamuka Magadzire 27.1 Introduction and Update 796 27.2 Basin Characteristics 799 27.3 Valley Configuration 801 27.4 Geomorphology 804 27.5 Water-surface Elevation, Gradient, and Discharge 804 27.6 Water Extent and Inundation Mapping 804 27.7 Mapping Sediment Concentration 808 27.8 Zambezi River –Water Type Mapping on Floodplains 809 27.9 Thermal Properties 811 27.10 Change Detection 811 27.10.1 Mesopotamian Marshlands 811 References 814 28 Channel Geometry Analysis Technique for the Lower Mississippi River 818Philip J. Soar, Colin R. Thorne, Oliver P. Harmar, David S. Biedenharn, and C. Fred Pinkard 28.1 Introduction 818 28.2 Context 819 28.3 Data Acquisition and Pre-processing 822 28.4 Analytical Approach and Methodology 827 28.5 Results 830 28.6 Interpretation and Commentary 830 28.7 Conclusion 835 Acknowledgements 836 References 837 29 The Management of Large Rivers: Technical and Political Challenges 838Ian C. Campbell 29.1 Introduction 838 29.2 The Challenges of River Management 842 29.3 Management of Rivers in Developing Countries 852 29.4 Conclusion 855 References 856 30 The Physical Diversity and Assessment of a Large River System: The Murray–Darling Basin, Australia 861Martin Thoms, Scott Rayburg, Mel Neave, Melissa Parsons, and Francis Chiew 30.1 Introduction 861 30.2 The Murray–Darling Basin 864 30.3 The Character of Rivers within the Murray–Darling Basin 869 30.4 Assessment of the Physical Condition of Rivers in the Murray–Darling Basin 874 30.5 Resilience and Large Rivers as Social-Ecological Systems – Future Directions 883 30.6 Conclusion 885 Acknowledgements 887 References 887 31 Spatial and Temporal Variations of Water and Sediment Discharges of the Yangtze River (Changjiang) from 1950 to 2018: Erosion of Lake, Channel, and Delta 891Kehui Xu, Shilun Yang, John D. Milliman, Zuosheng Yang, Haifei Yang, and Hui Xu 31.1 Introduction 891 31.2 Physical Setting 893 31.3 Data and Methods of Study 893 31.4 Spatial Variations of Water and Sediment 894 31.5 Temporal Variations of Water and Sediment 895 31.6 Discussion 900 31.7 Channel and Coastal Responses to Declining Sediment Discharge 905 31.8 Future Water and Sediment Discharges 906 31.9 Climatic and Anthropogenic Impacts on Other Global Rivers – the Mississippi Example 907 Acknowledgements 910 References 911 32 Large River Systems and Climate Change 916Michael D. Blum 32.1 Introduction 916 32.2 A Brief History of Ideas 916 32.3 Fluvial Response to Climate Change: Some General Concepts 921 32.4 Fluvial Response to Past Climate Change: Contrasting Examples 932 32.5 Epilog: Large Rivers and Climate Change, Past to Future 946 References 951Index 959

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Book SynopsisPlant Breeding Reviews presents state-of-the-art reviews on plant genetics and the breeding of all types of crops by both traditional means and molecular methods. Many of the crops widely grown today stem from a very narrow genetic base; understanding and preserving crop genetic resources is vital to the security of food systems worldwide. The emphasis of the series is on methodology, a fundamental understanding of crop genetics, and applications to major crops.Table of Contents1. Hari Deo Upadhyaya: Plant Breeder, Geneticist and Genetic Resources Specialist 1Sangam L Dwivedi Abbreviations 3 I. Introduction 3 II. Biographical Sketch 5 III. Contributions 5 A. Genetic Resources Management and Use 6 1. Representative Subsets 6 2. Climate]resilient Germplasm 8 3. Seed Nutrient]dense Germplasm 8 4. Bioenergy 9 5. Germplasm Use in Breeding 9 6. On]farm Conservation and Use of Diversity 10 7. Wild Relatives and Cultigen Genepool 10 8. Gaps in Collections 12 B. Molecular Biology and Biometrics 13 1. Population Structure and Diversity 13 2. Genome]wide Association Mapping 13 3. Candidate Genes Associated with Agronomically Useful Traits 15 4. Ethnolinguistic Groups Shaped Sorghum Diversity in Africa 15 5. Genome Sequencing 16 C. Groundnut Breeding 16 1. Early Maturity 16 2. Drought Tolerance 18 3. Aflatoxin Resistance 18 4. Farmers Participatory Varietal Selection 19 D. Chickpea Breeding 20 IV. Upadhyaya, the Man 20 A. Personality 20 B. Educator and Leader 27 C. International Collaborations 28 D. Recognition 28 1. Awards 28 2. Honours 30 3. Service 30 V. Publications 30 VI. Products 31 A. Cultivars 31 B. Registrations 31 References cited and further reading 33 2. Crop Improvement Using Genome Editing 55Nathaniel M Butler, Jiming Jiang and Robert M Stupar Abbreviations 56 I. Introduction 57 II. Conceptual Framework for Genome Editing 60 A. Development of Sequence]Specific Nucleases 60 1. Early Nucleases 62 2. Designer Nucleases 62 3. RNA]guided Nucleases 65 B. DNA Repair Pathways 66 1. Non]homologous End]joining 66 2. Homologous Recombination 69 C. Modes of Modifications 70 1. NHEJ]mediated Modifications 70 2. HR]mediated Modifications 71 III. Plant Transformation Strategies 72 A. Agrobacterium]mediated Transformation 73 B. Protoplasts and Biolistics 75 C. Plant Viral Systems 76 IV. Harnessing Breaks for Targeted Mutagenesis 77 A. Detecting and Stabilizing Targeted Mutations 78 B. Targeted Mutagenesis in Polyploids 81 V. Precision Gene Editing via HomologousRecombination 82 VI. Genome Editing at the Genome Level 85 A. Large Deletions 85 B. Chromosomal Rearrangements 86 C. Epigenetic Remodelling and Base Editing 87 VII. Future Perspectives 88 A. Nuclease Decisions and Considerations 89 B. Crop Challenges and Advantages 90 C. Regulation of Nuclease Technology 91 Acknowledgements 92 Literature Cited 92 3. Development and Commercialization of CMS Pigeonpea Hybrids 103KB Saxena, D Sharma, and MI Vales Abbreviations 105 I. Introduction 106 II. Reproductive Cycle and Morphology of Pigeonpea 108 A. Induction of Flowering 108 B. Maturity Range 109 C. Flower Structure 110 D. Flowering Pattern 111 E. Pollination and Fertilization 111 F. Natural Cross]pollination 112 1. Cross]pollinating Agents 112 2. Extent of Out]crossing 114 III. Crop Production 115 A. General Agronomy 115 B. Major Production Constraints 115 1. Diseases 115 2. Insect Pests 117 3. Waterlogging 117 IV. Extent and Nature of Heterosis in Pigeonpea 118 V. Genetic Male Sterility]based Hybrid Technology 119 A. Genetic Male Sterility Systems 119 B. Heterosis in GMS]based Hybrids 121 C. Release of the First GMS]based Pigeonpea Hybrid 121 D. Hybrid Seed Production Technology 122 E. Assessment of GMS]based Hybrid Technology 123 VI. Temperature]sensitive Male Sterility 124 VII. Cytoplasmic]nuclear Male Sterility]based Hybrid Technology 125 A. Early Efforts to Produce CMS System 126 B. Breakthrough in Breeding Stable CMS Systems 126 C. Diversification of Cytoplasm 127 1. A1 CMS System from Cajanus sericeus (Benth. ex Bak.) van der Maesen 128 2. A2 CMS System from Cajanus scarabaeoides (L.) Thou 128 3. A3 CMS System from Cajanus volubilis (Blanco) Blanco. 128 4. A4 CMS System from Cajanus cajanifolius (Haines) Maesen 129 5. A5 CMS System from Cajanus cajan (L.) Millsp 129 6. A6 CMS System from Cajanus lineatus (W & A) van der Maesen 130 7. A7 CMS from Cajanus platycarpus (Benth.) van der Maesen 130 8. A8 CMS System from Cajanus reticulatus (Aiton) F. Muell 130 9. A9 CMS System from Cajanus cajan (L.) Millsp 131 D. Effect of Pigeonpea Cytoplasm on Yield 131 E. Fertility Restoration of A4 CMS System 132 VIII. Breeding New Hybrid Parents 133 A. Fixing Priorities 133 B. Selection of Hybrid Parents from Germplasm and Breeding Populations 134 C. Isolation of Fertility]Restoring Inbred Lines from Heterotic Hybrids 136 D. Breeding Dwarf Parental Lines 137 E. Breeding Determinate/Non]determinate Parental Lines 137 F. Disease]resistant Parental Lines 138 G. Use of a Naked]Eye Polymorphic Marker in Hybrid Breeding 139 H. Formation of Heterotic Groups 140 I. Inbreeding Depression 141 IX. Application of Genomics in Breeding Hybrids 142 A. Understanding the Molecular Genetics Basis of the A4 CMS System 143 B. Tagging Fertility]restoring Genes 143 C. Assessment of Genetic Purity 144 D. Potential Role in Breeding Two]line Hybrids 145 X. Commercialization of Hybrid Pigeonpea Technology 146 A. Standard Heterosis 146 1. Early]maturing Hybrids 146 2. Medium] and Late]maturing Hybrids 147 B. Release of the World’s First Commercial Legume Hybrid 149 C. Hybrid Seed Production Technology 152 D. Economics of Hybrid Seed Production 153 XI. Outlook 154 Acknowledgements 157 Literature Cited 157 4. The Evolution of Potato Breeding 169Shelley H Jansky and David M Spooner Abbreviations 170 I. Introduction 170 II. Classification of Cultivated Potato 171 III. Origin of the Cultivated Potato 173 IV. Dynamics of Potato Landrace Evolution 176 V. Origin of the European Potato 178 VI. Nineteenth Century Potato Breeding 179 VII. Early Twentieth Century Potato Breeding 184 VIII. Conventional Potato Breeding 189 IX. Late Twentieth Century Potato Breeding 191 X. Twenty]first Century Potato Breeding 196 A. Is Tetraploidy Necessary for High Tuber Yield in Potato? 196 B. What are the Advantages of Moving to the Diploid Level and Developing Inbred Lines? 198 C. Is It Possible to Develop Diploid Inbred Lines in Potato? 200 XI. Conclusions 202 Literature Cited 203 5. Flavour Evaluation for Plant Breeders 215JC Dawson and GK Healy Abbreviations 217 I. Introduction 217 A. Scope of the Chapter 218 B. Justification for Rapid Sensory Methods 219 C. History 220 II. Types of Rapid Sensory Analysis Methods 221 A. Performance Relative to Conventional Methods 222 B. Methods of Rapid Sensory Evaluation 224 1. Evaluation of Individual Product Attributes 224 Method 1: Intensity Scales 224 Method 2: Flash Profiling 225 Medhod 3: Check All That Apply (CATA) 226 2. Evaluation of Global Differences 227 Method 4: Sorting 227 Method 5: Projective Mapping 228 3. Evaluation in Comparison to a Reference 230 Method 6: Paired Comparisons 230 Method 7: Polarized Sensory Positioning 231 Method 8: Open]ended Evaluations 232 4. Use of Professional Experts in Evaluation 232 C. Numbers of Assessors and Numbers of Samples for Trained, Untrained and Expert Panels 235 III. Data Analysis for Rapid Sensory Methods 236 A. Principal Component Analysis 237 B. Multi]dimensional Scaling 237 C. Multiple Correspondence Analysis 238 D. Generalized Procrustes Analysis 239 E. Multiple Factor Analysis 239 IV. Example of Using Sensory Analysis for Breeding 241 A. Background, Goals and Partners 241 1. Participant Recruitment and Priority Setting 241 2. Cultivar Trials 243 B. Flavour Evaluation Methods Used 243 1. Evolution of Flavour Evaluation Methods 243 2. Intensity Scaling Methods Used with Crew Members 244 3. Chef Projective Mapping Evaluation 245 C. Statistical Methodology 246 1. ANOVA with Intensity Scaling Methods 246 2. Principal Component Analysis of Field Crew Flavour Evaluation Means 246 3. Multiple Factor Analysis of Chef Projective Mapping Data 247 D. Results 247 1. Field Crew Flavour Evaluation with Intensity Scaling 247 2. Chef Flavour Evaluations 250 3. Participant Feedback and Next Steps 253 V. Outlook 254 Acknowledgements 256 Literature Cited 256 6. The Genetic Improvement of Black Walnut for Timber Production 263James R McKenna and Mark V Coggeshall Abbreviations 264 I. Introduction 265 II. Biology of Black Walnut 268 A. Leafing Date 268 B. Flowering 268 1. Female Flowers 269 2. Male Flowers 270 C. Pollen Collection 270 D. Artificial Pollination 271 III. Breeding 272 A. Breeding Strategies 272 B. Selection 272 C. Age]to]Age Correlations 273 D. Improvement 274 E. Analysis 274 IV. Evaluation of Heritable Traits 274 A. Geographic Variation 274 B. Growth 275 C. Timber Quality 275 D. Wood Quality 276 V. Host Plant Resistance to Pathogens and Insect Pests 277 A. Insect Resistance 277 B. Anthracnose 277 C. Thousand Cankers Disease 278 D. Bunch Disease – Witches Broom 278 VI. Propagation 279 A. Seed Propagation 279 B. Grafting 280 C. Rooting 281 VII. Plot Management 281 A. Progeny Tests 281 B. Clone Banks 282 C. Seed Orchards 283 VIII. Future Directions 283 Literature Cited 283 7. A Life in Horticulture and Plant Breeding: The Extraordinary Contributions of Jules Janick 291Irwin L Goldman and Rodomiro Ortiz Abbreviations 292 I. Introduction 292 II. Honors and Commendations 297 III. Students and Teaching 297 IV. Editorial Work 299 V. Books and Proceedings 303 VI. Research 306 A. Patents 307 B. Book Chapters, Reviews and Introductions 307 C. Journal Publications 310 D. Popular and Extension Articles 320 E. Book Reviews 329 F. Encyclopaedia Articles 331 VII. Public Addresses, Invited Seminars and Speeches 332 VIII. Service Contributions 355 IX. Epilogue 358 Literature Cited 360 Index

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Book SynopsisHorticultural Reviews presents state-of-the-art reviews on topics in horticultural science and technology covering both basic and applied research. Topics covered include the horticulture of fruits, vegetables, nut crops, and ornamentals. These review articles, written by world authorities, bridge the gap between the specialized researcher and the broader community of horticultural scientists and teachers.Table of ContentsContributors ix Dedication: Jules Janick xiiiIan Warrington 1. The Flowers of Fragaria × ananassa: Morphology, Response to Photoperiod, and Genetics of Induction 1Andrew Petran and Emily Hoover I. Introduction 2 II. Strawberry Growth, Reproduction, and Commercial Management 2 III. Inflorescence Architecture 13 IV. Genetics of Flower Induction 16 V. Conclusions 26 Literature Cited 27 2. Small Unmanned Aircraft Systems (sUAS): An Emerging Technology for Horticulture 33James A. Robbins I. Introduction 35 II. Aircraft 36 III. Sensors and Data Processing 42 IV. Horticultural Applications 52 V. Challenges 61 VI. Conclusions 64 Literature Cited 64 3. Leaf Blackening: A Serious Impediment to Long‐Term Cold Storage, Transport, and Extended Vase Life in Protea Cut Flowers 73Eleanor W. Hoffman, Waafeka Vardien, Gerard Jacobs, and Nicole E. Windell I. Introduction 74 II. Variation in Expression of Leaf Blackening 76 III. Physiological Causes of Leaf Blackening 80 IV. The Biochemical Mechanisms of Leaf Blackening 87 V. Control of Leaf Blackening 90 VI. Conclusions 99 Literature Cited 100 4. Sapota (Manilkara achras Forb.): Factors Influencing Fresh and Processed Fruit Quality 105Babak Madani, Amin Mirshekari, Elhadi Yahia, and John B. Golding I. Introduction 107 II. Nutritive Value 111 III. Physiological and Biochemical Changes During Fruit Maturation and Ripening 114 IV. Preharvest Effects on Postharvest Quality 120 V. Physiological Disorders 121 VI. Postharvest Diseases 122 VII. Postharvest Technology 123 VIII. Postharvest Treatments 126 IX. Non‐Destructive Methods for Identifying Fruit Maturity and Quality 131 X. Processing 132 XI. Summary and Future Prospects 134 Literature Cited 136 5. The Citron (Citrus medica L.) in China 143David Karp and Xulan Hu I. Introduction 145 II. History and Culture 145 III. Nomenclature 147 IV. Current Citron Cultivation in China 148 V. Major Cultivars of Chinese Citron and Select Citron Hybrids 158 VI. Germplasm Status; Regional and Global Perspective 190 Literature Cited 192 6. Apple Rootstocks: History, Physiology, Management, and Breeding 197Richard P. Marini and Gennaro Fazio I. Introduction 198 II. History 199 III. Rootstock–Scion Interactions 204 IV. Stresses Influencing Rootstock Performance 225 V. Interstems 259 VI. Influence of Rootstock on Fruit Characteristics 262 VII. Genetics and Breeding 266 VIII. Rootstock Evaluation 277 Literature Cited 282 7. Canopy Growth and Development Processes in Apples and Grapevines: Responses to Temperature 313Dennis H. Greer I. Introduction 315 II. Phenology 316 III. Dormant Buds in Apple Trees and Grapevines 317 IV. Winter Chilling in Apple Trees and Grapevines 319 V. Budbreak and Shoot Development in Apple Trees and Grapevines 320 VI. Fruit Growth 332 VII. Biomass Partitioning 338 VIII. Photosynthesis and the Carbon Economy 340 IX. Abiotic Stress Effects on Canopy Physiology 349 X. Impact of Climate Change on Phenology 355 XI. Conclusions 357 Literature Cited 358 8. Organic Acids in Fruits: Metabolism, Functions and Contents 371Robert P. Walker and Franco Famiani I. Introduction 373 II. The Function of the Flesh of Fruits and its Implication for their Organic Acid Contents 375 III. Acids that Contain a Benzene Ring: The Aromatic Acids 377 IV. The Inter‐Related Acids: Ascorbic, Oxalic, Tartaric, and Galacturonic 385 V. Fatty Acids 398 VI. Malic, Citric, and Metabolically Related Acids 399 VII. Conclusions 412 Literature Cited 413 Subject Index 431 Cumulative Subject Index 435 Cumulative Contributor Index 473

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Book SynopsisPresents a multidisciplinary analysis of the integration among reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS). Since plants are the main source of our food, the improvement of their productivity is the most important task for plant biologists. In this book, leading experts accumulate the recent development in the research on oxidative stress and approaches to enhance antioxidant defense system in crop plants. They discuss both the plant responses to oxidative stress and mechanisms of abiotic stress tolerance, and cover all of the recent approaches towards understanding oxidative stress in plants, providing comprehensive information about the topics. It also discusses how reactive nitrogen species and reactive sulfur species regulate plant physiology and plant tolerance to environmental stresses. Reactive Oxygen, Nitrogen and Sulfur Species in Plants: Production, Metabolism, Signaling and Defense MechanismsTable of ContentsVolume 1 Section I Reactive oxygen species metabolism and antioxidant defense 1. Regulated Suicide for Survival: Towards Programmed Cell Death during Reactive Species Mediated-Oxidative Stress of Plant CellsDibyendu Talukdar 2. Iron and its catalytic properties on radical generation: Role of chelators on the Labile Iron Pool (LIP)Elizabeth Robello, Andrea Galatro, Susana Puntarulo 3. Superoxide Dismutases (SODs) and their Role in Regulating Abiotic Stress induced Oxidative Stress in PlantsPanchanand Mishra and Pallavi Sharma 4. The Role of Ascorbate-Glutathione Pathway in Reactive Oxygen Species Balance under Abiotic StressesLiudmyla O. Sakhno, Alla I. Yemets, and Yaroslav B. Blume 5. Oxidative stress and antioxidant defense under combined waterlogging and salinity stressesSavita Duhan, Anita Kumari, Manohar Lal and Sunita Sheokand 6. Role of Polyamines in Protecting Plants from Oxidative StressPooja, Vinod Goyal, Sarita Devi and Renu Munjal 7. Role of Glutathione in Plant Abiotic Stress ToleranceAditya Banerjee, Aryadeep Roychoudhury 8. Molecular approaches in enhancing antioxidant defence in plantsKanika Khanna, Neha Handa, Poonam Yadav, Vandana Gautam, Vinod Kumar, Puja Ohri, Renu Bhardwaj 9. Omics in oxidative stress tolerance in cropsCeyhun kayihan, Füsun Eyidoğan 10. Role of reactive oxygen species signaling in plant growth and developmentNeveen B. Talaat 11. Oxidative Stress and Antioxidant Defense in Germinating Seeds: A Q&A SessionAndrea Pagano, Chiara Forti, Carla Gualtieri, Alma Balestrazzi, Anca Macovei 12. Oxidative stress and antioxidant defense in plants under salinityCaparrós, Mirza Hasanuzzaman, and María Teresa Lao 13. ROS modulation in crop plants under drought stressGiti Verma, Dipali Srivastava, Poonam Tiwari, and Debasis Chakrabarty 14. Oxidative Stress and Antioxidant Defense in Plants under High TemperaturePooja and Renu Munjal 15. Oxidative stress and antioxidant defense in plants exposed to metal/metalloid toxicityMuhammad Arif Ali, Shah Fahad, Idrees Haider, Niaz Ahmed, Shakeel Ahmad, Sajjad Hussain, Muhammad Arshad 16. Oxidative Stress and Antioxidant Defense in Plants Exposed To Ultraviolet RadiationJainendra Pathak, Rajneesh, Haseen Ahmed, Deepak K. Singh, Prashant R. Singh, Deepak Kumar, Vinod K. Kannaujiya, Shailendra P. Singh and Rajeshwar P. Sinha 17. Methods/protocols for determination of oxidative stress in crop plantsVenkidasamy Baskar, Mahima Karthikeyan and Sathishkumar Ramalingam 18. Does seed priming play a role in regulating reactive oxygen species under saline conditions?Mohamed Magdy F. Mansour, Esmat Farouk Ali, Karima Hamid A. Salama 19. Computer-assisted image analysis of the distribution and intensity of reactive oxygen species accumulation in plant leavesJoanna Sekulska-Nalewajko, Jarosław Gocławski, Elżbieta Kuźniak Section-II: Reactive nitrogen species metabolism and signalling 20. Role of nitric oxide in physiological and stress responses of plants under darknessPéter Poór, Zalán Czékus, Attila Ördög 21. Nitric oxide and phytohormones cross-talk during abiotic stresses responses in plantsTariq Shah, Sumbal Wahid, Muhammad Ilyas, Mirza Hasanuzzaman 22. The role of nitric oxide in the antioxidant defense of plants exposed to UV-B radiationRaúl Cassia, Melina Amenta, María Belén Fernández, Macarena Nocioni, and Valeria Dávila 23. Reactive oxygen species and nitric oxide production, regulation and function during defence responseEliana Molina-Moya, Laura C. Terrón-Camero, Leyre Pescador-Azofra, Luisa M. Sandalio, María C. Romero-Puertas 24. Role of nitric oxide in growth regulation and re-orientation of pollen tubesTariq Shah, Mehmood Ali Noor and Mirza Hasanuzzaman 25. Nitric oxide (NO)-Mediated Plant Stress SignalingL.V. Dubovskaya and Y.S. Bakakina 26. S-nitrosoglutathione (GSNO) and plant stress responsesAnjali Khajuria, Shagun Bali, Priyanka Sharma, Ravinderjit Kaur, Shivam Jasrotia, Poonam Saini, Puja Ohri and Renu Bhardwaj Volume 2 Section-III: Reactive sulfur species metabolism and signaling 27. Hydrogen sulfide in guard cell signalingCarlos García-Mata 28. Hydrogen sulfide: a new gasotransmitter in plant defensesYanjie Zhang, Yanxi Pei, and Guangdong Yang 29. Interplay between Hydrogen Sulfide and Calcium Signaling in Plant Abiotic Stress Response and AdaptationZhong-Guang Li 30. Reactive Sulfur species-Key regulators of abiotic stress tolerance in plantsFahim Nawaz, Sadia Majeed, Khawaja Shafique Ahmad, Muhammad Aqib, Muhammad Asif Shehzad, Muhammad Aurangzaib and Muhammad Shahbaz 31. Reactive Sulfur Species: A new player in plant physiology?Martin Clemens Gruhlke 32. Role of reactive sulfur species in the oxidative metabolism in plantsMuhammad Ija, Qasim Ali, Shah Fahad, Sana Ashraf, Muhammad Shahid and Shakeel Ahmad 33. Hydrogen Sulfide in Plant Abiotic Stress Tolerance: Progress and PerspectivesParankusam Santisree, Srivani S Adimulam, Pradeepreddy Bommineni, Pooja Bhatnagar-Mathur and Kiran K. Sharma Section-IV: Crosstalk among reactive oxygen, nitrogen and sulfur species 34. Reactive oxygen species, reactive nitrogen species and oxidative metabolism under waterlogging stressManohar Lal, Anita Kumari, Pooja Dhansu and Sunita Sheokand 35. Reactive Oxygen and Nitrogen Species in Stress-Induced Programmed Death of Plant Cultured CellsMassimo Malerba, and Raffaella Cerana 36. Finding a Place for NO in Everyday Plant LifeSvetlana Batasheva, Farit Abdrakhimov, Guzel Akhtyamova, Larisa Khamidullina, Vladimir Chikov 37. H2O2, NO and H2S: Tailoring in suiting plants against abiotic stressesCristiane J. da-Silva, Ana Claudia Rodrigues, Luzia V. Modolo 38. Cross talk among reactive oxygen, nitrogen and sulfur during abiotic stress in plantsParminder Kaur, Neha Handa, Vinod Verma, Palak Bakshi, Rashami Kalia, Shelja Sareen, Avinash Nagpal, Adarsh Pal Vig, Bilal Ahmad Mir and Renu Bhardwaj 39. Emerging technologies for enhancing ROS/RNS homeostasisAllAlla I. Yemets, Yuriy V. Karpets, Yuriy E. Kolupaev, and Yaroslav B. Blume 40. Compartmentalization of reactive oxygen species and nitric oxide production in plant cellsMartina Janků, Tereza Tichá, Lenka Luhová, Marek Petřivalský

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Book SynopsisWater harvesting is gaining more and more recognition as a sustainable and resilient water supply options. It is economically viable, socially compatible and environmentally friendly. Water harvesting has proven to be a robust solution to overcome or reduce water shortages all over the world. It is important to understand how to apply this practice in a sustainable and effective way to make full use of its potential in a world increasingly threatened by water scarcity. The Handbook of Water Harvesting and Conservation: Basic Concepts and Fundamentals is the most comprehensive, up-to-date and applied handbook on water harvesting and conservation yet published. The book's 30 chapters -- written by 84 outstanding international experts from approximately 20 selected countries faced by drought -- explore, critique and develop concepts and systems for water harvesting. The editors bring together many perspectives into a synthesis that is both academically based and practicalTable of ContentsList of Contributors xxi About the Editors xxvii Part A Concepts and Standards for a Secure Water Harvesting 1 1 Concept and Technology of Rainwater Harvesting 3Fayez Abdulla, Cealeen Abdulla, and Saeid Eslamian 1.1 Introduction 3 1.2 Concept of Rainwater Harvesting 4 1.3 Technologies of Rainwater Harvesting 5 1.4 Advantages and Disadvantages of Rainwater Harvesting 8 1.5 Feasibility of Rainwater Harvesting across Different Climatic Zones 10 1.6 Roof Rainwater Harvesting System Components 11 1.7 Calculation of Potential HarvestedWater 13 1.8 Water Quality and its Health and Environmental Impacts 14 1.9 System Operation and Maintenance 14 1.10 Conclusion 15 References 15 2 Rainwater Harvesting: Recent Developments and Contemporary Measures 17Aline Pires Veról, Marcelo Gomes Miguez, Elaine Garrido Vazquez, Fernanda Rocha Thomaz, Bruna Peres Battemarco, and Assed Naked Haddad 2.1 Introduction 17 2.2 Water Resource Management 18 2.3 Water Management at the Building Scale 25 2.4 Analysis of Payback of Rainwater Harvesting Systems 34 2.5 Conclusion 35 Acknowledgment 35 References 36 3 Standards for Rainwater Catchment Design 39Sisuru Sendanayake and Saeid Eslamian 3.1 Introduction 39 3.2 Catchment Surface 40 3.3 Conveyance System 42 3.4 Storage Tank 44 3.5 Pre-treatment of Roof Collection 53 3.6 Distribution System and Related Regulations 54 3.7 Conclusion 54 References 55 4 Water Security Using Rainwater Harvesting 57Adebayo Eludoyin, Oyenike Eludoyin, Tanimola Martins, Mayowa Oyinloye, and Saeid Eslamian 4.1 Introduction 57 4.2 Concept of Rainwater Harvesting 57 4.3 Rainwater Collection Systems 58 4.4 Rainwater Storage 61 4.5 Importance of Rainwater Harvesting 61 4.6 Quality Assessment of Harvested Rainwater 64 4.7 Problems Associated with Rainwater Harvesting 64 4.8 Conclusion 65 References 65 Part B Water Harvesting Resources 69 5 Single-Family Home and Building Rainwater Harvesting Systems 71Duygu Erten 5.1 Introduction 71 5.2 Historical Development of RWH and Utilization 71 5.3 Pros and Cons of RWH Systems 72 5.4 Current Practices Around theWorld 78 5.5 Health Risks of Roof-Collected Rainwater 78 5.6 Guides, Policy, and Incentives 79 5.7 Green Building Certification Systems and RWH 82 5.8 Conclusion 84 References 85 6 Water Harvesting in Farmlands 87Elena Bresci and Giulio Castelli 6.1 Introduction 87 6.2 Water Harvesting: Definitions 87 6.3 Floodwater Harvesting in Farmlands 88 6.4 Macro-CatchmentWater Harvesting in Farmlands 91 6.5 Micro-CatchmentWater Harvesting in Farmlands 94 6.6 RooftopWater Harvesting in Farmlands 95 6.7 Water Harvesting and Fertilization 96 6.8 Conclusions and Future Perspectives 96 References 97 7 Rainwater Harvesting for Livestock 101Billy Kniffen 7.1 Introduction 101 7.2 Rainfall Harvesting on the Land 101 7.3 AnimalWater Requirements 102 7.4 Harvested Rainfall as a Source for Livestock 103 7.5 Requirements for Harvesting Rainwater for Livestock 104 7.6 Distribution ofWater for Livestock 107 7.7 Rainwater System Maintenance 107 7.8 Conclusion 107 References 108 8 Road Water Harvesting 109Negin Sadeghi and Saeid Eslamian 8.1 Introduction 109 8.2 Water Harvesting Systems and Their Characteristics 110 8.3 RoadWater Harvesting 113 8.4 Conclusion 123 References 124 Part C Hydroinformatic and Water Harvesting 127 9 Application of RS and GIS for Locating Rainwater Harvesting Structure Systems 129Dhruvesh Patel, Dipak R. Samal, Cristina Prieto, and Saeid Eslamian 9.1 Introduction 129 9.2 Experimental Site 131 9.3 Methodology 131 9.4 Results and Discussions 137 9.5 Conclusion 141 References 142 10 Information Technology in Water Harvesting 145S. Sreenath Kashyap, M.V.V. Prasad Kantipudi, Saeid Eslamian, Maryam Ghashghaie, Nicolas R. Dalezios, Ioannis Faraslis, and Kaveh Ostad-Ali-Askari 10.1 Introduction 145 10.2 Water Harvesting Methods 145 10.3 The Internet of Things (IoT) 147 10.4 Assessing the Available Subsurface Resources Using the IoT 148 10.5 The IoT Devices for Efficient Agricultural/Irrigation Usage 150 10.6 Conclusions 151 References 151 11 Global Satellite-Based Precipitation Products 153Zhong Liu, Dana Ostrenga, Andrey Savtchenko, William Teng, Bruce Vollmer, Jennifer Wei, and David Meyer 11.1 Introduction 153 11.2 Precipitation Measurements from Space 154 11.3 Overview of NASA Satellite-Based Global Precipitation Products and Ancillary Products at GES DISC 155 11.4 Data Services 159 11.5 Examples 163 11.6 Conclusion 171 Acknowledgments 172 References 172 12 Risk Analysis of Water Harvesting Systems 177Maria Do Céu Almeida, Nelson Carriço, João Santos and Saeid Eslamian 12.1 Introduction 177 12.2 Concepts and Terminology 177 12.3 General Approaches to Risk Management Applicable to RWHS 177 12.4 Supporting Risk Management for RWHS 181 12.5 Hazards and Exposure Modes 182 12.6 Rainwater Collection Reliability asWater Source 183 12.7 Specific Risk Treatment Actions 185 12.8 Process Control and Monitoring 186 12.9 Conclusion 187 References 187 Part D Hydrological Aspects of Water Harvesting 191 13 Return Period Determination for Rainwater Harvesting System Design 193Sandeep Samantaray, Dillip K. Ghose, and Saeid Eslamian 13.1 Introduction 193 13.2 Study Area 194 13.3 Overview of Rainwater Harvesting 197 13.4 Methodology 198 13.5 Results and Discussions 201 13.6 Conclusions 203 References 203 14 Rainwater Harvesting Impact on Urban Groundwater 207A. Jebamalar, R. Sudharsanan, G. Ravikumar, and Saeid Eslamian 14.1 Introduction 207 14.2 State of the Art 208 14.3 Study Area and Data Collection 209 14.4 Methodology 213 14.5 Temporal Analysis of Groundwater Level 214 14.6 Spatial Analysis of Groundwater Table 215 14.7 Impact of RWH on Groundwater Recharge 215 14.8 Model Simulations for Impact of RWH Systems 217 14.9 Model Predictions for the Future 218 14.10 Conclusion 222 Acknowledgement 223 References 223 15 Effects of Water Harvesting Techniques on Sedimentation 225Siavash Fasihi, and Saeid Eslamian 15.1 Introduction 225 15.2 Qualitative Effects and Data Collection 226 15.3 Sedimentation in Small Check Dams 228 15.4 Revised Universal Soil Loss Equation (RUSLE) 229 15.5 Limburg Soil Erosion Model (LISEM) 235 15.6 Conclusion 238 References 238 Part E Hydrometeorological Water Harvesting 243 16 Principles and Applications of Atmospheric Water Harvesting 245Mousa Maleki, Saeid Eslamian, and Boutaghane Hamouda 16.1 Introduction 245 16.2 AtmosphericWater Harvesting Necessity 245 16.3 Methods of AtmosphericWater Harvesting 246 16.4 Energy Requirements of AMH andWater Production Costs 247 16.5 Atmospheric Vapor Harvesting Systems 248 16.6 Conclusion 256 References 257 17 Dew Harvesting on High Emissive Natural and Artificial Passive Surfaces 261Jose Francisco Maestre-Valero, Bernardo Martin-Gorriz, Victoriano Martínez-Alvarez, and Saeid Eslamian 17.1 Introduction 261 17.2 Passive Surfaces for the Case Studies 262 17.3 Data Collection 264 17.4 Case Studies for Dew Collection 265 17.5 Dew Modeling 267 17.6 Conclusion 270 Acknowledgments 271 References 271 18 Atmospheric Water Harvesting Using Waste Energy from Landfills and Oilfields 273Enakshi Wikramanayake, Onur Ozkan, Aritra Kar, and Vaibhav Bahadur 18.1 Introduction 273 18.2 Refrigeration-Based AtmosphericWater Harvesting Systems 275 18.3 ModelingWaste Natural Gas-Based AtmosphericWater Harvesting 276 18.4 Landfill Gas-Based AtmosphericWater Harvesting 277 18.5 Oilfield Gas-Based AtmosphericWater Harvesting 283 18.6 Sensitivity of theWater Harvest to Various Parameters 284 18.7 Comparison of AWH to Other Techniques for ProducingWater 285 18.8 Perspectives on AtmosphericWater Harvesting 285 18.9 Conclusions 286 Acknowledgements 286 References 286 Part F Environmental Aspects of Water Harvesting 289 19 Treatment Techniques in Water Harvesting 291Brandon Reyneke, Monique Waso, Thando Ndlovu, Tanya Clements, Sehaam Khan, and Wesaal Khan 19.1 Introduction 291 19.2 Pretreatment of Harvested Rainwater: Prevention of Debris Entry and Sedimentation 292 19.3 Chemical Disinfection 293 19.4 Physical Disinfection 295 19.5 Biological Treatment 298 19.6 Conclusion 300 References 301 20 Water Recycling from Palm Oil Mill Effluent 307Hossein Farraji, Irvan Dahlan, and Saeid Eslamian 20.1 Introduction 307 20.2 Problem Statement 307 20.3 Palm Oil Production 308 20.4 POME as an Agro-IndustryWastewater 308 20.5 Characteristics of POME 308 20.6 POME Treatment Methods 312 20.7 Water Recycling by Membrane Technique 313 20.8 Application of the SBR in POME Treatment 314 20.9 Discussions 316 20.10 Conclusion 316 References 316 Part G Green Water Harvesting 321 21 Vegetation Advantages for Water and Soil Conservation 323Hadis Salehi Gahrizsangi, Saeid Eslamian, Nicolas R. Dalezios, Anna Blanta, and Mohadaseh Madadi 21.1 Introduction 323 21.2 Background 323 21.3 Vegetation Advantage for Soil andWater Conservation in Artificial Plots 329 21.4 Conclusions 334 References 335 22 Water Harvesting in Forests: An Important Step in Water-Food-Energy Nexus 337Rina Kumari and Saeid Eslamian 22.1 Introduction 337 22.2 GlobalWater Scarcity 337 22.3 Change in Land Use-Land Cover and its Impact on Forest andWater Resources 339 22.4 Forest Hydrology 339 22.5 Rainwater Harvesting in Forests 343 22.6 Deforestation and its Impact 345 22.7 Forest Management andWatershed Development 346 22.8 Knowledge Gaps 347 22.9 Forests andWater in International Agreements 348 22.10 Role of Geospatial Technologies 348 22.11 Managing the Climate-Water-Forest Nexus for Sustainable Development 349 22.12 Case Studies 350 22.12.1 CombatingWater Scarcity in Latin America 350 22.12.2 Amazon River 350 22.12.3 Case Study of Southeast Asia 350 22.13 Conclusions 350 References 351 23 Rainwater and Green Roofs 355Sara Nazif, Seyed Ghasem Razavi, Pouria Soleimani, and Saeid Eslamian 23.1 Introduction 355 23.2 Green Roof Components 355 23.3 Green Roof Types 358 23.4 Green Roof Irrigation 359 23.5 Green Roof Standards 359 23.6 Green Roofs for Rainwater Collection and Storage 360 23.7 Green Roof Effect on Runoff Quality 363 23.8 Other Functions of Green Roofs 364 23.9 Cost and Benefit Analysis of Green Roofs 367 23.10 Conclusion 369 References 369 24 Green Landscaping and Plant Production with Water Harvesting Solutions 373Saeid Eslamian, Saeideh Parvizi, and Sayed Salman Ghaziaskar 24.1 Introduction 373 24.2 Water Harvesting 374 24.3 Rainwater Harvesting 374 24.4 The Goals and Benefits of Rainwater Harvesting 376 24.5 Impact of RWHR on Infiltration and Surface Runoff Processes 376 24.6 Climate Change and RWH 376 24.7 Landscape Functions and RWH 377 24.8 Hydrological Functions and RWH 377 24.9 Soil Fertility and Biomass Production 378 24.10 Discussions 380 24.11 Conclusions 381 References 381 Part H Reliable Rainwater Harvesting and Storage Systems 385 25 Comparing Rainwater Storage Options 387Sara Nazif, Hamed Tavakolifar, Hossein Abbasizadeh, and Saeid Eslamian 25.1 Introduction 387 25.2 History of Rainwater Harvesting 387 25.3 Benefits of Rainwater Storage 388 25.4 Main Rainwater Storage Options 389 25.5 Comparing Rainwater Storage Options 395 25.6 Conclusion 398 References 398 26 Rainwater Harvesting Storage-Yield-Reliability Relationships 401John Ndiritu 26.1 Introduction 401 26.2 The Rainwater Harvesting Storage-Yield-Reliability Problem 401 26.3 Modeling Storage-Yield-Reliability Relationships 402 26.4 Key Considerations 411 26.5 Conclusions 412 References 413 27 Towards Developing Generalized Equations for Calculating Potential Rainwater Savings 417Monzur A. Imteaz, Muhammad Moniruzzaman and, Abdullah Yilmaz 27.1 Introduction 417 27.2 State of the Art 418 27.3 Methodology 419 27.4 Study Area and Data 420 27.5 Results 421 27.6 Conclusions 423 Acknowledgement 424 References 424 Part I Sustainable Water Harvesting and Conservation in a Changing Climate 427 28 Water Harvesting, Climate Change, and Variability 429Jew Das, Manish Kumar Goyal, and N.V. Umamahesh 28.1 Introduction 429 28.2 Water Harvesting 431 28.3 Case Study 437 28.4 Results and Discussion 439 28.5 Conclusion 443 References 444 29 Water Harvesting and Sustainable Tourism 447Neda Torabi Farsani, Homa Moazzen Jamshidi, Mohammad Mortazavi, and Saeid Eslamian 29.1 Introduction 447 29.2 Water Management: An Approach to Sustainable Tourism 447 29.3 Tourism andWater Harvesting Economy 451 29.4 Conclusion 453 References 453 30 Rainwater Harvesting Policy Issues in the MENA Region: Lessons Learned, Challenges, and Sustainable Recommendations 457Muna Yacoub Hindiyeh, Mohammed Matouq, and Saeid Eslamian 30.1 Introduction 457 30.2 Definitions of RWH 457 30.3 Rainwater Harvesting Toward Millennium and Sustainable Development Goals 458 30.4 Water Administration and Legislation 459 30.5 Policy and Regulatory Approaches to RWH Use 459 30.6 Considerations When Establishing a Municipal Rainwater Harvesting Program 463 30.7 Regulatory Approaches in Other Countries 464 30.8 Challenges and Limitations 469 30.9 Future Recommendations for the MENA Region 470 30.10 Conclusion 470 References 471 Index 475

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Book SynopsisTable of ContentsContributors Preface 1 Achieving Complexity at the Bottom Through the Flavylium Cation-Based Multistate. A Comprehensive Kinetic and Thermodynamic StudyJohan Mendoza and Fernando Pina 1.1 Introduction 1.2 Flavylium cation as a metamorphosis generator 1.3 Extending the multistate of anthocyanins and related compounds to the basic region 1.4 The kinetic processes 1.5 Conclusions and perspectives 2 Proanthocyanidin Oligomers with Doubly-Linked (A-Type) Interflavan Connectivity: Structure and SynthesisKen Ohmori and Keisuke Suzuki 2.1 Introduction 2.2 Structure 2.3 Synthetic studies 2.4 Conclusion 3 Answering the Call of the Wild: Polyphenols in Traditional Therapeutic PracticeMary Ann Lila and Kriya Dunlap 3.1 Introduction 3.2 The wildcrafting tradition 3.3 How wildcrafted edible plants differ from agricultural commodities 3.4 Animal mimickry/Zoopharmacognosy 3.5 Probing the mechanisms behind polyphenol-rich traditional medicines bioactivity 3.6 Commercialization prospects for wildcrafted polyphenol-rich plants 3.7 Acknowledgements 4 Causes and Consequences of Condensed Tannin Variation in Populus: A Molecules to Ecosystems PerspectiveKennedy F. Rubert-Nason and Richard L. Lindroth 4.1 Introduction 4.2 Condensed tannin biosynthesis 4.3 Allocational tradeoffs influence CT production 4.4 Causes of quantitative and qualitative variation in Populus CTs 4.5 Roles of CT variation in Populus-environment interactions 4.6 Importance of CTs in Populus-dominated ecosystems of the Anthropocene 4.7 Conclusions and challenges 5 Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of Proanthocyanidins to Determine Authenticity of Functional Foods and Dietary SupplementsDaniel Esquivel-Alvarado, Jess D. Reed, and Christian G. Krueger 5.1 Introduction 5.2 Introduction to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) 5.3 Mass spectrometry of proanthocyanidins 5.4 Deconvolution of isotope patterns of A- to B-type interflavan bonds in proanthocyanidins 5.5 Multivariate analysis of MALDI-TOF MS spectra data 5.6 Conclusion 6 Challenges in Analyzing Bioactive ProanthocyanidinsWayne E. Zeller and Irene Mueller-Harvey 6.1 Introduction 6.2 Structural diversity of proanthocyanidins 6.3 Noted challenges in proanthocyanidin analysis 6.4 Fate of proanthocyanidins in digestive tract and during plant fermentation 6.5 Definition and possible origins of non-extractable proanthocyanidins (NEPAs) 6.6 Universal problems of proanthocyanidin analysis 6.7 Proanthocyanidin characterization by depolymerization 6.8 Mass spectrometry 6.9 Nuclear Magnetic Resonance Spectroscopy 6.10 Colorimetry 6.11 Infra-red spectroscopy 6.12 Conclusions 7 Lignin Monomers Derived from the Flavonoid and Hydroxystilbene Biosynthetic PathwaysJosé C. del Río, Jorge Rencoret, Ana Gutiérrez, Wu Lan, Hoon Kim and John Ralph 7.1 Lignin monomers derived from the monolignol biosynthetic pathway 7.2 Flavonoid and hydroxystilbene biosynthetic pathways 7.3 Radical coupling of flavonoids and hydroxystilbenes with monolignols – flavonolignans and stilbenolignans 7.4 Lignin monomers derived from the flavonoid and hydroxystilbene biosynthetic pathways 7.5 Conclusions and future prospects 7.6 Acknowledgements 8 Complex Regulation of Proanthocyanidin Biosynthesis in Plants by R2R3 MYB Activators and RepressorsDawei Ma and C. Peter Constabel 8.1 Introduction to PAs and flavan-3-ols 8.2 Regulation of PA and flavonoid biosynthesis by MYB transcription factors 8.3 The importance of repressor MYBs in PA and flavonoid metabolism 8.4 The complex interaction of PA MYB activators, MYB repressors and bHLH transcription factors 8.5 Developmental and plant hormone-mediated regulation of the PA pathway via MYBs 8.6 Stress activation of PA synthesis by MYBs in poplar and other woody plants 8.7 Summary and conclusions 8.8 Acknowledgements 9 Conservation and Divergence Between Bryophytes and Angiosperms in the Biosynthesis and Regulation of Flavonoid ProductionKevin M. Davies, Rubina Jibran, Nick W. Albert, Yanfei Zhou and Kathy E. Schwinn 9.1 Introduction 9.2 Flavonoid biosynthesis in basal plants 9.3 Origins of the phenylpropanoid biosynthetic pathway and conservation across the embryophytes 9.4 Notable phenylpropanoids of bryophytes 9.5 Regulation of flavonoid production 9.6 Concluding remarks 9.7 Acknowledgements 10 Matching Proanthocyanidin Use with Appropriate Analytical MethodJames A. Kennedy 10.1 Introduction 10.2 General proanthocyanidin structure and analysis 10.3 Red Wine Mouthfeel 10.4 Biological Activity 10.5 Summary 11 Imaging Polyphenolic Compounds in Plant TissuesMarisa S. Otegui 11.1. Introduction 11.2. The chemical nature and intrinsic fluorescence properties of polyphenols 11.3. Microscopy-based methods for imaging plant phenolic compounds 11.4 Polyphenols and microscopy imaging 11.5 Future challenges and opportunities in imaging plant metabolites Acknowledgments References Index

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Book SynopsisLearn basic Python programming to create functional and effective visualizations from earth observation satellite data sets Thousands of satellite datasets are freely available online, but scientists need the right tools to efficiently analyze data and share results. Python has easy-to-learn syntax and thousands of libraries to perform common Earth science programming tasks. Earth Observation Using Python: A Practical Programming Guide presents an example-driven collection of basic methods, applications, and visualizations to process satellite data sets for Earth science research. Gain Python fluency using real data and case studies Read and write common scientific data formats, like netCDF, HDF, and GRIB2 Create 3-dimensional maps of dust, fire, vegetation indices and more Learn to adjust satellite imagery resolution, apply quality control, and handle big files Develop useful workflows and learn to share cTable of ContentsForeword Introduction 1 A Tour of Current Satellite Missions and Products 1.1 History of Computational Scientific Visualization 1.2 Brief catalog of current satellite products 1.2.1 Meteorological and Atmospheric Science 1.2.2 Hydrology 1.2.3 Oceanography and Biogeosciences 1.2.4 Cryosphere 1.3 The Flow of Data from Satellites to Computer 1.4 Learning using Real Data and Case Studies 1.5 Summary 1.6 References 2 Overview of Python 2.1 Why Python? 2.2 Useful Packages for Remote Sensing Visualization 2.2.1 NumPy 2.2.2 Pandas 2.2.3 Matplotlib 2.2.4 netCDF4 and h5py 2.2.5 Cartopy 2.3 Maturing Packages 2.3.1 xarray 2.3.2 Dask 2.3.3 Iris 2.3.4 MetPy 2.3.5 cfgrib and eccodes 2.4 Summary 2.5 References 3 A Deep Dive into Scientific Data Sets 3.1 Storage 3.1.1 Single-values 3.1.2 Arrays 3.2 Data Formats 3.2.1 Binary 3.2.2 Text 3.2.3 Self-describing data formats 3.2.4 Table-Driven Formats 3.2.5 geoTIFF 3.3 Data Usage 3.3.1 Processing Levels 3.3.2 Product Maturity 3.3.3 Quality Control 3.3.4 Data Latency 3.3.5 Re-processing 3.4 Summary 3.5 References 4 Practical Python Syntax 4.1 "Hello Earth" in Python 4.2 Variable Assignment and Arithmetic 4.3 Lists 4.4 Importing Packages 4.5 Array and Matrix Operations 4.6 Time Series Data 4.7 Loops 4.8 List Comprehensions 4.9 Functions 4.10 Dictionaries 4.11 Summary 4.12 References 5 Importing Standard Earth Science Datasets 5.1 Text 5.2 NetCDF 5.3 HDF 5.4 GRIB2 5.5 Importing Data using xarray 5.5.1 netCDF 5.5.2 GRIB2 5.5.3 Accessing datasets using OpenDAP 5.6 Summary 5.7 References 6 Plotting and Graphs for All 6.1 Univariate Plots 6.1.1 Histograms 6.1.2 Barplots 6.2 Two Variable Plots 6.2.1 Converting Data to a Time Series 6.2.2 Useful Plot Customizations 6.2.3 Scatter Plots 6.2.4 Line Plots 6.2.5 Adding data to an existing plot 6.2.6 Plotting two side-by-side plots 6.2.7 Skew-T Log-P 6.3 Three Variable Plots 6.3.1 Filled Contour 6.3.2 Mesh Plots 6.4 Summary 6.5 References 7 Creating Effective and Functional Maps 7.1 Cartographic Projections 7.1.1 Projections 7.1.2 Plate Carrée 7.1.3 Equidistant Conic 7.1.4 Orthographic 7.2 Cylindrical Maps 7.2.1 Global plots 7.2.2 Changing projections 7.2.3 Regional Plots 7.2.4 Swath Data 7.2.5 Quality Flag Filtering 7.3 Polar Stereographic Maps 7.4 Geostationary Maps 7.5 Plotting datasets using OpenDAP 7.6 Summary 7.7 References 8 Gridding Operations 8.1 Regular 1D grids 8.2 Regular 2D grids 8.3 Irregular 2D grids 8.3.1 Resizing 8.3.2 Regridding 8.3.3 Resampling 8.4 Summary 8.5 References 9 Meaningful Visuals through Data Combination 9.1 Spectral and Spatial Characteristics of Different Sensors 9.2 Normalized Difference Vegetation Index (NDVI) 9.3 Window Channels 9.4 RGB 9.4.1 True Color 9.4.2 Dust RGB 9.4.3 Fire/Natural RGB 9.5 Matching with Surface Observations 9.5.1 With user-defined functions 9.5.2 With Machine Learning 9.6 Summary 9.7 References 10 Exporting with Ease 10.1 Figures 10.2 Text Files 10.3 Pickling 10.4 NumPy binary files 10.5 NetCDF 10.5.1 Using netCDF4 to create netCDF files 10.5.2 Using Xarray to create netCDF files 10.5.3 Following Climate and Forecast (CF) metadata conventions 10.6 Summary 11 Developing a Workflow 11.1 Scripting with Python 11.1.1 Creating scripts using text editors 11.1.2 Creating scripts from Jupyter Notebooks 11.1.3 Running Python scripts from the command line 11.1.4 Handling output when scripting 11.2 Version Control 11.2.1 Code Sharing though Online Repositories 11.2.2 Setting-up on GitHub 11.3 Virtual Environments 11.3.1 Creating an environment 11.3.2 Changing environments from the command line 11.3.3 Changing environments in Jupyter Notebook 11.4 Methods for code development 11.5 Summary 11.6 References 12 Reproducible and Shareable Science 12.1 Clean Coding Techniques 12.1.1 Stylistic conventions 12.1.2 Tools for Clean Code 12.2 Documentation 12.2.1 Comments and docstrings 12.2.2 README file 12.2.3 Creating useful commit messages 12.3 Licensing 12.4 Effective Visuals 12.4.1 Make a Statement 12.4.2 Undergo Revision 12.4.3 Are Accessible and Ethical 12.5 Summary 12.6 References Conclusion A Installing Python A.1 Download and Install Anaconda A.2 Package management in Anaconda A.3 Download sample data for this book B Jupyter Notebooks B.1 Running on a Local Machine (New Coders) B.2 Running on a Remote Server (Advanced) B.3 Tips for Advanced Users B.3.1 Customizing Notebooks with Configuration Files B.3.2 Starting and Ending Python Scripts B.3.3 Creating Git Commit templates C Additional Learning Resources D Tools D.1 Text Editors and IDEs D.2 Terminals E Finding, Accessing, and Downloading Satellite Datasets E.1 Ordering data from NASA EarthData E.2 Ordering data from NOAA/CLASS F Acronyms Acknowledgements

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Book SynopsisOPEN CHANNEL DESIGN A fundamental knowledge of flow in open channels is essential for the planning and design of systems to manage water resources. Open channel design has applications within many fields, including civil engineering, agriculture, hydrology, geomorphology, sedimentology, environmental fluid and sediment dynamics and river engineering. Open Channel Design: Fundamentals and Applications covers permissible velocity, tractive force, and regime theory design methodologies and applications. Hydraulic structures for flow control and measurement are covered. Flow profiles and their design implications are covered. Sediment transport mechanics and moveable boundaries in channels are introduced. Finally, a brief treatment of the St. Venant equations and Navier-Stokes equations are introduced as topics to be explored in more advanced courses. The central goal is to prepare students for work in engineering offices where they will be involved with aspects of lanTable of ContentsPreface ix Acknowledgments xi About the Companion Website xii 1 Basic Principles and Flow Classifications 1 Fluid Mechanics Foundations 2 Hydrologic Foundations 7 Presentation Organization 8 Problems and Questions 10 References 11 2 Channel Fundamentals 12 Goals 12 Channel Elements and Nomenclature 12 General Flow Relationships 17 Uniform Flow Relationships 17 Theoretical Considerations 23 Natural, Compound, or Sustainable Channels 25 Lined Channels, Optimum Channels, and Velocity Constraints 28 Channel Installation 43 Summary 43 Problems and Questions 47 References 51 3 Vegetated Waterways and Bioswales 53 Goals 53 Background 53 Channel Planning 54 Basic Design Procedures 56 Bioswales 60 Vegetated Filter Strips 62 Temporary Linings 62 Summary 66 Problems and Questions 68 References 69 4 Tractive Force Methods for Earthen Channels 71 Goals 71 Riprap-Lined or Earthen Waterways (Earthen II) 71 Tractive Force for Vegetated Waterways 77 Details and Origins of The Parabolic Cross-section 82 Costing Channel Designs 92 Steady Uniform Flow Conclusion 94 Problems and Questions 95 References 97 5 The Energy Equation and Gradually Varied Flows 98 Goals 98 Energy Preliminaries – Velocity Profiles and Boundary Effects 98 Longer Transitions – Gradually Varied Flow Analyses 115 Conclusions 126 Problems and Questions 126 References 127 6 Momentum Equation for Analyzing Varied Steady Flows and Spatially Varied Increasing Flows 128 Goals 128 Rapidly Varying Steady Flows (dQ/dt = 0, dQ/dx = 0, dy/dx varies) 128 Spatially Varying Steady Flow (dQ/dt = 0, dQ/dx varies, dy/dx varies) 137 Conclusions 142 Problems and Questions 142 References 143 7 Hydraulics of Water Management Structures 144 Goals 144 Structure Types 145 Hydraulic Concepts 147 Stage–Discharge Relationships of Weir Inlets and Flumes 150 Discharge Relations of Orifices and Sluice Gates Inlet Devices 156 Flow Hydraulics of Closed Conduits 157 Stage–Discharge Curves for Culverts and Spillways 167 Closed Conduit Systems for Urban Stormwater Collection 169 Ecologic Suitability 171 Summary and Conclusions 177 Problems and Questions 179 References 182 8 Gradually Varied Unsteady Flow 185 Goals 185 Hydrologic Routing Approaches 187 Kinematic Wave Method 194 Diffusion Wave Method 199 Dynamic Routing 203 Summary and Conclusions 209 Problems and Questions 210 References 211 9 Rapidly Varying Unsteady Flow Applications – Waves 213 Goals 213 Surface Irrigation 213 Sluice Gate and Related Operations 217 The Dam-Break Problem 223 Oscillatory Waves 230 Summary and Conclusions 233 Problems and Questions 234 References 235 10 Channel Design Emphasizing Fine Sediments and Survey of Alluvial Channel Sediment Transport 236 Goals 236 Alluvial Channel vs. Earthen Channel and Other Preliminaries 237 Early Approaches to Sediment Transport 237 Incipient Motion 238 Riprap or Revetment Specification 243 Bedform Descriptions and Analysis 244 Sediment Fall Velocity 245 A Probabilistic Approach to Sediment Transport 249 Einstein (1950)–Laursen (1958)–Graf (1971) Stage–Discharge and Other Hydraulic Calculations 254 Van Rijn (1984) Stage–Discharge and Total Load 259 Total Load by Regression Approaches 264 Sediment Measurement 268 Sediment Routing Through Detention Ponds and Streams 268 Software Support for Estimating Sediment Transport 270 Implications of Sediment Transport on Infrastructure 271 Empirical Channel Design Approaches Leading to Sustainable Channels 274 Forces Impacting Channel Cross Sections – Stream Restoration 281 Summary and Future Directions 286 Problems and Questions 289 References 290 Appendix A  Software and Selected Solutions 294 Appendix B  Solution Charts for Vegetated Waterways Using the Permissible Velocity Method 305 Appendix C  Selected Cost Data for Channel Excavation and Lining Materials 310 Appendix D  Design Strategy Summary for Uniform Flow Channels 315 Index 317

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Book SynopsisPOLLUTANTS AND WATER MANAGEMENT Pollutants and Water Management: Resources, Strategies and Scarcity delivers a balanced and comprehensive look at recent trends in the management of polluted water resources. Covering the latest practical and theoretical aspects of polluted water management, the distinguished academics and authors emphasize indigenous practices of water resource management, the scarcity of clean water, and the future of the water system in the context of an increasing urbanization and globalization. The book details the management of contaminated water sites, including heavy metal contaminations in surface and subsurface water sources. It details a variety of industrial activities that typically pollute water, such as those involving crude oils and dyes. In its discussion of recent trends in abatement strategies, Pollutants and Water Management includes an exploration of the application of microorganisms, like bacteria, actinomycetes, fuTable of ContentsList of Contributors vii Part I Water Pollution and Its Security 1 1 Water Security and Human Health in Relation to Climate Change: An Indian Perspective 3Ravishankar Kumar, Prafulla Kumar Sahoo, and Sunil Mittal 2 Assessment of Anthropogenic Pressure and Population Attitude for the Conservation of Kanwar Wetland, Begusarai, India: A Case Study 22Ajeet Kumar Singh, M. Sathya, Satyam Verma, Agam Kumar, and S. Jayakumar 3 Grossly Polluting Industries and Their Effect on Water Resources in India 47Zeenat Arif, Naresh Kumar Sethy, Swati, Pradeep Kumar Mishra, and Bhawna Verma Part II Phytoremediation of Water Pollution 67 4 Phytoremediation: Status and Outlook 69Kajal Patel, Indu Tripathi, Meenakshi Chaurasia, and K.S. Rao 5 Phytoremediation of Heavy Metals from the Biosphere Perspective and Solutions 95Indica Mohan, Kajol Goria, Sunil Dhar, Richa Kothari, B.S. Bhau, and Deepak Pathania 6 Phytoremediation for Heavy Metal Removal: Technological Advancements 128Monika Yadav, Gurudatta Singh, and R.N. Jadeja Part III Microbial Remediation of Water Pollution 151 7 Advances in Biological Techniques for Remediation of Heavy Metals Leached from a Fly Ash Contaminated Ecosphere 153Krishna Rawat and Amit Kumar Yadav 8 Microbial Degradation of Organic Contaminants in Water Bodies: Technological Advancements 172Deepak Yadav, Sukhendra Singh, and Rupika Sinha 9 The Fate of Organic Pollutants and Their Microbial Degradation in Water Bodies 210Gurudatta Singh, Anubhuti Singh, Priyanka Singh, Reetika Shukla, Shashank Tripathi, and Virendra Kumar Mishra Part IV Removal of Water Pollutants by Nanotechnology 241 10 Detection and Removal of Heavy Metals from Wastewater Using Nanomaterials 243Swati Chaudhary, Mohan Kumar, Saami Ahmed, and Mahima Kaushik 11 Spinel Ferrite Magnetic Nanoparticles: An Alternative for Wastewater Treatment 273Sanjeet Kumar Paswan, Pawan Kumar, Ram Kishore Singh, Sushil Kumar Shukla, and Lawrence Kumar 12 Biocompatible Cellulose-Based Sorbents for Potential Application in Heavy Metal Ion Removal from Wastewater 306Shashikant Shivaji Vhatkar, Kavita Kumari, and Ramesh Oraon Part V Advances in Remediation of Water Pollution 327 13 Advances in Membrane Technology Used in the Wastewater Treatment Process 329Naresh K. Sethy, Zeenat Arif, K.S. Sista, P.K. Mishra, Pradeep Kumar, and Avinash K. Kushwaha 14 Occurrence, Fate, and Remediation of Arsenic 349Gurudatta Singh, Anubhuti Singh, Reetika Shukla, Jayant Karwadiya, Ankita Gupta, Anam Naheed, and Virendra Kumar Mishra 15 Physical and Chemical Methods for Heavy Metal Removal 377Monika Yadav, Gurudatta Singh, and R.N. Jadeja Part VI Policy Dimensions on Water Security 399 16 The Role of Government and the Public in Water Resource Management in India 401Jitesh Narottam Vyas and Supriya Nath Index 416

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Book SynopsisPHYSIOLOGY OF SALT STRESS IN PLANTS Discover how soil salinity affects plants and other organisms and the techniques used to remedy the issue In Physiology of Salt Stress in Plants, an editorial team of internationally renowned researchers delivers an extensive exploration of the problem of soil salinity in modern agricultural practices. It also discusses the social and environmental issues caused by salt stress. The book covers the impact of salt on soil microorganisms, crops, and other plants, and presents that information alongside examinations of salt's effects on other organisms, including aquatic fauna, terrestrial animals, and human beings. Physiology of Salt Stress in Plants describes the morphological, anatomical, physiological, and biochemical dimensions of increasing soil salinity. It also discusses potential remedies and encourages further thought and exploration of this issue. Readers are encouraged to consider less hazardous fertilizers and pesticides, to use safer doses, and to explore and work upon salt resistant varieties of plants. Readers will also benefit from the inclusion of: Thorough introductions to salt stress perception and toxicity levels and the effects of salt stress on the physiology of crop plants at a cellular levelExplorations of the effects of salt stress on the biochemistry of crop plants and salt ion transporters in crop plants at a cellular levelPractical discussions of salt ion and nutrient interactions in crop plants, including prospective signalling, and the effects of salt stress on the morphology, anatomy, and gene expression of crop plantsAn examination of salt stress on soil chemistry and the plant-atmosphere continuum Perfect for researchers, academics, and students working and studying in the fields of agriculture, botany, entomology, biotechnology, soil science, and plant physiology, Physiology of Salt Stress in Plants will also earn a place on the bookshelves of agronomists, crop scientists, and plant biochemists.Table of ContentsList of Contributors xiii Preface xix 1 An introduction to salt stress perception and toxicity level -Worldwide report at a glanceAtun Roy Choudhury, Neha Singh, Ayushi Gupta and P Sankar Ganesh 1.1 Soil Salinity: An Introduction 1.2 Salt stress perception and current scenario 1.3 Types of salt stress 1.4 Origin of problem 1.5 Salt toxicity level: A worldwide report 1.6 Effect of salt stress on flora and fauna of the ecosystem 1.7 Role in sustainable agriculture 1.8 Unintended effects of salt-containing substance application in agricultural land 1.9 Role of salt toxicity in operation of green revolution 1.10 Reaching the current status and conclusion References 2 Effects of salt stress on physiology of crop plants: At cellular levelVivekanand Tiwari, Abhay Kumar and Pratibha Singh 2.1 Soil salinity and plants 2.2 Crop loss due to salt toxicity- An estimation worldwide 2.3 Effect of salt stress on target and non-target plants and microorganisms 2.4 Effect of salt stress on physiology of crop plants 2.4.1 Effect of salt stress on chlorophyll biosynthesis, chloroplast functioning and photophosphorylation 2.4.1.1 Chlorophyll biosynthesis in salt stress 2.4.1.2 Salt stress affects chloroplast function 2.4.1.3 Photophosphorylation in salt stress 2.4.2 Glycolysis, Kreb’s cycle enzymes, oxidative phosphorylation, and other mitochondrial functioning 2.4.2.1 Glycolytic pathway in salt stress 2.4.2.2 TCA cycle in salt stress 2.4.2.3 Salt stress and oxidative phosphorylation 2.4.3 Peroxisome functioning 2.5 Halophytes and their physiology 2.5.1 Ion homeostasis in a halophyte 2.5.2 Osmotic adjustment 2.5.3 Physiological and metabolic adaptation of halophytes 2.6 Halophytes in agriculture and land management 2.7 Conclusion and future perspectives References 3. Effects of salt stress on biochemistry of crop plantsPoonam Yadav and Durgesh Kumar Jaiswal 3.1 Introduction 3.2 Effects of salt stress on lipid metabolism 3.3 Effects of salt stress on amino acid synthesis and nitrogen metabolism 3.4 Effects of salt stress on protein biosynthesis 3.5 Effect of salt stress on oxidation of membrane proteins 3.6 Effect of salt stress on nucleic acid formation 3.7 Binding to DNA and RNA and formation of cross-links 3.8 Effect of salt stress on dephosphorylation of RNA and DNA 3.9 Future advances and conclusion References 4. Salt ion transporter in crop plant at cellular levelRia Khare, Gurpreet Sandhu, Aruba Khan, Prateek Jain 4.1 Introduction 4.2 Absorption of Na+ from soil and its compartmentalization in plant cells 4.3 Salt ions regulation in plants cells and tissues 4.4 Role of ion channels and salt ion transporter in crop plants at cellular level 4.5 Transport of Na+ through SOS signal transduction pathway: At cellular level 4.6. Role of salt tolerance responsive genes in transport of Na+ and Cl- ions: At cellular level 4.7 Role of ions in salt stress tolerance 4.8 Reaching the current status and conclusion References 5. Salt ion and nutrient interactions in crop plants: Prospective signallingRia Khare and Prateek Jain 5.1. Introduction 5.2. Effects of salt stress on nutrient absorption 5.3 Effects of salt stress on nutrient cycling in crop plants 5.4 Salt ion and nutrient interactions in crop plants 5.5 Effect of salt stress on nutrient transporters 5.5.1 K transporters 5.5.2 N transporters 5.5.3 P transporters 5.5.4 S transporters 5.6 Role of nutrient interactions: Prospective signalling 5.7 Future prospective and conclusion References 6. Effects of salt stress on the morphology, anatomy and gene expression of crop plantsPragati Kumari, Arvind Gupta, Harish Chandra, Pratibha Singh and Saurabh Yadav 6.1 Introduction 6.2 Salt stress and effects on morphology of plants 6.3 Photosynthetic pigments and osmolytes accumulation 6.4 Effect of saline stress on floral organs 6.5 Anatomical features and salt stress 6.6 Yield and related traits 6.7 Salt stress and its effects on Gene expression 6.8 Conclusion References 7. Effect of salt stress on soil chemistry and plant-atmosphere continuum (SPAC)Gunjan Goyal, Aruna Yadav and Gunjan Dubey 7.1 Introduction 7.2 Effect of salt stress on soil component 7.2.1 Effect of salt stress on abiotic component of soil and soil health 7.2.2 Effects of salt stress on biotic component of soil and soil health 7.3 Soil chemistry affecting factors in agricultural land 7.4 Soil salinity effect on crop plants 7.4.1 Germination 7.4.2 Growth 7.4.3 Photosynthesis and photosynthetic pigments 7.4.4 Mineral uptake and assimilation 7.4.5 Oxidative stress 7.4.6 Yield 7.5 An introduction to Soil plant-atmosphere continuum (SPAC) 7.6 Salt absorption by roots tissues and their effect on plant-atmosphere continuum (SPAC) 7.7 Translocation of salt ions in the vascular system of crop plants 7.7.1 Mechanism of sodium influx into cytosol 7.7.2 Mechanism of Na+ compartmentalization in vacuoles 7.7.3 The SOS pathway 7.7.4 Effect of salt stress on Xylem transport 7.7.5 Effect of salt stress on Phloem loading 7.8 Current status and conclusion Acknowledgement References 8 Effects of salt stress on nutrient cycle and uptake of crop plantsLav Kumar Jaiswal, Prabhakar Singh, Rakesh Kumar Singh, Tanamyee Nayak, Ankush Gupta 8.1 Introduction 8.2 Limitation of nutrient cycle and uptake of nutrients 8.2.1 Phosphorus limitation 8.2.2 Nitrogen limitation 8.3 Nutrient cycle or Biogeochemical cycle 8.3.1 Water cycle or Hydrological cycle 8.3.2 Carbon cycle 8.3.3 Nitrogen cycle 8.3.4 Oxygen cycle 8.3.5 Phosphorus cycle 8.3.6 Sulfur cycle 8.3.7 Calcium cycle 8.4 Effect of salt stress on carbon cycle 8.5 Effect of salt stress on oxygen and water cycle 8.5.1 Effect of salt stress on oxygen cycle 8.5.2 Effect of salt stress on water cycle 8.6 Effect of salt stress on nitrogen fixing bacteria and biogeochemical cycle of nitrogen 8.7 Effect of salt stress on phosphorus bacteria and biogeochemical cycle of phosphorus 8.8 Effect of salt stress on sulphur bacteria and biogeochemical cycle of sulphur 8.9 Future prospective and conclusion References 9 Salt induced effects on crop plants and counteract mitigating strategy by antioxidants systemIndrajeet Kumar, Umesh Kumar, Prince Kumar Singh, Rajesh Kumar Sharma 9.1 Introduction 9.2 Formation of salt induced indirect products (oxidative biomarkers) in crops 9.3 Effect of salt stress on crop plants 9.4 Consequences effect of oxidative biomarkers in crop plants 9.4.1 Lipid peroxidation 9.4.2 Effect on Proteins 9.4.3 Effects on Carbohydrates 9.4.4 Effect on polynucleic acids 9.5 Generation of self-defence mitigating strategy in crop plants 9.5.1 Counteract mitigating strategy by enzymatic antioxidants system 9.5.1.1 Superoxide dismutase (SOD) 9.5.1.2 Catalase (CAT) 9.5.1.3 Ascorbate-Glutathione (AsA-GSH) Cycle Enzymes 9.5.1.4 Ascorbate Peroxidases (APX) 9.5.1.5 Monodehydroascorbate reductase (MDHAR) and dehydroascorbate reductase (DHAR) 9.5.1.6 Glutathione Reductase (GR) 9.5.1.7 Guaiacol peroxidase (GPOX) 9.5.2 Counteract mitigating strategy by non-enzymatic antioxidants system 9.6 Conclusion and Future prospective References 10 Effects of salt stress on osmolyte metabolism of crop plants and mitigating strategy by osmolyteAbreeq Fatima, Garima Singh, Anuradha Patel, Sanjesh Tiwari, Divya Gupta, Anurag Dubey, Dilip Kumar Prajapati and Sheo Mohan Prasad 10.1 Introduction 10.2 Groups and biosynthetic pathways of osmolytes in crop plant 10.2.1 Polyamines and biosynthetic pathways in the cell organelles of crop plant 10.2.2 Betaeine and their biosynthetic pathways in the cell organelles of crop plant 10.2.3 The biosynthetic pathway of carbohydrate sugar, sugar alcohol and amino acids in the cell organelles of crop plant 10.3 Effect of salt stress on osmolyte production and work action 10.4 The osmotic and ionic adjustment under salt stress; tolerance mechanism 10.5 Conclusion References 11 Salt stress toxicity amelioration by phytohormone, synthetic products and nutrient amendment practicesDivya Gupta, Garima Singh, Sanjesh Tiwari, Anuradha Patel, Abreeq Fatima Anurag Dudey, Neha Naaz, Jitendra Pandey and Sheo Mohan Prasad 11.1 Introduction 11.2 Structure and mechanism of action of phytohormones under salt stress 11.3 Structural, physiological and biochemical nature of phytohormones under salt stress 11.3.1 Abscisic acid (ABA) 11.3.2 Cytokinins (CKs) 11.3.3 Gibberellins (GAs) 11.3.4 Auxins (AUXs) 11.3.5 Brassinosteroids (BRs) 11.3.6 Salicylic acid (SA) 11.3.7 Jasmonic acid (JA) 11.4 Salt stress toxicity amelioration by exogenous / endogenous phytohormones 11.4.1 Auxin 11.4.2 Gibberellins 11.4.3 Cytokinin 11.4.4 Brassinosteroids 11.4.5 Salicylic acid 11.5 Salt toxicity amelioration by exogenous synthetic products 11.6 Salt toxicity amelioration by exogenous nutrient amendment practices 11.7 Future prospective and conclusion References 12 Crop plants develop extracellular signalling products against salt stressSantwana Tiwari, Nidhi Verma, Shikha Singh, Shivam Gupta, Jitendra Pandey and Sheo Mohan Prasad 12.1 Introduction 12.2 Site of synthesis of extracellular signaling products 12.3 Release of extracellular products by cells of cyanobacteria, algae and crop plant under salt stress: antioxidants, enzymes and proteins 12.3.1 Antioxidants 12.3.2 Enzymes 12.3.3 Proteins 12.4 Release of extracellular products by cells of cyanobacteria, algae and crop plants under salt stress: amino acids, osmolytes, nitrogen, nitric oxide, ammonia 12.4.1 Amino acids 12.4.2 Osmolytes 12.4.3 Nitrogen and its derivatives 12.5 Release of extracellular products by cells of cyanobacteria and crop plants under salt stress: phytols, sterols, terpenoid, fatty acids, phenols 12.5.1 Phenols 12.5.2 Terpenoids 12.5.3 Phytols 12.5.4 Sterols 12.5.5 Fatty Acids 12.6 Release of extracellular products by cells of cyanobacteria and crop plants under salt stress: Photoprotective compounds, polysaccharides, halogenated compounds and phytohormones 12.6.1 Photoprotective compounds 12.6.2 Polysaccharides and halogenated compounds 12.7 Uncovering potential and applications of extracellular signaling products in biology, agriculture and medicine 12.8 Current status and future prospects References

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Book SynopsisProvides detailed information about the use of nanotechnology in remediating waste and pollution in agriculture Nano-Technological Intervention in Agricultural Productivityexplores sustainable, eco-friendly technologies for remediating wastes and contaminated areas in both water and land ecosystems. Focusing on nano-technological innovations that use microbes and microbial agents to improve the quality and pollutant discharge of contaminated sites, this comprehensive volume also discusses molecular approaches for the characterization of nanoparticles, the biosynthetic pathways of microbes,geneand protein expression studies for bio-deterioration techniques, and more. Organized intoninechapters, the book opens with a thorough overview of the functions, classification, properties, synthesis, and applications of nanoparticles. Following a discussion of the environmental and agricultural implications of nanotechnology, the authors examine the current role andfTable of ContentsAbout the Authors xi About the Book xiii 1 Nanotechnology and Nanoparticles 1 1.1 Nanoparticles and Their Functions 1 1.2 Classification of NPs 2 1.2.1 Carbon-Based NPs 2 1.2.2 Metal Nanoparticles 2 1.2.3 Ceramic NPs 3 1.2.4 Semiconductor NPs 3 1.2.5 Polymeric NPs 3 1.2.6 NPs Based on Lipids 4 1.3 Synthesis of Nanoparticles 4 1.3.1 Top-Down Synthesis 4 1.3.2 Bottom-Up Synthesis 5 1.4 NPs and Characterization 6 1.4.1 Morphological Characterization 6 1.4.1.1 SEM Technique 6 1.4.1.2 TEM Technique 6 1.4.2 Structural Characteristics 7 1.4.2.1 XRD 7 1.4.2.2 Energy-Dispersive X-ray (EDX) 7 1.4.2.3 XPS 7 1.4.2.4 FT-IR and Raman Spectroscopies 8 1.4.3 Particle Size and Surface Area Characterization 8 1.4.4 Optical Characterizations 8 1.5 Physicochemical Properties of NPs 9 1.5.1 Mechanical and Optical Properties 9 1.5.2 Magnetic Properties 9 1.5.3 Mechanical Properties 10 1.5.4 Thermal Properties 10 1.6 Functions of NPs 10 1.6.1 Drugs and Medications 11 1.6.2 Materials and Manufacturing 11 1.6.3 Environment 12 1.6.4 Electronics 12 1.6.5 Energy Harvesting 12 References 13 2 Implications of Nanotechnology and Environment 21 2.1 Ecotoxicological Implications of Nanoparticles 21 2.1.1 Ecotoxicity of Fullerenes 23 2.1.2 Ecotoxicity of Carbon Nanotubes 23 2.1.3 Ecotoxicity of Metal Nanoparticles 23 2.1.4 Ecotoxicity of Nanocomposites 24 2.1.5 Ecotoxicity of Oxide Nanoparticles 25 2.2 Nanotechnology and Agriculture 26 2.3 Risk Assessment Factors and Modulation of Nanomaterials 27 References 30 3 Nanotechnology and Disease Management 37 3.1 Recent Advancements in Plant Nanotechnology 37 3.1.1 Cerium Oxide (CeO2) NPs 38 3.1.2 Silver NPs 38 3.1.3 Titanium Dioxide (ToO2) NPs 39 3.1.4 Zinc Oxide (ZnO) NPs 41 3.1.5 Cupric Oxide (CuO) NPs 41 3.1.6 Gold NPs (GNPs) 42 3.1.7 Carbon Nanotubes 42 3.1.8 Nickel Oxide NPs 43 3.2 Nanotechnology: Role in Plant-Parasitic Control 43 3.2.1 Nanocapsules: Liposomes and Polymers 44 3.2.1.1 Potential Uses in Controlling ParasiticWeeds 44 3.3 Abiotic Stress-Tolerant Transgenic Crops and Nanotechnology 45 3.3.1 Nanotechnology in Gene Transfer Experiments 45 3.4 Plant Pathogens and Nanoparticle Biosynthesis 46 3.4.1 Bacteria-Mediated Biosynthesis 47 3.4.2 Fungal Mediated Biosynthesis 48 3.5 Nanomaterial and Plant Protection Against Pests and Pathogens 49 3.6 Future Perspectives 51 References 51 4 Nanotechnology in Agri-Food Production 59 4.1 Nanomaterials 59 4.2 Nanotechnology and Food Systems: Food Packing 60 4.3 Nano-Nutraceuticals 61 4.3.1 Issues with Nano-Nutraceuticals 62 4.4 Nanotechnological Advancement in Antimicrobial Peptides (AMPs) 63 4.4.1 Passive Nano-Delivery Systems 63 4.4.1.1 Cyclosporin A 63 4.4.1.2 Nisin 64 4.4.1.3 Polymyxin 64 4.4.2 Antimicrobial Peptides in Targeted Nano-Delivery Systems 64 4.5 Assessment of Nanotechnology for Enhanced Food Security 65 4.5.1 Framework for Assessing the Potential Role of Nanotechnology in Food 65 4.5.2 Assessment of Nanotechnology Potential Through Literature Survey 65 4.6 Future Perspectives 66 References 66 5 Nanotechnology: Improvement in Agricultural Productivity 73 5.1 Nanoparticle Biosynthesis and Use in Agriculture 73 5.1.1 Silver Nanoparticles 73 5.1.2 Zinc Oxide Nanoparticles 74 5.1.3 Titanium Dioxide (TiO2) Nanoparticles 75 5.2 Nanorobots 76 5.2.1 Environment Monitoring 77 5.2.2 Nanorobot Sensors 79 5.2.3 Pollutant and Chemical Detection 79 5.2.4 Metal Identification 80 5.2.5 Nanorobot Data Transmission 81 5.2.6 Nanorobot System on Nanotechnology Chip 82 5.3 Natural Nanostructures in Food 82 5.3.1 Protein-Based Nanostructures 83 5.3.1.1 β-Lactoglobulin 84 5.3.1.2 Serum Albumin 85 5.3.1.3 α-Lactalbumin and Lysozyme (Lys) 85 5.3.1.4 Ovalbumin and Avidin 86 5.3.1.5 Transferrins 86 5.3.1.6 Osteopontin and Osteopontin Lactoperoxidase (OPN) 87 5.3.2 Formation of Natural Nanostructure Subsequently to Molecular Interaction/Complexation 88 5.3.2.1 Lipid-Based Nanostructures 89 References 90 6 Lignin Nanoparticles: Synthesis and Application 97 6.1 Overview of Lignin Nanoparticles 97 6.2 Lignin Nanoparticle Synthesis (LNPs) 98 6.2.1 Polymerization 98 6.2.2 Acid Precipitation 98 6.2.3 Solvent Exchange Method 99 6.2.4 Ultrasonication 100 6.2.5 Biological Method 100 6.3 Application of Lignin Nanoparticles (LNPs) 101 6.3.1 Antibacterial Activity 101 6.3.2 Antioxidant Activity 102 6.3.3 UV Absorbents 102 6.3.4 Hybrid Nanocomposites 103 6.3.5 Drug Delivery System 103 6.3.6 Adsorbents to Remove Dyes 104 6.3.7 As a Capacitor 104 6.3.8 As a Nano-trap 105 References 105 7 Contemporary Application of Nanotechnology in Agriculture 109 7.1 Introduction 109 7.2 Nanofertilizers 110 7.3 Nanocomposites 111 7.4 Nanobiosensors 112 7.4.1 Nanosensors in Agriculture 113 7.4.2 Monitoring Soil Conditions and Plant Growth Regulators 113 7.4.3 Plant Pathogen Recognition 114 7.4.4 Detection of Pesticide Residues 114 7.5 Nanopesticides 115 7.6 Natural Nanoparticles: Environmental and Health Implications 118 7.6.1 Water Quality 118 7.6.2 Interactions with Contaminants and Other Organisms 119 7.6.3 Environmental Risks and Biogeochemistry of NNPs 120 7.6.4 Environmental Issues 120 7.7 Future Perspective 121 References 121 8 Nanotechnology: Advances in Plant and Microbial Science 131 8.1 Engineered Nanomaterials and Soil Remediation 131 8.1.1 ENMs: Role in Soil Remediation 132 8.1.1.1 Immobilization 132 8.1.1.2 Photocatalytic Degradation 134 8.2 Fate and Interactions of Nanomaterials in Soil 135 8.2.1 Nanoparticles and Plants 136 8.2.2 Suppressive Effects on Plants 136 8.2.3 Promontory Plant Effects 136 8.2.4 Nanoparticles and Impacts on Soil Microbes 138 8.2.5 Zinc and Sulfur Nanoparticles 138 8.2.6 Copper and Silica Nanoparticles 139 8.3 Nanomaterials and Metal Components: Accumulation and Translocation Within Plants 139 8.3.1 NPS: Uptake and Translocation in Plants 140 8.3.2 NPS: Root Uptake and Translocation 141 8.3.3 Assimilated Root Uptake and Translocation Pathways of Nanoparticles 142 8.3.4 NPS: Transformation in the Rhizosphere 144 8.4 Biotransformation of ENPs in Plants 145 8.5 Effect of Nanomaterials on Plants 146 8.5.1 Positive Effects 146 8.5.2 Toxicity 147 References 148 9 Food Application and Processing: Nanotechniques and Bioactive Delivery Systems 161 9.1 Introduction 161 9.2 Phytochemicals and Nanoparticles 164 9.3 Bioactive Delivery Systems 167 9.3.1 Nanotechnology of Natural Products and Drug Delivery 169 9.4 Bioactive Delivery Systems 173 9.4.1 Protein-Based Nanoscale Delivery Systems 173 9.4.2 Polysaccharide-Based Nanoscale Delivery Systems 175 9.4.3 Complex or Hybrid Nanoscale Delivery Systems 177 9.5 Toxicity of Biodegradable Nanoparticles 180 9.6 Future Perspectives 181 References 182 Index 197

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Book SynopsisMATHEMATICAL MACROEVOLUTION IN DIATOM RESEARCH Buy this book to learn how to use mathematics in macroevolution research and apply mathematics to study complex biological problems. This book contains recent research in mathematical and analytical studies on diatoms. These studies reflect the complex and intricate nature of the problems being analyzed and the need to use mathematics as an aid in finding solutions. Diatoms are important components of marine food webs, the silica and carbon cycles, primary productivity, and carbon sequestration. Their uniqueness as glass-encased unicells and their presence throughout geologic history exemplifies the need to better understand such organisms. Explicating the role of diatoms in the biological world is no more urgent than their role as environmental and climate indicators, and as such, is aided by the mathematical studies in this book. The volume contains twelve original research papers as chapters. Macroevolutionary science topics covered arTable of ContentsList of Figures xviii List of Tables xxx Preface xxxv Acknowledgments xxxvii Prologue -- Introductory Remarks xxxix Part I: Morphological Measurement in Macroevolutionary Distribution Analysis 1 1 Diatom Bauplan, As Modified 2D Valve Face Shapes of a 3D Capped Cylinder and Valve Shape Distribution 3 1.1 Introduction 3 1.1.1 Analytical Valve Shape Geometry 5 1.1.2 Valve Shape Constructs of Diatom Genera 8 1.2 Methods: A Test of Recurrent Diatom Valve Shapes 10 1.2.1 Legendre Polynomials, Hypergeometric Distribution, and Probabilities of Valve Shapes 12 1.2.2 Multivariate Hypergeometric Distribution of Diatom Valve Shapes as Recurrent Forms 15 1.3 Results 18 1.4 Discussion 22 1.4.1 Valve Shape Probability Distribution 22 1.4.2 Hypergeometric Functions and Other Shape Outline Methods 22 1.4.3 Application: Valve Shape Changes and Diversity during the Cenozoic 25 1.4.4 Diatom Valve Shape Distribution: Other Potential Studies 25 1.5 Summary and Future Research 26 1.6 Appendix 26 1.7 References 34 2 Comparative Surface Analysis and Tracking Changes in Diatom Valve Face Morphology 39 2.1 Introduction 39 2.1.1 Image Matching of Surface Features 40 2.1.2 Image Matching: Diatoms 41 2.2 Purpose of this Study 42 2.3 Background on Image and Surface Geometry 42 2.3.1 The Geometry of the Digital Image and the Jacobian 42 2.3.2 The Geometry of the Diatom 3D Surface Model and the Jacobian 45 2.3.3 The Image Gradient and Jacobian 46 2.4 Image Matching Kinematics via the Jacobian 47 2.4.1 Position and Motion: The Kinematics of Image Matching 47 2.4.2 Displacement and Implicit Functions 48 2.4.3 Displacement and Motion: Position and Orientation 49 2.4.4 Surface Feature Matching via the Jacobian 50 2.4.5 The Jacobian of Whole Surface Matching 52 2.5 Methods 53 2.5.1 Fiducial Outcomes of Image Matching of Surface Features 53 2.6 Results 54 2.6.1 Surface Feature Image Matching and the Jacobian 56 2.6.2 Whole Valve Images, Matching of Crest Lines and the Jacobian 60 2.6.3 Image Matching of more than Two Images 65 2.7 Discussion 71 2.7.1 Utility of Jacobian-Based Methods and Image Matching 72 2.7.2 The Image Jacobian and Rotation in A Reference Frame: Potential Application to Diatom Images 73 2.7.3 Deformation and Registration of Image Surfaces: An Alternative Jacobian Calculation 75 2.8 Summary and Future Research 77 2.9 References 77 3 Diatom Valve Morphology, Surface Gradients and Natural Classification 81 3.1 Introduction 81 3.2 Purposes of this Study 82 3.2.1 The Genus Navicula 83 3.3 Methods 84 3.3.1 Naviculoid Diatom Surface Analysis 84 3.3.2 Gradients of Digital Image Surfaces 84 3.3.3 Histogram of Oriented Gradients and Surface Representation 89 3.3.4 Application to Diatom Valve Face Digital Images 90 3.3.5 Support Vector Regression and Classification 90 3.3.6 Using HOG as Combination Gradient Magnitude and Direction Input Data for SVR 91 3.3.7 Computational Efficiency and Cost 95 3.4 Diatom Valve Surface Morphological Analysis 95 3.4.1 SVR Model Fit of Naviculoid Taxa 95 3.4.2 Valve Surface Morphological Classification and Regression of Naviculoid Diatoms 96 3.5 Results 96 3.5.1 HOG Data Analysis 96 3.5.2 Goodness-of-Fit SVR Model Using 4D HOG Data from Naviculoid LMs 100 3.5.3 SVR of Naviculoid 2D HOG Data 102 3.5.4 Second Round of SVR Analysis of Remaining Naviculoid 2D HOG Data 105 3.5.5 Last Round of SVR Analysis of Remaining Naviculoid 2D HOG Data 106 3.5.6 Classification Results from SVR Analysis of Naviculoid Taxa 106 3.6 Discussion 106 3.6.1 Characteristics of SVM and SVR 107 3.6.2 Advantages in Using HOG Data and SVR 108 3.6.3 Potential Utility of HOG Data and SVR in Diatom Research 108 3.7 Summary and Future Research 109 3.8 References 110 Part II: Macroevolutionary Systems Analysis of Diatoms 115 4 Probabilistic Diatom Adaptive Radiation in the Southern Ocean 117 4.1 Introduction 117 4.1.1 Diatoms in the SO 120 4.1.2 Chaetocerotales and Bacillariales Speciation Rates 120 4.1.3 Chaetocerotales and Bacillariales: Fe, NO3 and SiO2 Availability in the SO 121 4.1.4 Modeling Diatom Adaptive Radiation 122 4.2 Purposes of this Study 123 4.3 Mathematical Modeling of Adaptive Radiation 123 4.3.1 Quantitative Phenotypic Trait Measurement and Adaptive Radiation 123 4.3.2 Adaptive Radiation: Implicit Stochastic Models 125 4.3.3 Adaptive Radiation Models: Time Evolution of a Stochastic System 127 4.3.4 Adaptive Radiation as an Optimal Control Problem 128 4.3.5 Exit Probabilities as Boundaries for Completion of Adaptive Radiation 130 4.3.6 Exit Times for the Adaptive Radiation Process 131 4.3.7 Adaptive Radiation: A Study of Southern Ocean Diatoms and Niche Filling 132 4.4 Methods 133 4.4.1 Niche Filling and Adaptive Radiation 134 4.5 Results 134 4.5.1 Ecological Niche Preference, Photosynthesis Efficiency, Nutrient Enrichment or Limitation, and Adaptive Radiation 140 4.5.2 Ecological Niche Preference and Photosynthesis Efficiency Rankings Representing Niche Filling as Adaptive Radiation 141 4.5.3 Niche Filling and the Lyapunov modified OU Adaptive Radiation Model 141 4.6 Discussion 145 4.6.1 More on Specifications for Adaptive Radiation Modeling 146 4.6.2 Diatom Adaptive Radiation Short-Term Trends as a Result of Niche Filling in the SO 147 4.6.3 Other Potential Mathematical Modeling Regimes of Adaptive Radiation 148 4.7 Summary and Future Directions 149 4.7.1 Caveats in Adaptive Radiation Studies to be Considered 149 4.8 References 150 5 Cenozoic Diatom Origination and Extinction and Influences on Diversity 159 5.1 Introduction 159 5.1.1 Cenozoic Diatoms and Environmental Conditions 160 5.1.2 Diatom Diversity during the Cenozoic 161 5.1.3 Diversity as a Result of the Frequency of Origination and Extinction Events 162 5.2 Purposes of this Study 163 5.3 Methods and Background 163 5.3.1 Reconstructed Diatom Origination, Extinction and Diversity during the Cenozoic 163 5.3.2 Cumulative Functions and the Frequency of Cenozoic Origination nd Extinction 165 5.3.3 Origination and Extinction: Heaviside Functions and Switching 167 5.3.4 Origination and Extinction as a Sequence of Steps and Accumulated Switches during the Cenozoic 168 5.3.5 Piecewise Continuous Switching via the Laplace Transform of the Heaviside Functions 168 5.3.6 Overlapping of Origination and Extinction: A Convolution Product 169 5.3.7 Non-Overlapping Origination and Extinction: A Poisson Process 170 5.3.8 Test of Switch Reversibility, Cenozoic Events and a Lyapunov Function 171 5.3.9 Origination and Extinction: Relation to Diversity 172 5.4 Results 173 5.4.1 Cumulative Frequency of Cenozoic Diatom Origination and Extinction Events 173 5.4.2 Switching from Diatom Origination to Extinction over the Cenozoic 176 5.4.3 Origination and Extinction Sequential Steps and Accumulated Switches during the Cenozoic 181 5.4.4 Overlapping via a Convolution Product of Origination and Extinction 183 5.4.5 Origination and Extinction as Poisson Processes 184 5.4.6 Test of Origination and Extinction Switches: Stochastic or Deterministic Chaos? 184 5.4.7 Diversity and Its Relation to Origination and Extinction for Cenozoic Diatoms 185 5.5 Discussion 189 5.5.1 Diversity and the Effects from Origination and Extinction of Cenozoic Diatoms 189 5.5.2 Cenozoic Events and Diatom Diversity, Origination and Extinction 192 5.5.3 Origination and Extinction Related to Diversity: Markov Chain, Martingale, Ergodic Processes, and Lyapunov Functions 193 5.6 Summary and Future Research 194 5.7 References 194 6 Diatom Food Web Dynamics and Hydrodynamics Influences in the Arctic Ocean 199 6.1 Introduction 199 6.2 Purposes of this Study 200 6.3 Background on Arctic Ocean Diatoms 200 6.3.1 Diatoms and their Relation to Sea Ice 200 6.3.2 Sea Ice, Upwelling and Diatom Productivity 201 6.3.3 Diatom Lipid Content as a Proxy for Biomass 203 6.3.4 Diatom Biomass and the Hydrodynamics of Upwelling 203 6.4 Lattice Boltzmann Model 205 6.5 Lattice Boltzmann Model and Hydrodynamics 207 6.5.1 Upwelling and Buoyancy 207 6.5.2 Collisions and Streaming Densities of Diatom Genera during Upwelling 209 6.5.3 Buoyancy and Ice 210 6.5.4 Upwelling and the Splitting of the Cylindrical Rotation of Currents 211 6.6 Lattice Boltzmann Model: Diatom Bloom Density, Sea Ice and Upwelling 211 6.7 Lattice Boltzmann Model: Specifications for Simulation 213 6.7.1 Overview of 2D LBM with Respect to Diatom Genera Lattice Nodes 216 6.7.2 Buoyancy, Upwelling and Diatom Blooms in LBM via p and u 219 6.8 Methods 220 6.9 Results 220 6.10 Discussion 226 6.10.1 Arctic Diatom Food Web Dynamics: Other Potential Outcomes 229 6.10.2 Diatom Blooms: Influences over Time and Space 230 6.11 Summary and Future Research 231 6.12 References 231 Part III: General and Special Functions in Diatom Macroevolutionary Spaces 241 7 Diatom Clade Biogeography: Climate Influences, Phenotypic Integration and Endemism 243 7.1 Introduction 243 7.1.1 Biogeography and Climate 245 7.1.2 Mapping Biogeographic Patterns 246 7.1.3 Biogeography as an Optimization Problem 246 7.1.4 Biogeographic Pattern and Spatial Rate of Change 247 7.1.5 Biogeography, Phenotypic Integration and Phenotypic Novelty 248 7.2 Purposes of this Study 249 7.3 Methods 250 7.3.1 Freshwater Diatom Dispersal Biogeography and the Traveling Salesman Problem 251 7.3.2 Freshwater Diatom Biogeographic Patterns with Respect to Climate 252 7.3.3 Diatom Biogeographic Patterns and Distance Decay 252 7.3.4 Endemism and Continental Area 253 7.3.5 Endemism and Dispersal Distance 253 7.3.6 Endemism, Phenotypic Integration and Phenotypic Novelty: The Raphe 254 7.4 Results 254 7.4.1 Clade Shortest Tours from Continent to Continent with Respect to Climate 257 7.4.2 Magnitude of Clade Tour Stops from Continent to Continent with Respect to Climate 258 7.4.3 Ecological Similarity, Biogeographical Distribution and Distance Decay 262 7.4.4 Biogeographical Distribution of Freshwater Diatom Genera 262 7.4.5 Endemics in each Clade and on each Continent 265 7.4.6 Phenotypic Integration and Relation to Geographic Distribution 266 7.5 Discussion 267 7.5.1 Freshwater Diatom Clade Dispersal and Climate 268 7.5.2 Distance Decay as the Pattern of Dispersal in Freshwater Diatom Biogeography 269 7.5.3 Phenotypic Integration and Diatom Biogeography 269 7.6 Summary and Future Research 270 7.7 References 270 8 Cell Division Timing and Mode of the Diatom Life Cycle 277 8.1 Introduction 277 8.1.1 Evolution of Diatom Cell Division Dynamics 278 8.1.2 Diatom Life Cycle as a Dynamical System 278 8.1.3 Diatom Cell Division and Growth Rate 279 8.1.4 Diatom Cell Size Diminution during Mitosis 280 8.1.5 Diatom Cell Division during Meiosis 281 8.1.6 Diatom Cell Division after Meiosis 282 8.2 Purposes of this Study 283 8.3 Background on the Diatom Cell Cycle 283 8.3.1 Diatom Life Cycle Timing: Stages 283 8.3.2 Diatom Life Cycle Timing: Switches 284 8.3.3 Diatom Life Cycle Timing: Cell Behavior 285 8.4 Modeling the Diatom Life Cycle: Timing of Stages and Switches 286 8.4.1 Delay Differential Equations 286 8.4.2 Solutions to DDEs 286 8.4.3 Mackey-Glass System of DDEs 287 8.4.4 Mackey-Glass System: Stage 1 of the Diatom Life Cycle 288 8.4.5 Mackey-Glass System: Stage 2 of the Diatom Life Cycle 289 8.4.6 Mackey-Glass System: Stages 3 and 4 of the Diatom Life Cycle 289 8.4.7 Mackey-Glass System: The Diatom Life Cycle Switches 290 8.5 Methods 291 8.6 Results 292 8.7 Discussion 300 8.7.1 Cell Size Control and the Diatom Cell Cycle Structure 303 8.7.2 Potential Alterations to the Mackey-Glass System when Applied to the Diatom Life Cycle 304 8.7.3 Mackey-Glass Systems: Utility and Applications 305 8.7.4 Potential Additional Analyses of Results from Mackey-Glass Systems 305 8.8 Summary and Future Research 305 8.9 References 306 9 Diatom Morphospaces, Tree Spaces and Lineage Crown Groups 313 9.1 Introduction 313 9.1.1 Euclidean Spaces are Subspaces of Hilbert and Banach Spaces 315 9.1.2 From Geometrical to Topological Spaces as Mathematical Morphospaces 315 9.2 Occupied and Unoccupied Morphospace 316 9.3 Purposes of this Study 318 9.4 Morphospace Structure and Dynamics 318 9.4.1 Morphospace Networks and All Possible Morphologies 318 9.4.2 Networks, Hierarchy and Morphospace 319 9.5 Phylogeny Structure and Phylogenetic Dynamics 320 9.5.1 Phylogenetic Trees and Mapped Traits 320 9.5.2 Phylogenetic Trees and the Geometry of Tree Spaces 321 9.6 Measuring Occupied Morphospace: Clustering Coefficients 322 9.7 A Brief Background on Diatom Morphospaces 323 9.8 Mathematical Morphospaces in the Context of a Diatom Phylogeny 324 9.9 Methods 325 9.9.1 Input Data for Morphospace Analysis 325 9.9.2 Diatom Lineage Crown Groups Embedded in a Metric Space 326 9.9.3 Diatom Submorphospaces Embedded in a Metric Morphospace 333 9.9.4 Clustering Coefficients as Measures of Occupied Morphospace 334 9.10 Results 334 9.11 Discussion 336 9.11.1 Trees, Networks and Morphospaces 345 9.11.2 Probabilistic Distances in Lineage Crown Group Morphospace 345 9.11.3 Diatom Novelties Versus Repetitive Forms in Occupied Morphospace 345 9.11.4 Diatom Teratologies and Mutagenicities: Influences on Morphology 346 9.11.5 Understanding Diatom Evolution via Morphospace and Phylogenetic Analyses 347 9.12 Summary and Future Research 347 9.12.1 What is Morphological Data? 347 9.12.2 Tempo and Mode of Phylomorphogenetic Spaces 348 9.13 References 348 Part IV: Macroevolutionary Characteristics of Diatoms 355 10 Diatom Morphological Complexity Over Time as a Measurable Dynamical System 357 10.1 Introduction 357 10.1.1 Complexity and Evolution 360 10.2 Diatom Morphological Complexity 360 10.3 Purposes of this Study 361 10.4 Characterizing Morphological Complexity 361 10.5 Information and Morphology 362 10.6 Information and Complexity 363 10.7 Markov Chains and their Properties 364 10.7.1 Markov Chains and Lyapunov Exponents 366 10.8 Ergodicity and Chaoticity 367 10.8.1 Entropy Rates 368 10.9 Kolmogorov Complexity and Entropy 370 10.10 Methods 372 10.10.1 Transition Probability Matrix and Properties of a Markov Chain 372 10.10.2 Measuring Morphological Kolmogorov Complexity 375 10.10.3 Diatom Morphological Complexity over Geologic Time and Comparison of Cretaceous and Cenozoic Taxa 375 10.11 Results 376 10.12 Discussion 385 10.13 Summary and Future Research 389 10.13.1 Is Morphological Complexity Related to Morphological Symmetry? 390 10.14 References 390 11 Diatom Surface Symmetry, Symmetry Groups and Symmetry Breaking 399 11.1 Introduction 399 11.1.1 Geometry as a Basis for Form, Surfaces and Symmetry 399 11.1.2 Inverse Functions as a Basis for Symmetry and Stability 400 11.2 Symmetry of 3D Organismal Surfaces 400 11.2.1 Shape versus Surface Symmetries 401 11.2.2 Geometry of Non-Flat 3D Surfaces: Bidirectional Curvature and Its Relation to Twists and Writhes 402 11.2.3 Knots: Geometry and Topology of Closed Curved Surfaces 403 11.2.4 From Hyperbolic Geometry and Surfaces to Hyperbolic Knots 404 11.2.5 Closed Helices, Hyperbolic Knots and Mobius Surfaces 405 11.3 Symmetry Groups 405 11.3.1 Diatom Surface Symmetry Groups: Cyclic, Reflective, Dihedral, Glide, Scale, and Knot 406 11.3.2 States of Symmetry 407 11.4 Purposes of this Study 409 11.5 Methods 410 11.5.1 Systems of Parametric 3D Equations for Exemplar Diatom Surface Models 411 11.5.2 Symmetry Groups: Cyclic, Reflective, Dihedral, Glide, Scale, and Knot 411 11.5.3 From Partial Derivatives to Ordinary Derivatives to Assess Stability 411 11.5.4 Inverse Jacobian Eigenvalues and Surface Symmetry Analysis 411 11.5.5 Stability and Inverse Jacobian Eigenvalues 414 11.5.6 Diatom Surface Symmetries and Symmetry Group Assessment 415 11.5.7 Vegetative Size Reduction and Symmetry Breaking 416 11.5.8 Relative Stability and Symmetry 416 11.5.9 Symmetry Gradients 416 11.6 Results 417 11.7 Discussion 428 11.7.1 Diatom Surface Symmetries and the Intricacies of Assessment 428 11.7.2 More on Diatom Surface Symmetries and Handedness 429 11.7.3 Diatom Vegetative Reproduction and Symmetry Breaking 429 11.7.4 Symmetry Breaking, Vegetative Reproduction, Size Reduction, and Stability 430 11.7.5 Eigenvalues and Variance: Instability and Fluctuating Asymmetry 430 11.7.6 Symmetry Groups and Evolutionary Dynamics: Symmetry in Diatoms and Adaptation 431 11.8 Summary and Future Research 431 11.9 References 432 12 Evolvability of Diatoms as a Function of 3D Surface Phenotype 437 12.1 Introduction 437 12.1.1 3D Surface Properties -- An Overview 438 12.1.2 From Differential Geometry to the Characterization of 3D Surfaces 438 12.1.3 The Phenotype Characterized via a 3D Surface and Its Geometric Characteristics 440 12.1.4 From Geometric Phenotype to Evolvability 441 12.1.5 Evolvability and Phenotypic Novelty 441 12.1.6 Evolvability and Diatoms 442 12.1.7 Diatom Exemplar Phenotypic and Valve Plication Characteristics 443 12.1.8 Diatom Architecture and the Geometric Phenotype 444 12.2 Purposes of this Study 445 12.3 Methods 445 12.3.1 Phenotypic Inertia 446 12.3.1.1 Measurement of Phenotypic Inertia: Christoffel Symbols 446 12.3.2 Phenotypic Robustness 447 12.3.2.1 Measurement of Phenotypic Robustness: the Hessian 448 12.3.3 Phenotypic Stability 449 12.3.3.1 Measurement of Phenotypic Stability: the Laplacian 449 12.3.4 Evolvability of each Diatom Genus: Actinoptychus, Arachnoidiscus and Cyclotella 450 12.3.5 Evolvability Among Diatom Genera 452 12.3.6 Contribution of Phenotypic Inertia, Robustness and Stability to Evolvability 452 12.3.7 Phenotypic Novelty Measurement 454 12.3.8 Evolvability and Phenotypic Novelty 455 12.4 Results 455 12.4.1 Phenotypic Inertia, Robustness and Stability 460 12.4.2 Evolvability across Genera 463 12.4.3 Evolvability and the Fitness Function Components of Phenotypic Inertia, Robustness and Stability 465 12.4.4 Phenotypic Novelty and Comparison to Evolvability 465 12.5 Discussion 467 12.6 Summary and Future Research 469 12.7 References 470 Epilogue -- Findings and the Future 475 Index 479

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Book SynopsisA clear and engaging introduction to the philosophy of science, exploring the role of science within the broader framework of human knowledge and engagement with the world What are the central features and advantages of a scientific worldview? Why do even reasonable scientists sometimes disagree with each other? How are scientific methods different than those of other disciplines? Can science provide an objective account of reality? This is Philosophy of Science introduces the most important philosophical issues that arise within the empirical sciences. Requiring no previous background in philosophy, this reader-friendly volume covers topics ranging from traditional questions about the nature of explanation and the confirmation of theories to practical issues concerning the design of physical experiments and modeling. Incisive and accessible chapters with relevant case-studies and informative illustrations examine the function of thought experiments, discTable of ContentsPreface ix Acknowledgments xi About the Companion Website xii 1 Pillars of Science: Reasons, Knowledge, and Truth 1 1.1 Epistemic Reasons 2 1.2 Reasoning from Evidence 7 1.3 Knowledge and Truth 11 1.4 Facts, Hypotheses, and Theories 12 1.5 Conclusion 17 2 Evidence, Observation, and Measurement 19 2.1 The Promises of Evidence 19 2.2 Basic Evidence and Derived Evidence 21 2.3 Measurement 26 2.4 Conclusion 31 3 Uses of Evidence 33 3.1 From Observation to Hypothesis 33 3.2 Theory Appraisal 36 3.3 The Demarcation Problem 42 3.4 Conclusion 49 4 Evidence, Rationality, and Disagreement 51 4.1 From Weak to Strong Evidence 51 4.2 Evidence and Rationality 60 4.3 Explaining Scientific Disagreement 63 4.4 Conclusion 69 5 The Nature of Probability 71 5.1 Basics of Probability 71 5.2 Interpretations of Probability 73 5.3 Probabilities as Credences 74 5.4 Epistemic Probabilities 79 5.5 Probabilities as Objective Chances 81 5.6 Probabilities and Defeasible Reasoning 84 5.7 Fallacies 86 5.8 Conclusion 87 6 Do Not Be Misled: Confounds and Controls 88 6.1 Trials and Errors 88 6.2 Treatment and Control 89 6.3 Randomization 94 6.4 Conclusion 99 7 Physical Experiments and Their Design 101 7.1 Historical Remarks 101 7.2 Setting Experimental Parameters 102 7.3 Dependent and Independent Variables 103 7.4 Learning from Experiment 106 7.5 Types of Errors: Pick Your Poison 112 7.6 Relationships between Experiment and Theory 113 7.7 Conclusion 117 8 Experimental Methods That They Don’t Teach 119 8.1 Found and Natural Experiments 119 8.2 Thought Experiments 122 8.3 The Structure and Evidential Value of Thought Experiments 133 8.4 Learning from TEs 136 8.5 The Ubiquity of Thought Experiments 139 8.6 Are Computer Simulations Thought Experiments? 141 8.7 Conclusion 142 9 Models: Useful Lies and Informative Fictions 144 9.1 The Nature of Models 146 9.2 Modelling Techniques 153 9.3 Analogies 156 9.4 Learning from Models 159 9.5 Conclusion 165 10 Causation and Causal Inference 167 10.1 What’s the Problem with Causation? 167 10.2 Hume’s Challenge 168 10.3 Causation as Mere Regularities 170 10.4 Conserved Quantities to the Rescue? 171 10.5 Causation and Manipulation 173 10.6 Conclusion 177 11 Strange Causation – Time Travel and Remote Action 179 11.1 On Influencing the Past 180 11.2 Quantum Mechanics and Locality 191 11.3 Conclusion 196 12 But Is Any of It Real? 198 12.1 Theories and Truth 198 12.2 A Map of the Views 199 12.3 Are Groups Real? 201 12.4 Laws of Nature 205 12.5 Is Everything Real Observable? 208 12.6 Realism vs. Antirealism 213 12.7 Structural Realism 218 12.8 Realism and Explanation 219 12.9 Conclusion 221 13 Explanation and Understanding 223 13.1 The Deductive-Nomological Model 224 13.2 The Causal Model 229 13.3 The Unificationist Model 231 13.4 The Pragmatic Model 234 13.5 What about Realism? 237 13.6 Conclusion 238 14 Fundamental Theories and the Organization of Science 240 14.1 The Layer Cake Model 242 14.2 Classical Reductionism 243 14.3 Functional Concepts 248 14.4 The Functional Model 250 14.5 Emergence 253 14.6 Interdisciplinary Research 257 14.7 Conclusion 259 15 Scientific Progress 262 15.1 Science and Technology 263 15.2 Goals of Science 264 15.3 Reduction in the Limit 265 15.4 How Theories Are Born 266 15.5 What Kind of Progress? 269 15.6 From Theories to Research Programmes 275 15.7 Methodological Anarchism 277 15.8 Incommensurability 279 15.9 Structural Realism and Progress 284 15.10 Conclusion 286 Index 288

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