Biology, life sciences Books

Book SynopsisPopulation Genetics and Microevolutionary Theory Explore the fundamentals of the biological implications ofpopulation genetic theoryIn the newly revised Second Edition of Population Genetics and Microevolutionary Theory, accomplished researcher and author Alan R. Templeton delivers a fulsome discussion of population genetics with coverage of exciting new developments in the field, including new discoveries in epigenetics and genome-wide studies. The book prepares students to successfully apply population genetics analytical tools by providing a solid foundation in microevolutionary theory. The book emphasizes that population structure forms the underlying template upon which quantitative genetics and natural selection operate and is a must-read for future population and evolutionary geneticists and those who wish to work in genetic epidemiology or conservation biology. You'll learn about a wide array of topics, including quantitative genetics, the interactions of natural selection with other evolutionary forces, and selection in heterogeneous environments and age-structured populations. Appendices that cover genetic survey techniques and probability and statistics conclude the book. Readers will also benefit from the inclusion of:A thorough introduction to population genetics, including the scope of the subject, its premises, and the Hardy-Weinberg Model of MicroevolutionAn exploration of systems of mating, including a treatment of the use of runs of homozygosity to show pedigree inbreeding in distant ancestorsA practical discussion of genetic drift, including the use of effective sizes in conservation biology (with a discussion of African rhinos as an example)A concise examination of coalescence, including a treatment of the infinite sites modelPerfect for graduate students in genetics and evolutionary biology programs and advanced undergraduate biology majors, Population Genetics and Microevolutionary Theory will also earn a place in the libraries of students taking courses in conservation biology, human genetics, bioinformatics, and genomics.Table of ContentsPreface to the 2nd Edition ix Chapter 1. The Scope and Basic Premises of Population Genetics 1-1 Basic Premises of Population Genetics 1-1 Population Genomics1-12 Section 1: Population Structure and History Chapter 2. Modeling Evolution and the Hardy-Weinberg Law 2-1 How to Model Microevolution 2-1 The Hardy-Weinberg Model 2-4 Hardy-Weinberg for Two Loci2-19 Chapter 3. Systems of Mating 3-1 Inbreeding 3-1 Assortative Mating3-25 Disassortative Mating3-45 Chapter 4. Genetic Drift 4-1 Basic Evolutionary Properties of Genetic Drift 4-2 Founder and Bottleneck Effects 4-7 Genetic Drift and Disequilibrium4-11 Genetic Drfit, Disequilibrium, and System of Mating4-13 Effective Population Size4-18 Chapter 5. Genetic Drift in Large Populations and Coalescence 5-1 Newly Arisen Mutations 5-1 Neutral Alleles 5-3 The Coalescent5-22 Chapter 6. Gene Flow and Population Subdivision 6-1 Gene Flow Between Two Local Populations 6-1 The Balance of Gene Flow and Drift 6-6 An Example of the Balance of Drift and Gene Flow6-27 Factors Influencing The Amount and Patter of Gene Flow6-42 Total Effective Population Size in Subdivided Populations6-62 Multiple Modes of Inheritance and Population Structure6-71 Admixture6-76 Identifying Subpopulations and Population Structure6-81 A Final Warning6-96 Chapter 7. Population History 7-1 Inferring Historical Effective Population Sizes 7-6 Inferring Historical Gene Flow Patterns and Admixture 7-11 Using Haplotype Trees to Study Population History 7-19 Model Based Approaches to Phylogeographic Analysis 7-56 Direct Studies Over Space and Past Times 7-70 Historical Population Genetics and Macroevolution 7-75 Section 2: Genotype and Phenotype Chapter 8. Basic Quantitative Genetic Definitions and Theory 8-1 “Simple” Mendelian Phenotypes 8-2 Nature Versus Nurture? 8-7 The Fisherian Model of Quantitative Genetics8-13 Chapter 9. Quantitative Genetics: Unmeasured Genotypes 9-1 Correlation Between Relatives 9-2 The Distinction Between Heritability and Inheritance9-17 Response to Selection9-19 The Problem of Between-Population Differences in Mean Phenotype 9-21 Controlled Crosses for the Analysis of Between Population Differences 9-30 The Balance Between Mutation, Drift, and Gene Flow Upon Phenotypic Variance 9-36 Chapter 10. Quantitative Genetics: Measured Genotypes 10-1 Marker Association Studies 10-5 Candidate Loci10-35 Candidate Loci and Genetic Architecture10-51 Section 3: Natural Selection and Adaptation Chapter 11. Natural Selection 11-1 The Fundamental Equation of Natural Selection: Measured Genotypes 11-4 Sickle-Cell Anemia as an Example of Natural Selection 11-10 Adaptation as a Polygenic Process 11-24 The Fundamental Theorem of Natural Selection: Unmeasured Genotypes 11-29 Some Implications of the Fundamental Equations of Natural Selection 11-33 The Course of Adaptation and Natural Selection 11-47 Chapter 12. Interactions of Natural Selection with Other Evolutionary Forces and the Detection of Natural Selection 12-1 The Interaction of Natural Selection with Mutation 12-3 The Interaction of Natural Selection with Mutation and System of Mating 12-8 The Interaction of Natural Selection with Gene Flow 12-12 The Interaction of Natural Selection with Genetic Drift 12-21 The Interactions of Natural Selection, Genetic Drift, and Gene Flow 12-28 The Interactions of Natural Selection, Genetic Drift, and Mutation 12-45 The Interactions of Natural Selection, Genetic Drift, Mutation, and Recombination 12-65 Candidate Loci 12-71 Quantitative Genetic Approaches to Detecting Selection 12-75 The Neutralist/Selectionist Debate 12-80 Chapter 13. Units and Targets of Selection 13-1 The Unit of Selection 13-4 Targets of Selection Below the Level of the Individual 13-18 Targets of Selection Above the Level of the Individual 13-51 Chapter 14. Selection in Heterogeneous Environments 14-1 Coarse-Grained Spatial Heterogeneity 14-4 Coarse-Grained Temporal Heterogeneity 14-34 Fine-Grained Heterogeneity 14-56 Coevolution 14-74 Chapter 15. Selection in Age-Structured Populations 15-1 Life History and Fitness 15-3 The Evolution of Senescence 15-13 Abnormal Abdomen: An Example of Selection in an Age-Structured Population 15-24 Overview 15-63 Appendices Appendix 1. Genetic Survey Techniques A1-1 Appendix 2. Probability and Statistics A2-1 References R-1 Index

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Book SynopsisHistory of Anatomy: An International Perspective is unique in its global approach to studying the development of human anatomy. Though it references widely known anatomists, such as Aristotle, Galen, and Bell, the book also pay homage to less famous contributors to the field and explains their findings.Table of ContentsPreface xi Acknowledgments xiii 1 Africa 1 1.1 Egypt 2 1.1.1 The Edwin Smith Papyrus 2 1.1.2 The Ebers Papyrus 2 1.1.3 The Kahun Papyrus 3 1.1.4 Egyptian Anatomy in General 3 1.1.5 Neurological Anatomy 4 1.1.6 Cardiovascular Anatomy 6 1.1.7 Reproductive Anatomy 6 1.2 Algeria 7 1.2.1 Jean Baptiste Paulin Trolard 7 Bibliography 11 2 Asia 13 2.1 China 13 2.1.1 Correcting the Errors in the Forest of Medicine 14 2.1.2 Hua Tuo 17 2.1.3 Conclusion 19 2.2 Japan 19 2.2.1 Feudal Japan (1186–1868) 19 2.2.2 Shinnin Kawaguchi 23 2.2.3 Genpaku Sugita 24 2.2.4 Ryotaku Maeno 25 2.2.5 Shoteki Fuseya 27 2.2.6 Otsuki Gentaku 27 2.2.7 Koji Harada and Ryoetsu Hoshino 28 2.2.8 Human Dissection 28 2.2.9 Seishu Hanaoka 29 2.2.10 Buntaro Adachi 31 2.2.11 Sunao Tawara 36 2.3 India 39 2.3.1 Sushruta 39 Bibliography 44 3 Europe 49 3.1 Austria 50 3.1.1 Heinrich Obersteiner 50 3.1.2 Emil Zuckerkandl 55 3.2 Czechoslovakia 59 3.2.1 Vincent Alexander Bochdalek 59 3.3 England 62 3.3.1 Richard Lower 63 3.3.2 John Browne 71 3.3.3 James Drake 75 3.3.4 Francis Sibson 81 3.3.5 William Turner 87 3.4 France 90 3.4.1 Jacobus Sylvius 90 3.4.2 Charles Estienne 94 3.4.3 Raymond de Vieussens 96 3.4.4 Pierre Dionis 98 3.4.5 Félix Vicq d’Azyr 101 3.4.6 Marie‐François Xavier Bichat 105 3.4.7 François Magendie 109 3.4.8 Jules Germain Cloquet 114 3.4.9 Augusta Déjerine‐Klumpke 120 3.5 Germany 122 3.5.1 Adam Christian Thebesius 122 3.5.2 Franz Kaspar Hesselbach 125 3.5.3 Hubert von Luschka 128 3.5.4 Adolf Wallenberg 132 3.5.5 Korbinian Brodmann 135 3.6 Greece 141 3.6.1 Aristotle 141 3.6.2 Galen 145 3.6.3 Polybus 147 3.7 Holland 148 3.7.1 Franciscus Sylvius 149 3.7.2 Niels Stensen 150 3.7.3 Pieter Camper 154 3.8 Ireland 160 3.8.1 Abraham Colles 160 3.9 Italy 164 3.9.1 Leonardo da Vinci 165 3.9.2 Vidus Vidius (Guido Guidi) 167 3.9.3 Giambattista Canano 170 3.9.4 Matteo Realdo Colombo 172 3.9.5 Costanzo Varolio (Constantius Varolius) 174 3.9.6 Giulio Cesare Casseri 176 3.9.7 Giovanni Maria Lancisi 180 3.9.8 Giovanni Battista Morgagni 188 3.9.9 Ruggero Ferdinando Antonio Guiseppe Vincenzo Oddi 192 3.10 Norway 196 3.10.1 Johan Georg Ræder 196 3.11 Scotland 200 3.11.1 Andrew Fyfe the Elder 200 3.11.2 Sir John Struthers 204 3.11.3 Charles Bell 208 3.12 Spain 213 3.12.1 Antonio de Gimbernat y Arbós 213 3.13 Sweden 216 3.13.1 Emanuel Swedenborg 216 3.14 Switzerland 219 3.14.1 Wilhelm His Senior 219 3.14.2 Wilhelm His Junior 221 Bibliography 222 4 Middle East 251 4.1 Anatomy in the Bible and Talmud 251 4.1.1 Neuroanatomy 251 4.1.2 General Anatomy 255 4.2 Anatomy in the Qur’an and Hadeeth 256 4.2.1 History of the Qur’an and Hadeeth 257 4.2.2 The Cardiovascular System 257 4.2.3 Contributions to Medicine 258 4.3 Persia 259 4.3.1 Following the Establishment of the Persian Empire (Sixth to Seventh Century CE) 259 4.3.2 Abu Zakariya Yuhanna ibn Masawaih, Mesue 262 4.3.3 Ali ibn Sahl Rabban al‐Tabari 262 4.3.4 Abubakr Muhammad Ibn Zakaria Razi, Rhazes 262 4.3.5 Abubakr Rabi ibn Ahmad Joveini Bukhari 263 4.3.6 Ali ibn Abbas al‐Majusi, Hally Abbas 264 4.3.7 Abu Ali al‐Hussain ibn Abdallah ibn Sina, Avicenna 265 4.3.8 Zinn‐ol‐Abedin Seyed Esmail ibn al‐Hussain ibn Mohammad ibn Ahmad al‐Jorjani, Hakim Jorjani 267 4.4 From the Mongol Invasion of Persia to the Foundations of Modern Anatomy 268 4.4.1 Nasir al‐Din Tusi 268 4.4.2 Mansur ibn Muhammad ibn Ahmad ibn Yusuf ibn Ilyas, Ibn Ilyas 269 4.4.3 The Safavid Period (1501–1722 CE) and the Reconciliation of Prophetic and Galenic Traditions 274 4.5 Baghdad 275 4.5.1 Ibn Jazlah 275 Bibliography 277 5 North America 285 5.1 United States 285 5.1.1 Henry Jacob Bigelow 285 5.1.2 Oliver Wendell Holmes 288 Bibliography 295 Index 297

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Book SynopsisEvolutionary developmental biology jumps a step further in Evolutionary Developmental Anthropology to survey the correlation between evolutionary developmental anthropology and primate and human morphological evolution.Table of ContentsContributors vii Foreword: Humans from Embryos ix Günter P. Wagner 1 Introduction to Evo‐Devo‐Anthro 1 Campbell Rolian and Julia C. Boughner 2 Chondrocranial Growth, Developmental Integration and Evolvability in the Human Skull 17 Neus Martínez‐Abadías, Mireia Esparza, Torstein Sjøvold and Benedikt Hallgrímsson 3 The Tooth of the Matter: The Evo‐Devo of Coordinated Phenotypic Change 35 Julia C. Boughner 4 Genetic Regulation of Amelogenesis and Implications for Hominin Ancestors 61 Rodrigo S. Lacruz 5 Evo‐Devo Sheds Light on Mechanisms of Human Evolution: Limb Proportions and Penile Spines 77 Philip L. Reno 6 Out on a Limb: Development and the Evolution of the Human Appendicular Skeleton 101 Nathan M. Young and Terence D. Capellini 7 Tinkering with Growth Plates: A Developmental Simulation of Limb Bone Evolution in Hominoids 139 Campbell Rolian 8 Origin, Development, and Evolution of Primate Muscles, with Notes on Human Anatomical Variations and Anomalies 167 Rui Diogo and Bernard Wood 9 The Evolutionary Biology of Human Neurodevelopment: Evo‐Neuro‐Devo Comes of Age 205 Bernard Crespi and Emma Leach 10 Evolving the Developing Cortex: Conserved Gradients of Neurogenesis Scale and Channel New Functions in Primates 231 Christine J. Charvet and Barbara L. Finlay 11 Growing Up Fast, Maturing Slowly: The Evolution of a Uniquely Modern Human Pattern of Brain Development 261 Philipp Gunz 12 FOXP2 and the Genetic and Developmental Basis of Human Language 285 Carles Lalueza‐Fox 13 Assembly Instructions Included 297 Kenneth Weiss and Anne Buchanan Index 317

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Book SynopsisNeurodevelopmental disorders arise from disturbances to various processes of brain development, which can manifest in diverse ways. They encompass many rare genetic syndromes as well as common, heritable conditions such as intellectual disability, autism, ADHD, schizophrenia and many types of epilepsy.Table of ContentsList of Contributors vii ForewordKevin J. Mitchell ix 1 The Genetic Architecture of Neurodevelopmental Disorders 1Kevin J. Mitchell 2 Overlapping Etiology of Neurodevelopmental Disorders 29Eric Kelleher and Aiden Corvin 3 The Mutational Spectrum of Neurodevelopmental Disorders 49Nancy D. Merner, Patrick A. Dion, and Guy A. Rouleau 4 The Role of Genetic Interactions in Neurodevelopmental Disorders 69Jason H. Moore and Kevin J. Mitchell 5 Developmental Instability, Mutation Load, and Neurodevelopmental Disorders 81Ronald A. Yeo and Steven W. Gangestad 6 Environmental Factors and Gene–Environment Interactions 111John McGrath 7 The Genetics of Brain Malformations 129M. Chiara Manzini and Christopher A. Walsh 8 Disorders of Axon Guidance 155Heike Blockus and Alain Chédotal 9 Synaptic Disorders 195Catalina Betancur and Kevin J. Mitchell 10 Human Stem Cell Models of Neurodevelopmental Disorders 239Peter Kirwan and Frederick J. Livesey 11 Animal Models for Neurodevelopmental Disorders 261Hala Harony-Nicolas and Joseph D. Buxbaum 12 Cascading Genetic and Environmental Effects on Development: Implications for Intervention 275Esha Massand and Annette Karmiloff-Smith 13 Human Genetics and Clinical Aspects of Neurodevelopmental Disorders 289Gholson J. Lyon and Jason O'Rawe 14 Progress Toward Therapies and Interventions for Neurodevelopmental Disorders 319Ayokunmi Ajetunmobi and Daniela Tropea Subject Index 345 Gene Index 353

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Book SynopsisStem Cell Nanoengineeringreviews theapplications ofnanotechnology in the fields of stem cells, tissue engineering, and regenerative medicine. Topics addressed include various types of stem cells, underlying principles of nanobiotechnology, the making of nano-scaffolds, nano tissue engineering, applications of nanotechnology in stem cell tracking and molecular imaging, nano-devices, as well asstem cell nano-engineering from bench to bedside. Written by renowned experts in their respective fields, chapters describe and explore a wide variety of topics in stem cellnanoengineering, making the book a valuable resource for both researchers and clinicians in biomedical and bioengineering fields.Table of ContentsAbout the Editors ix Contributors xi Preface xvii Part 1 An Introduction to Stem Cells 1 1 Adult Stem Cells 3 Andreas Nussler and Sahar Olsadat Sajadian 2 Pluripotent Stem Cells 25 Hossein Azizi, Akbar Hajizadeh Moghaddam, and Thomas Skutella 3 Interactions of Stem Cells and Components of the Extracellular Matrix 35 Anna K. Blakney, Julie J. Antetomaso, Winnie W. Leung, and Deok-Ho Kim 4 Regenerative Medicine and Cell Therapy: Past, Present, and Future 47 Hooman Sadri-Ardekani and Anthony Atala Part 2 An Introduction to Nanotechnology 67 5 Principles of Nanotechnology 69 Jerzy Leszczynski 6 Stem-Cell Nanoengineering: Explorations in a Rapidly Moving Field 87 Abhalaxmi Singh and Sanjeeb K. Sahoo Part 3 Nanostructures for Stem-Cell Engineering – Engineering Approach 97 7 Nanopatterned Surfaces for Stem-Cell Engineering 99 Waleed Ahmed El-Said, Tae-Hyung Kim, Ki-Bum Lee, and Jeong-Woo Choi 8 Biomimetic Nanostructures by Electrospinning and Electrospraying 123 Elham Vatankhah, Molamma P. Prabhakaran, and Seeram Ramakrishna 9 Nanoparticles for Stem-Cell Engineering 143 Esmaiel Jabbari 10 Toxicology of Nanobiomaterials 171 Shahin Bonakdar and Omid Mashinchian Part 4 Control of Stem-Cell Fate by Engineering of Microenvironment 185 11 Stem-Cell Responses to Surface Nanotopographies 187 Peng-Yuan Wang and Wei-Bor Tsai 12 Control of Mesenchymal Stem-Cell Fate by Engineering the Nanoenvironment 205 Habib Nikukar, Stuart Reid, Mathis O. Riehle, Adam S.G. Curtis, and Matthew J. Dalby 13 Delivery of Molecules and Genes/Small Interfering RNA into Stem Cells by Nanoengineering 223 Mohsen Ashjari Part 5 Nanotissue Engineering – Biological Approach along with Differentiation 243 14 Expansion of Stem Cells by Nanotissue Engineering 245 Amir Mellati and Hu Zhang 15 Nanotissue Engineering of Neural Cells 265 Sasan Jalili-Firoozinezhad, Fahimeh Mirakhori, and Hossein Baharvand 16 Nanotechnology and Cardiovascular Tissue Engineering 285 Savneet Kaur and Upasana Rishiraj 17 Nanotissue Engineering of Musculoskeletal Cells 299 Mohamadreza Baghaban Eslaminejad, Leila Taghiyar, and Fatemeh Safari 18 Nanotissue Engineering of Skin Cells 315 Daisy M. Ramos, Aditi Subramanian, Aja Aravamudhan, Matthew Harmon, Roshan James, Namdev B. Shelke, and Sangamesh G. Kumbar 19 High-Throughput Screening of Stem Cell Self-Renewal and Differentiation on Nanomaterials 327 Perry T. Yin, Tae-Hyung Kim, Jeong-Woo Choi, and Ki-Bum Lee Part 6 Nanotechnology in Stem-Cell Imaging 345 20 Nanotechnology for Cellular Imaging 347 Miroslaw Janowski, P. Walczak, and J.W.M. Bulte Part 7 Nanotissue Engineering and Clinical Applications 363 21 Advancing Translational Nanotechnology to Clinical Application 365 Michelle Griffin, Shima Salmasi, Naghmeh Naderi, Peter E. Butler, and Alexander M. Seifalian 22 Stem-Cell Nanoengineering from Bench to Bed 381 Omid Mashinchian, Shahin Bonakdar, Shahriar Sharifi, and Morteza Mahmoudi Index 397

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Book SynopsisThe Handbook of Behavioral Genetics and Phenotyping represents an integrative approach to neurobehavioural genetics; worldwide experts in their field will review all chapters. Advanced overviews of neurobehavioural characteristics will add immense value to the investigation of animal mutants and provide unique information about the genetics and behavioural understanding of animal models, under both normal and pathological conditions. Cross-species comparisons of neurobehavioural phenotypes will pave the way for an evolutionary understanding of behaviour. Moreover, while biological sciences are progressing towards a holistic approach to investigate the complexity of organisms (i.e., systems biology approach), an integrated analysis of behavioural phenotyping is still lacking. The Handbook of Behavioral Genetics and Phenotyping strengthens the cross-talk within disciplines that investigate the fundamental basis of behaviour and genetics. This will be the first volume in which traditioTable of ContentsList of Contributors xix Preface xxv 1 Genetic Screens in Neurodegeneration 1Abraham Acevedo Arozena and Silvia Corrochano Introduction 1 The Genetics of Neurodegenerative Disorders 2 Neurodegeneration Disease Models 4 Genetic Approaches to Discover New Genes Related to Neurodegeneration Using Disease Models 5 Saccharomyces cerevisiae 6 Caenorhabditis elegans 8 Drosophila melanogaster 9 Danio rerio 10 Mus musculus 11 Human Cellular Models and Post-mortem Material 14 The Future 14 Acknowledgments 15 References 15 2 Computational Epigenomics 19Mattia Pelizzola Background 19 Profiling and Analyzing the Methylation of Genomic DNA 19 Experimental Methods 20 Data Analysis 20 Array-based Methods 20 Sequencing-based Methods 20 Profiling and Analyzing Histone Marks 26 Experimental Methods 26 Data Analysis 27 Issues of Array-based Methods 27 Issues of NGS-based Methods 27 Integration with Other Omics Data 31 Chromatin States 32 Unraveling the Cross-talk Between Epigenetic Layers 33 References 33 3 Behavioral Phenotyping in Zebrafish: The First Models of Alcohol Induced Abnormalities 37Robert Gerlai Introduction 37 Alcohol Related Human Disorders: A Growing Unmet Medical Need 37 Unraveling Alcohol Related Mechanisms: The Importance of Animal Models 38 Face Validity: The First Step in Modeling a Human Disorder 39 Acute Effects of Alcohol in Zebrafish: A Range of Behavioral Responses 39 Chronic Alcohol Exposure Induced Behavioral Responses in Zebrafish 41 Effects of Embryonic Alcohol Exposure 42 Behavioral Phenotyping: Are We There Yet? 46 Assembling the Behavioral Test Battery 49 Concluding Remarks 50 References 50 4 How does Stress Affect Energy Balance? 53Maria Razzoli, Cheryl Cero, and Alessandro Bartolomucci Introduction 53 Stress 54 Energy Balance and Metabolic Disorders 55 Pro-adipogenic Stress Mediators 57 Pro-lipolytic Effect of Stress Mediators 57 How does Stress Affect Energy Balance? 57 Animal Models of Chronic Stress and their Impact on Energy Balance 58 Physical and Psychological (non-social) Chronic Stress Models 58 Mild Chronic Pain Models – Mild Tail Pinch, Foot Shock 58 Thermal Models – Cold and Heat Stress 64 Chronic Mild Stress Models: Chronic Mild Stress, Chronic Variable Stress, etc. 64 Restraint or Immobilization 65 Chronic Social Stress Models 66 Social Isolation, Individual Housing 66 Unstable Social Settings 66 Visible Burrow System 67 Intermittent Social Defeat (Resident/Intruder Procedure) 67 Chronic Psychosocial Stress, Sensory Contact, and Chronic Defeat stress 68 Stress, Recovery, and Maintenance: Insights on Adaptive and Maladaptive Effects of Stress 69 Molecular Mechanisms of Stress-Induced Negative and Positive Energy Balance 70 Serotonin (5-hydroxytryptamine, 5HT) 71 Orexin 71 Neuropeptide Y (NPY) 72 Ghrelin and Growth Hormone Secretagogue Receptor (GHSR) 72 Glucagon like Peptide 1 (GLP1) 73 Leptin 73 Amylin 74 Norepinephrine and β3-Adrenergic Receptor 74 Conclusion 74 References 75 5 Interactions of Experience-Dependent Plasticity and LTP in the Hippocampus During Associative Learning 91Agnès Gruart, Noelia Madroñal, María Teresa Jurado-Parras, and José María Delgado-García Introduction: Study of Learning and Memory Processes in Alert Behaving Mammals 91 Changes in Synaptic Strength During Learning and Memory 92 Classical Conditioning 92 Instrumental Conditioning 95 Changes in Synaptic Strength Evoked by Actual Learning can be Modified by Experimentally Evoked Long-term Potentiation 96 Other Experimental Constraints on the Study of the Physiological Basis of Learning Processes 100 Factors Modifying Synaptic Strength (Environment, Aging, and Brain Degenerative Diseases) 101 Different Genetic and Pharmacological Manipulations Able to Modify Synaptic Strength 103 Functional Relationships Between Experimentally Evoked LTP and Associative Learning Tasks 106 Future Perspectives 108 Context and Environmental Constraints 108 Other Forms of Learning and Memory Processes 109 Cortical Circuits and Functional States During Associative Learning 109 References 110 6 The Genetics of Cognition in Schizophrenia: Combining Mouse and Human Studies 115Diego Scheggia and Francesco Papaleo Background 115 Genetics of Schizophrenia 116 Cognitive (dys)functions in Schizophrenia 117 Translating Cognitive Symptoms in Animal Models 119 Executive Control 120 Performance in Schizophrenia 122 Animal Models 124 Working Memory 125 Performance in Schizophrenia 126 Animal Models 127 Control of Attention 128 Performance in Schizophrenia 130 Animal Models 130 Concluding Remarks 131 References 132 7 The Biological Basis of Economic Choice 143David Freestone and Fuat Balci Introduction 143 Translating from Animals to Humans 144 Reinforcement Learning in the Brain 145 Subjective Value 146 The Midbrain Dopamine System Updates Value 147 From Stimulus Value to Action Value 150 Model Based Learning 150 The Prefrontal Cortex Encodes Value 152 The Basal Ganglia Selects Actions 153 Optimal Decisions: Benchmarks for the Analysis of Choice Behavior 155 The Drift Diffusion Model 157 Temporal Risk Assessment 158 Timed-response Inhibition for Reward-rate Maximization 160 Timed Response Switching 163 Temporal Bisection 164 Numerical Risk Assessment 166 Rodent Version of Balloon Analog Risk Task 167 Conclusion 167 Acknowledgments 168 References 168 8 Interval-timing Protocols and Their Relevancy to the Study of Temporal Cognition and Neurobehavioral Genetics 179Bin Yin, Nicholas A. Lusk, and Warren H. Meck Introduction 179 Application of a Timing, Immersive Memory, and Emotional Regulation (Timer) Test Battery 190 Neural Basis of Interval Timing 191 What Makes a Mutant Mouse “Tick”? 193 Proposal of a TIMER Test Battery and Its Application in Reverse Genetics 199 Behavioral Test Battery Applications in Forward Genetics 202 Order of Behavioral Tasks 205 Location and Time of Behavioral Testing 205 Summary 205 References 206 Appendix I 226 Limitations of the individual-trials analysis for data obtained in the peak-interval (PI) procedure 226 9 Toolkits for Cognition: From Core Knowledge to Genes 229Giorgio Vallortigara and Orsola Rosa Salva Introduction 229 Core Knowledge: The Domestic Chick as a System Model 230 Numerical Competence 230 Physical Properties 230 Geometry of Space 232 Animate Agents 232 A Comparative Perspective on the Genetic and Evolutionary Bases of Social Behavior 236 From Social Experience to Genes 239 From Genes to Social Behavior 241 Future Directions 243 Conserved Mechanisms for Social Core Knowledge 243 Interactions Between Experience and Genomic Information 243 Neurogenetic Basis of Social Predispositions 243 Epigenetics and the Development of the Social Brain 244 Spatial Cognition, Another Promising Core-knowledge Domain 244 References 245 10 Quantitative Genetics of Behavioral Phenotypes 253Elzbieta Kostrzewa and Martien J.H. Kas Human Studies of Quantitative Traits 253 Mouse Studies of Quantitative Traits 254 Classical Inbred Mice 254 Quantitative Trait Loci (QTL) Analysis 254 Knock-out (KO) Mouse Lines 256 Use of Mice as Animal Model for Complex Human Traits 257 Comparative Genomic Approaches 257 Evolutionarily Conserved Behavioral Phenotypes 257 Physical Activity – Definitions and Methods of Phenotypic Measurement 258 Current Results of Quantitative Genetic Basis of PA in Humans 259 Current Results of Quantitative Genetic Basis of PA in Mice 260 KO Studies 260 QTL Studies 261 An Overlap of Genetic Findings Between the Species 261 Conclusions 265 References 265 11 Behavioral Phenotyping in Genetic Mouse Models of Autism Spectrum Disorders: A Translational Outlook 271Maria Luisa Scattoni, Caterina Michetti, Angela Caruso, and Laura Ricceri Introduction 271 Measuring Social behavior in ASD Mouse Models 272 Social Interaction Tests 272 Male-female 277 Female-female 278 Male-male 278 Social-approach 279 Sociability Test Phase 280 Social Novelty 280 Social Recognition 280 Repetitive Behavior 281 Motor Stereotypies 281 Restricted Interests 281 Behavioral Inflexibility 282 Behavioral Tests Targeting other ASD Symptoms 282 Anxiety 282 Epilepsy 283 Behavioral Phenotyping in ASD Mouse Pups 283 Future Directions: ASD Mouse Models as a Resource for Gene-environment Interaction Studies 284 Acknowledgments 285 References 285 12 Genetics of Human Sleep and Sleep Disorders 295Birgitte Rahbek Kornum The Mystery of Human Sleep 295 Sleep is Essential for Mammalian Life 295 The Function of Sleep 296 Extended Wakefulness Induces Sleep 296 Homeostatic and Circadian Regulation of Sleep and Wake 297 Adenosine and Sleep Homeostasis 298 Resistance to Sleep Loss is a Stable Phenotype 299 Genetic Markers of Response to Sleep Loss 299 A Unique Activity Pattern Characterizes the Sleeping Brain 300 Sleep Stages and Sleep Cycles 300 Genetics of the Human Sleep Electroencephalography 301 Normal Sleep Architecture is Lost in Fatal Familial Insomnia 303 Circadian Regulation of Sleep and Associated Disorders 304 Circadian Regulation of Sleep 304 Molecular Regulation of the Circadian Clock 305 The Central Circadian Clock is Entrained By Light 306 Circadian Rhythm Sleep Disorders 307 Advanced Sleep Phase Syndromes 307 Delayed Sleep Phase Syndromes 308 Short Sleep Times in Healthy Individuals 308 Destabilization of Sleep States and Narcolepsy 309 Normal Regulation of Sleep Architecture 309 Wakefulness is Associated with Cortical Activation 309 The Preoptic Area Contains Sleep-promoting Neurons 309 Mutual Inhibition Regulates Transitions Between Wake and Sleep 310 Regulation of REM Sleep 311 Narcolepsy, A Disorder of Wakefulness and REM Sleep 311 Narcolepsy with Cataplexy is Caused By Hypocretin Deficiency 312 Autoimmunity Toward Hypocretin Neurons 312 Genetic Evidence Supports the Autoimmune Hypothesis of Narcolepsy 313 Restless Legs Syndrome, A Developmental Sleep Disorder 314 Restless Legs Syndrome, A Mysterious Urge to Move 314 Restless Legs Syndrome and Dopamine Disturbances 315 Iron Deficiency Exacerbates RLS Symptoms 315 Genetic Studies Suggest Developmental Defects 316 Unresolved Issues and Future Perspectives 316 What is the Molecular and Neuroanatomical Basis for the Ultradian Rhythm of NREM-REM Sleep? 317 What is the Genetic Basis for Individual Variation in Complex Sleep Features such as Sleep Spindles and K-Complexes? 317 What is the Basis for the Individual Differences in Resistance to Sleep Loss? 317 Are Homeostatic and Circadian Mechanisms Genuinely Independent or Are They Intimately Linked? 318 What Controls the Molecular and Anatomical Diversity of Sleep Regulatory Networks Across Species? 318 References 319 13 The Endocannabinoid System in the Control of Behavior 323Edgar Soria-Gomez, Mathilde Metna, Luigi Bellocchio, Arnau Busquets-Garcia, and Giovanni Marsicano Introduction 323 Cannabinoid Effects and Endocannabinoid Functions 324 Role of the ECS in Memory Processes 325 Memory: General Background 325 Role of the ECS in Synaptic Plasticity 325 Memory Impairment Produced by Exogenous Cannabinoids 326 Cannabinoid Regulation of Memory: Neurobiological Mechanisms 327 Role of the ECS in Fear Processes 329 Fear: General Background 329 The ECS as an Endogenous Regulator of Fear Responses 331 Cannabinoid Regulation of Fear: Neurobiological Mechanisms 332 Implication of the ECS in Fear Coping Behaviors 333 Role of the ECS in Feeding Behavior 336 Feeding Behavior: General Background 336 The ECS as an Endogenous Regulator of Feeding Behavior 337 The ECS and Food Reward Circuits 338 The ECS in the Hypothalamic Appetite Network 338 The ECS in the Caudal Brainstem and Gastrointestinal Tract 340 Bimodal Control of Stimulated Food Intake by the ECS in the Brain 341 Paraventricular Hypothalamus Versus Ventral Striatum in Hypophagia induced by the ECS 342 The Olfactory Bulb and the Hyperphagic Action of the ECS 342 Conclusions 343 References 344 14 Epigenetics in Brain Development and Disease 357Elisabeth J. Radford, Anne C. Ferguson-Smith, and Sacri R. Ferrón Introduction 357 Epigenetics and Neurodevelopment 358 Histone Modifications 358 DNA Methylation 361 Hydroxymethylation 364 Genomic Imprinting 364 Non-coding RNAs 365 Neurodevelopmental Disorders with an Epigenetic Basis 366 Rett Syndrome 366 Coffin–Lowry Syndrome 367 Rubinstein–Taybi Syndrome 367 Alpha-thalassemia Mental Retardation Syndrome 367 Imprinted Neurodevelopmental Disorders 368 Trinucleotide Repeat Disorders 368 Fragile X Syndrome 370 Friedreich’s Ataxia 370 Myotonic Dystrophy 371 Huntington’s Disease (HD) 371 Epigenetics of Neurodegenerative Disorders 372 Parkinson´s Disease (PD) 372 Alzheimer´s Disease (AD) 373 The Impact of the Environment on the Epigenome 374 Epigenetic Therapy in Neurodevelopment 375 Untargeted Treatment 375 Targeted Epigenetic Modulation 377 Concluding Remarks 377 Acknowledgments 377 References 378 15 Impact of Postnatal Manipulations on Offspring Development in Rodents 395Diego Oddi, Alessandra Luchetti, and Francesca Romana D’Amato Introduction 395 Early Postnatal Environment in Laboratory Altricial Rodents 396 Rodents’ Responses to Postnatal Environment and Early Manipulations 397 Assessing Pups’ Responses to Postnatal Environment and Early Manipulation 397 Neonatal Ultrasonic Calls: Isolation-induced Vocalizations and Maternal Potentiation 397 Searching for Social Contact: Homing and Huddling Behaviors 398 Early-life Environment and Stress-Response 398 Separation from the Mother 399 Mother’s Stress 400 The Cross-fostering Paradigm 401 Repeated Cross-fostering as a Model of Early Maternal Environment Instability 403 Environmental Enrichment 405 Conclusions 406 References 407 16 Exploring the Roles of Genetics and the Epigenetic Mechanism DNA Methylation in Honey Bee (Apis Mellifera) Behavior 417Christina M. Burden and Jonathan E. Bobek Introduction 417 Genetics of Adult Honey Bee Biology and Behavior 418 Nurse to Forager Transition 418 Forager Preference 420 Techniques for Investigating the Genetic Bases of Behavior 420 QTL Mapping 421 RNA Techniques 421 Microarrays 421 RNA Sequencing 422 Experimentally Modulating the Genes Correlated with Specific Behaviors to Test Causality 422 DNA Methylation and Honey Bee Behavior 423 Honey Bee DNA Methylation Machinery and Genome-Wide Patterns 423 DNA Methylation and Task Specialization 424 DNA Methylation and Memory Consolidation 425 Techniques for Detecting and Assaying DNA Methylation 426 The Technological Bases for Most DNA Methylation Assays 426 Methylation-specific Restriction Endonucleases 426 Protein-mediated Precipitation of Methylated DNA 428 Bisulfite Conversion 428 Assaying Single CpGs, Short Sequences, and Target Regions 429 Analyzing Genome-wide DNA Methylation Patterns: Microarray-based Methodologies 431 Analyzing Genome-wide DNA Methylation Patterns: Sequencing-based Methodologies 432 Techniques for Manipulating DNA Methylation 434 Pharmacological Manipulation of DNA Methylation 434 RNA Interference as a DNMT Blockade 434 Concluding Remarks and Future Perspectives 435 References 436 17 Genetics and Neuroepigenetics of Sleep 443Glenda Lassi and Federico Tinarelli Defining Sleep 443 Sleep is Genetically Determined 445 EEG and Heritable Traits 445 Sleep Disorders and Genes 446 Sleep and Gene Expression 447 Epigenetics 448 DNA Methylation 450 Posttranslational Modifications (PTMs) 450 RNA interference 452 Neuroepigenetics 453 Two Neurodevelopmental Disorders with Opposing Imprinting Profiles and Opposing Sleep Phenotypes 453 Neuroepigenetics of Sleep 454 Fruit Fly 454 Rodent Models 454 Human Beings 456 Sleep and Parent-of-origin Effects 458 Conclusions 460 References 460 18 Behavioral Phenotyping Using Optogenetic Technology 469Stephen Glasgow, Carolina Gutierrez Herrera, and Antoine Adamantidis Introduction 469 Microbial Opsins 470 Fast Excitation Using Channelrhodopsin-2 and Its Variants 470 Fast Optical Silencing 474 Alternative strategies for cell-type specific modulation of neural activity 476 Targeting systems 476 Light Delivery in the Animal Brain 478 Recording Light-evoked Neuronal Activity 479 Behavioral Phenotyping 479 In-vivo Optogenetics: Defining Circuits 480 Perspectives 484 Acknowledgments 484 References 484 19 Phenotyping Sleep: Beyond EEG 489Sibah Hasan, Russell G. Foster, and Stuart N. Peirson Sleep Research 489 Phenotyping Sleep in Humans 490 Introduction 490 Actigraphy 490 Cardiorespiratory Signals 491 EEG 492 Phenotyping Sleep in Animal Models 494 Introduction 494 EEG 494 Introduction 494 Tethered EEG 496 Telemetered EEG 496 NeuroLogger EEG 498 Beyond EEG 498 Infrared Beam Break 499 Movement Based on Implanted Magnets 499 Piezo-electric Sensors 499 Video Tracking 500 Future Perspectives 501 Acknowledgements 502 References 502 20 A Cognitive Neurogenetics Screening System with a Data-Analysis Toolbox 507C.R. Gallistel, Fuat Balci, David Freestone, Aaron Kheifets, and Adam King Introduction 507 Mechanisms, Not Procedures 508 Functional Specificity 508 No Group Averages 509 Physiologically Meaningful Measures 509 Importance of Large-scale Screening and Minimal Handling 511 Utilizable Archived Data with Intact Data Trails 511 The System 512 The Toolbox 513 Core Commands 516 Powerful Graphics Commands 517 Results 518 Summary 523 References 524 21 Mapping the Connectional Architecture of the Rodent Brain with fMRI 527Adam J. Schwarz and Alessandro Gozzi Introduction 527 MRI Mapping of Functional Connectivity in the Rodent Brain 528 Networks of Functional Covariance 528 Connectivity of Neurotransmitter Systems 529 The Dopaminergic System 529 The Serotonergic System 531 Resting State BOLD fMRI 532 Connectivity Networks of the Rodent Brain 533 Do Rodent Brains have a Default Mode Network? 536 Use of Anesthesia and Other Methodological Considerations 539 Transgenic Models: Genetic Manipulation of Functional Connectivity Patterns 541 Future Perspectives 543 References 545 22 Cutting Edge Approaches for the Identification and the Functional Investigation of miRNAs in Brain Science 553Emanuela de Luca, Federica Marinaro, Francesco Niola, and Davide De Pietri Tonelli Introduction 553 History 553 Biology and Functions in the Brain 553 Identification of Novel MicroRNAs in the Brain 555 miRNA Extraction and Purification 556 miRNA Cloning 556 Computational Identification of Novel miRNAs 557 RNA Sequencing (RNA-Seq) 558 miRNA expression analysis in the brain 559 miRNA profiling 559 Analysis of miRNA Expression in Tissue 559 Target Identification 560 Computational Identification of Targets 561 Proteomics 561 RISC-associated miRNA Targets 562 RNomics 563 miRNA Manipulation/Target Validation 565 miRNA Inhibition 565 miRNA Over-expression 566 Target Validation 567 New Frontiers in Small RNA-based Technologies to Cure Nervous System Deficits 567 Use of miRNAs in Gene Therapy 567 Use of miRNAs in Gene Therapy in the Brain Requires Improved Delivery Strategies 571 Conclusion and Perspectives 572 Are Circulating miRNAs Novel Biomarkers for Brain Diseases? 572 Use of miRNAs in Cell Reprogramming Technology 573 Are miRNAs Just the “Tip of the Iceberg”? Emerging Classes of Noncoding RNAs and Novel Scenarios 574 Acknowledgments 575 Competing Financial Interests 575 References 575 Index 585

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Book Synopsis There is no escaping the fact that theisland biogeography of the North Atlantic Regionissingularlypeculiar. Sitting inthenorth of the Atlantic Ocean, these islands have been subjected to largescale shifts in climate over the last few million years, unlike the other island groups further south which were likelymorebuffered from thevicissitudes of Quaternary climate changes.Uniquely for a groupof islandsthere is only one documented extinctionin the North Atlantic(the Great Auk), and those in the insects are local eventsrelating to species that are distributed throughout the Palaearctic region. Over half the insect species in Iceland and Greenlandare introduced. The faunas, excluding Greenland, arepredominantlyofPalaearcticoriginand have close affinities with the faunas ofScandinavia andthe British Isles and.These unique physical and biological characteristics have interested biologists and biogeographers forcenturies. The key debates concerningthebiogeographyof the North Atlantic islandsstillrumble on:Do the biota reflect crypticrefugiaor otherwise, or tabula rasa and recolonization?How important werehuman communities in shaping the existing biota and biogeographical patterns?Throw into this mixcurrent concerns over global warming,and we can now ask,how resilient is the biota to change, either natural or anthropogenic? This volume draws together a range of researchers with longstanding research interests in the region, from diverseacademicbackgrounds, to evaluatesome ofthese questions.Table of ContentsList of Contributors vii Introduction xiJon P. Sadler and Eva Panagiotakopulu Section I: Remote Origins 1 1 The Opening of the North Atlantic 3Brian G. J. Upton 2 Cenozoic Vegetation and Phytogeography of the Sub-arctic North Atlantic 29Friðgeir Grímsson, Thomas Denk and Reinhard Zetter 3 Interglacial Biotas from the North Atlantic Islands 51Ole Bennike and Jens Böcher Section II: Origins of the Present Biota 83 4 Origin and Dispersal of the North Atlantic Vascular Plant Floras 85Christian Brochmann and Inger G. Alsos 5 The Aquatic Fauna of the North Atlantic Islands with Emphasis on Iceland 103Gísli Már Gíslason 6 The Vascular Floras of High-Latitude Islands with Special Reference to Iceland 113Thóra Ellen Thórhallsdóttir 7 Quaternary Vertebrates from the North Atlantic Islands 147Ole Bennike and Bernd Wagner 8 North Atlantic Insect Faunas, Fossils and Pitfalls 161Eva Panagiotakopulu Section III: Human Impact 185 9 Landnám and the North Atlantic Flora 187Kevin J. Edwards, Egill Erlendsson and J. Edward Schofield 10 Origin of the Northeast Atlantic Islands Bird Fauna: Scenarios of Ecosystem Development 215Aevar Petersen and Bergur Olsen 11 Human Impact on North Atlantic Biota: Farming and Farm Animals, Fishing, Sealing and Whaling 251Ingrid Mainland and Jennifer Harland Section IV: Conservation in a Warming World 273 12 A Fleet of Silver: Local Knowledge Perceptions of Sea Ice from Iceland and Labrador/Nunatsiavut 275Astrid E. J. Ogilvie, Brian T. Hill and Gaston R. Demarée 13 Biodiversity Conservation in the Faroe Islands Under Changing Climate and Land Use 293Anna Maria Fosaa 14 Biodiversity Conservation in Iceland Under Changing Climate 303Erlingur Hauksson 15 The Natural Environment and Its Biodiversity in Greenland During the Present Climate Change 339Ib Johnsen and Henning Heide-Jørgensen Index 359

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Book SynopsisWinner of the IENE Project Award 2016.Trade Review“In conclusion, the book provides a very important contribution to the understanding of the effects of linear infrastructures on wildlife. It is 'reader friendly' and practice driven, and I'm sure it will generate both further research and collaboration in the field, so that the highest beneficiary will be the natural vegetation and fauna.” (Bulletin of the Eurasian Dry Grassland Group, 1 November 2015) “Authors focused and wrote concisely, which means the contents are readily digestible and consequently easy to use for students in both academic and more technical and practical disciplines… Another major strength of the Handbook of Road Ecology is its comprehensive international coverage. Each of the three editors is from a different continent, and the other contributors cover an impressively diverse range of countries, developed and developing, and cultures. This means that in addition to providing a comprehensive compendium for people seeking information on ecologically sustainable road construction and planning, the volume is also valuable for learning from approaches and solutions applied in different regions…The cross-referencing of chapters is helpful and enables readers to find other chapters relevant to a particular topic with ease. The editors have clearly put considerable effort into ensuring the book is concise and easy to use for all those who are interested in the challenges of ecologically sustainable construction and planning of roads. Each chapter begins with a succinct summary and bullet points and ends with suggestions for further reading, which makes it easy to use as a reference work from which relevant information can be located easily and quickly. The book is richly illustrated with colored photographs and figures." Conservation Biology, 00: 0 (2017) Table of ContentsNotes on Contributors ix Foreword xx Richard T. T. Forman Preface xxii Acknowledgements xxiv About the companion website xxvi 1 The ecological effects of linear infrastructure and traffic: Challenges and opportunities of rapid global growth 1 Rodney van der Ree, Daniel J. Smith and Clara Grilo 2 Bad roads, good roads 10 William F. Laurance 3 Why keep areas road‐free? The importance of roadless areas 16 Nuria Selva, Adam Switalski, Stefan Kreft and Pierre L. Ibisch 4 Incorporating biodiversity issues into road design: The road agency perspective 27 Kevin Roberts and Anders Sjölund 5 Improving environmental impact assessment and road planning at the landscape scale 32 Jochen A. G. Jaeger 6 What transportation agencies need in environmental impact assessments and other reports to minimise ecological impacts 43 Josie Stokes 7 Principles underpinning biodiversity offsets and guidance on their use 51 Yung En Chee 8 Construction of roads and wildlife mitigation measures: Pitfalls and opportunities 60 Cameron Weller 9 Ensuring the completed road project is designed, built and operated as intended 65 Rodney van der Ree, Stephen Tonjes and Cameron Weller 10 Good science and experimentation are needed in road ecology 71 Rodney van der Ree, Jochen A. G. Jaeger, Trina Rytwinski and Edgar A. van der Grift 11 Field methods to evaluate the impacts of roads on wildlife 82 Daniel J. Smith and Rodney van der Ree 12 Case study: A robust method to obtain defendable data on wildlife mortality 96 Éric Guinard, Roger Prodon and Christophe Barbraud 13 Road–wildlife mitigation planning can be improved by identifying the patterns and processes associated with wildlife-vehicle collisions 101 Kari Gunson and Fernanda Zimmermann Teixeira 14 Incorporating landscape genetics into road ecology 110 Paul Sunnucks and Niko Balkenhol 15 Guidelines for evaluating use of wildlife crossing structures 119 Edgar A. van der Grift and Rodney van der Ree 16 Guidelines for evaluating the effectiveness of road mitigation measures 129 Edgar A. van der Grift, Rodney van der Ree and Jochen A. G. Jaeger 17 How to maintain safe and effective mitigation measures 138 Rodney van der Ree and Stephen Tonjes 18 Understanding and mitigating the negative effects of road lighting on ecosystems 143 Bradley F. Blackwell, Travis L. DeVault and Thomas W. Seamans 19 Ecological impacts of road noise and options for mitigation 151 Kirsten M. Parris 20 Fencing: A valuable tool for reducing wildlife-vehicle collisions and funnelling fauna to crossing structures 159 Rodney van der Ree, Jeffrey W. Gagnon and Daniel J. Smith 21 Wildlife crossing structures: An effective strategy to restore or maintain wildlife connectivity across roads 172 Daniel J. Smith, Rodney van der Ree and Carme Rosell 22 Recreational co‐use of wildlife crossing structures 184 Rodney van der Ree and Edgar A. van der Grift 23 Predator-prey interactions at wildlife crossing structures: Between myth and reality 190 Cristina Mata, Roberta Bencini, Brian K. Chambers and Juan E. Malo 24 Wildlife warning signs and animal detection systems aimed at reducing wildlife-vehicle collisions 198 Marcel P. Huijser, Christa Mosler‐Berger, Mattias Olsson and Martin Strein 25 Use of reflectors and auditory deterrents to prevent wildlife-vehicle collisions 213 Gino D’Angelo and Rodney van der Ree 26 Ecological effects of railways on wildlife 219 Benjamin Dorsey, Mattias Olsson and Lisa J. Rew 27 Impacts of utility and other industrial linear corridors on wildlife 228 A. David M. Latham and Stan Boutin 28 The impacts of roads and traffic on terrestrial animal populations 237 Trina Rytwinski and Lenore Fahrig 29 Insects, snails and spiders: The role of invertebrates in road ecology 247 Heinrich Reck and Rodney van der Ree 30 Case study: Protecting Christmas Island’s iconic red crabs from vehicles 258 Rob Muller and Mike Misso 31 Making a safe leap forward: Mitigating road impacts on amphibians 261 Andrew J. Hamer, Thomas E. S. Langton and David Lesbarrères 32 Reptiles: Overlooked but often at risk from roads 271 Kimberly M. Andrews, Tom A. Langen and Richard P. J. H. Struijk 33 Flight doesn’t solve everything: Mitigation of road impacts on birds 281 Angela Kociolek, Clara Grilo and Sandra Jacobson 34 Bats and roads 290 Isobel M. Abbott, Anna Berthinussen, Emma Stone, Martijn Boonman, Markus Melber and John Altringham 35 Carnivores: Struggling for survival in roaded landscapes 300 Clara Grilo, Daniel J. Smith and Nina Klar 36 Case study: Roads and jaguars in the Mayan forests 313 Eugenia Pallares, Carlos Manterola, Dalia A. Conde and Fernando Colchero 37 Case study: Finding the middle road – grounded approaches to mitigate highway impacts in tiger reserves 317 Sanjay Gubbi AND H.C. Poornesha 38 Case study: African wild dogs and the fragmentation menace 322 Brendan Whittington‐Jones and Harriet Davies‐Mostert 39 Roads, traffic and verges: Big problems and big opportunities for small mammals 325 Fernando Ascensão, Scott LaPoint and Rodney van der Ree 40 Reducing road impacts on tree‐dwelling animals 334 Kylie Soanes and Rodney van der Ree 41 Case study: Canopy bridges for primate conservation 341 Andrea Donaldson and Pamela Cunneyworth 42 Transportation and large herbivores 344 Patricia Cramer, Mattias Olsson, Michelle E. Gadd, Rodney van der Ree and Leonard E. Sielecki 43 Case study: The Mount Kenya elephant corridor and underpass 353 Susie Weeks 44 Form and function: A more natural approach to infrastructure, fish and stream habitats 357 Paul J. Wagner 45 Solutions to the impacts of roads and other barriers on fish and fish habitat 364 Fabrice Ottburg and Matt Blank 46 The function and management of roadside vegetation 373 Suzanne J. Milton, W. Richard J. Dean, Leonard E. Sielecki and Rodney van der Ree 47 Roads in the arid lands: Issues, challenges and potential solutions 382 Enhua Lee, David B. Croft and Tamar Achiron‐Frumkin 48 Road ecology in an urbanising world 391 Darryl Jones, Hans Bekker and Rodney van der Ree 49 Tropical ecosystem vulnerability and climatic conditions: Particular challenges for road planning, construction and maintenance 397 Miriam Goosem 50 The influence of economics, politics and environment on road ecology in South America 407 Alex Bager, Carlos E. Borghi and Helio Secco 51 Highway construction as a force in the destruction of the Amazon forest 414 Philip M. Fearnside 52 Road ecology in South India: Issues and mitigation opportunities 425 K. S. Seshadri and T. Ganesh 53 Planning roads through sensitive Asian landscapes: Regulatory issues, ecological implications and challenges for decision‐making 430 Asha Rajvanshi and Vinod B. Mathur 54 Setjhaba SA, South Afrika: A South African perspective of an emerging transport infrastructure 439 Wendy Collinson, Dan Parker, Claire Patterson‐Abrolat, Graham Alexander and Harriet Davies‐Mostert 55 Unfenced reserves, unparalleled biodiversity and a rapidly changing landscape: Roadways and wildlife in East Africa 448 Clinton W. Epps, Katarzyna Nowak , and Benezeth Mutayoba 56 Expected effects of a road across the Serengeti 455 Michelle E. Gadd 57 China: Building and managing a massive road and rail network and protecting our rich biodiversity 465 Yun Wang, Yaping Kong and Jiding Chen 58 Railways, roads and fences across Kazakhstan and Mongolia threaten the survival of wide‐ranging wildlife 472 Kirk A. Olson and Rodney van der Ree 59 Best‐practice guidelines and manuals 479 Marguerite Trocmé 60 Case study: The role of non‐governmental organisations (NGOs) and advocates in reducing the impacts of roads on wildlife 485 Patricia White 61 Case study: Building a community of practice for road ecology 488 Paul J. Wagner and Andreas Seiler 62 Wildlife/roadkill observation and reporting systems 492 Fraser Shilling, Sarah E. Perkins and Wendy Collinson Glossary 502 Species 509 Index 513

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Book SynopsisAs pressures on Australia''s inland waters intensify from population growth, expanding resource development and climate change, there is an urgent need to manage and protect these special areas. Understanding their ecology underpins their wise management and conservation. Australian Freshwater Ecology vividly describes the physical, chemical and biological features of wetlands, lakes, streams, rivers and groundwaters in Australia. It presents the principles of aquatic ecology linked to practical management and conservation, and explains the causes, mechanisms, effects and management of serious environmental problems such as altered water regimes, eutrophication, salinization, acidification and sedimentation of inland waters. Key features: contributions from a diverse, highly qualified team of aquatic ecologists whose expertise spans the ecology and management of standing and running waters in Australia sections covering groundwaters, biodivTrade Review“This excellent volume is certain to inspire a new generation of freshwater ecologists, in Australia and beyond, to go out and learn more about these incredibly diverse and vulnerable environments.” (Freshwater Biology, 2 June 2015) Table of ContentsAbout this book, xi About the companion website, xii PART I: PROCESSES IN AQUATIC ECOSYSTEMS, 1 1 Australian waters: diverse, variable and valuable, 3 1.1 The challenge for aquatic ecologists, 3 1.2 Defi ning some common terms, 6 1.3 Australian inland waters: their diversity and distribution, 6 1.4 The water regime: ‘where, when and to what extent water is present’, 7 1.4.1 Water budgets, scale issues and human influences on water regimes, 7 1.4.2 Components of the water regime, 8 1.4.3 Water regime variability, 9 1.5 Linkages in aquatic ecosystems: from molecular bonds to global exchanges, 11 1.5.1 Wonderful water and its molecular linkages, 11 1.5.2 Linkages at the catchment scale, 12 1.5.3 Linkages at the global scale: the hydrological cycle, 13 1.5.4 Continental linkages and surface waters in Australia, 15 1.5.5 Continental linkages and groundwaters in Australia, 19 1.6 The structure of this book, 20 2 Physical processes in standing waters, 21 2.1 Depth and physical processes, 21 2.2 Let there be light ..., 21 2.2.1 Light reaching the water surface, 21 2.2.2 Light below the water surface, 22 2.2.3 Seeing through water: Secchi discs and quantum sensors, 24 2.3 The euphotic zone, 24 2.4 Light and life, 25 2.5 Temperature and stratification, 25 2.5.1 Causes of stratifi cation, 26 2.6 Using circulation patterns to classify standing waters, 27 2.7 Ecological implications of the different types of stratifi cation and mixing, 29 2.8 Deep versus shallow standing waters: depth matters, 31 2.8.1 How deep standing waters form, 32 2.8.2 How shallow standing waters form, 32 2.9 Synthesis, 35 3 Chemical processes in standing waters, 37 3.1 ‘There’s a certain chemistry ...’, 37 3.2 Dissolved gases, 37 3.2.1 Oxygen, 38 3.2.2 Carbon dioxide, 41 3.2.3 Hydrogen, 42 3.2.4 Methane, 43 3.3 Sources of ions, 45 3.4 Ionic composition of Australian standing waters, 45 3.5 Conductivity, salinity and total dissolved solids, 45 3.6 Ionic composition and trophic state, 47 3.6.1 Some common anions, 47 3.6.2 Some common cations, 48 3.7 Redox reactions and redox potential, 50 3.8 Redox reactions and some common metals, 51 3.9 Nutrients, nutrient limitation and ecological stoichiometry, 52 3.9.1 Phosphorus, 53 3.9.2 Nitrogen, 55 3.9.3 Carbon, 58 3.10 Water regime, drying and water chemistry, 60 3.10.1 What happens to water chemistry during a wetting-drying cycle?, 60 3.11 Synthesis, 62 4 Biological processes in standing waters, 63 4.1 Biological players on a physical and chemical stage, 63 4.2 Major ecological zones and habitats, 64 4.3 Blurred boundaries and mobile assemblages, 66 4.4 Trophic groups and sources of energy, 66 4.5 Producers, 69 4.5.1 An ecological classification of producers, 72 4.5.2 Microscopic aquatic plants, 72 4.5.3 Macroscopic aquatic plants, 74 4.5.4 Plants living in water: benefits and constraints, 76 4.5.5 Alternative states: changes in plant dominance in shallow waterbodies, 77 4.6 Consumers, 80 4.6.1 Decomposers: the importance of microbes and fungi, 80 4.6.2 Invertebrate detritivores, 81 4.6.3 Invertebrate herbivores, 82 4.6.4 Invertebrate carnivores, 83 4.6.5 Vertebrate herbivores, 84 4.6.6 Vertebrate carnivores, 85 4.6.7 Predation and trophic cascades, 86 4.6.8 Trophic cascades and biomanipulation, 87 4.6.9 How vertebrates use waterbodies: linkages and subsidies, 87 4.7 Biological processes in temporary standing waters, 90 4.8 Biological processes in saline standing waters, 94 4.9 Synthesis, 95 5 Physical processes in running waters, 97 5.1 Flow and the diversity of running waters, 97 5.2 Scale, ecological hierarchies and networks, 97 5.3 A hierarchical classification of physical features, 99 5.3.1 Physical features and channel flows, 101 5.4 Hydrology and stream flow, 103 5.4.1 Measuring discharge, 103 5.4.2 Measuring current velocity, 104 5.5 Hydrographs, catchment characteristics and groundwater interactions, 106 5.6 Flow variability and its implications, 108 5.7 The physical process of transport, 110 5.7.1 The sources of sediment, 111 5.7.2 Sediment particle size and distribution, 112 5.7.3 Current velocity, erosion and transport, 113 5.7.4 Sediment dynamics and channel form, 114 5.7.5 Floodplain sedimentation and billabong formation, 115 5.8 River profi les and longitudinal changes in physical features, 118 5.9 Synthesis, 119 6 Chemical processes in running waters, 120 6.1 The complex web of factors, 120 6.2 Dissolved gases, 120 6.3 Ionic composition of Australian rivers, 123 6.4 Sources of ions, 124 6.5 Nutrients and nutrient spiralling, 126 6.5.1 Transport and retention of nutrients, 128 6.6 Carbon and organic matter, 129 6.6.1 Dissolved organic matter in rivers, 130 6.6.2 Solute processes: dissolved substances in running waters, 132 6.7 Longitudinal changes in chemical features, 133 6.8 Synthesis, 135 7 Biological processes in running waters, 136 7.1 Factors affecting biological processes at various scales, 136 7.2 Zones and habitats: parallels and contrasts with standing waters, 136 7.3 Living with flow, 138 7.4 Sources of energy in running waters, 142 7.4.1 Producers, 142 7.4.2 The distribution of different life-forms of producers, 143 7.4.3 Open-water producers in large rivers, 146 7.4.4 Classifying consumers in running waters, 146 7.4.5 Invertebrate herbivores, 147 7.4.6 Invertebrate carnivores, 149 7.4.7 Vertebrate herbivores, 150 7.4.8 Vertebrate carnivores, 151 7.4.9 Decomposers, 154 7.4.10 Functional feeding groups, 157 7.5 The fate of a dead eucalypt leaf that falls into a stream ..., 158 7.6 Conceptual models of running-water ecosystems, 160 7.7 The role of disturbance, 163 7.7.1 Post-disturbance recolonization processes, 164 7.7.2 Recolonization, dispersal and biogeography in Australian running waters, 168 7.7.3 Setting the biogeographic scene: ancient rocks, variable climates, 170 7.7.4 Some biogeographic patterns in Australian inland waters, 170 7.8 Synthesis, 173 8 Groundwater processes and management, 174 8.1 Out of sight, out of mind?, 174 8.2 An integrated definition of groundwaters, 174 8.3 Physical processes in groundwaters, 176 8.3.1 Groundwater discharge, permeability, porosity and Darcy’s Law, 178 8.3.2 Physical processes between groundwaters and surface waters, 180 8.3.3 Groundwater temperature, 183 8.4 Chemical processes in groundwaters, 184 8.4.1 Principal chemical processes in groundwater, 184 8.4.2 Chemical processes along gradients of dissolved oxygen, 186 8.5 Biological processes in groundwaters, 187 8.5.1 Groundwater microbiology, 188 8.5.2 Buried treasures in Australia: groundwater invertebrates and fishes, 190 8.5.3 Biodiversity and ecology of Australian groundwater fauna, 191 8.5.4 Physical, chemical and biological drivers of groundwater ecological processes, 193 8.5.5 Groundwater-dependent ecosystems (GDEs), 195 8.6 Management issues in Australian groundwaters, 197 8.7 Ecosystem services and conservation of Australian groundwaters, 201 8.8 Synthesis, 202 PART II: MANAGEMENT OF AQUATIC ECOSYSTEMS, 205 9 Management issues: water regime, 207 9.1 ‘When the well is dry ...’, 207 9.2 Changes to water regimes by humans in Australia: a brief history, 207 9.2.1 Changing water regime, changing processes, 210 9.3 Diverse impoundments with diverse effects, 211 9.3.1 Impoundments as ecological barriers, 214 9.3.2 Impoundments and estuaries, 215 9.4 Ecological effects of water extraction, 216 9.4.1 Ecological effects of drainage and irrigation, 218 9.4.2 Ecological effects of inter-basin transfers, 219 9.4.3 Ecological effects of urbanization, 220 9.5 Water regimes and environmental watering, 221 9.5.1 Environmental watering: ecological objectives and outcomes, 223 9.5.2 Environmental watering: risks and tactics, 225 9.6 ‘Breaking down the barriers’: fishways and dam removal, 226 9.7 Synthesis, 227 10 Management issues: physical features, 229 10.1 Changing physical features, changing processes, 229 10.2 Human activities and the physical environment, 230 10.2.1 Human changes to catchments, 230 10.2.2 Human changes to basins and channels, 232 10.3 Sedimentation: a physical process with negative fallout, 235 10.3.1 Human activities and sedimentation, 236 10.3.2 Ecological effects of sedimentation, 238 10.3.3 Management of sedimentation, 239 10.4 Physical processes and land-water interfaces, 241 10.4.1 Ecological roles of fringing and riparian zones, 241 10.4.2 Threats to land-water interfaces, 243 10.4.3 Management of land-water interfaces, 245 10.5 Recovering natural physical complexity, 248 10.6 Synthesis, 249 11 Management issues: water quality, 250 11.1 What is water quality?, 250 11.2 Managing water quality, 250 11.3 Eutrophication, 253 11.3.1 Natural and anthropogenic eutrophication, 253 11.3.2 Drivers, stressors and processes of eutrophication, 253 11.3.3 Ecological impacts and effects on ecosystem services, 256 11.3.4 Management of eutrophication, 258 11.4 Salinization, 259 11.4.1 Natural and anthropogenic salinization, 259 11.4.2 Drivers, stressors and processes of salinization, 259 11.4.3 Ecological impacts and effects on ecosystem services, 261 11.4.4 Management of salinization, 262 11.5 Acidifi cation, 264 11.5.1 Natural and anthropogenic acidifi cation, 264 11.5.2 Drivers, stressors and processes of acidification, 264 11.5.3 Ecological impacts and effects on ecosystem services, 267 11.5.4 Management of acidification, 268 11.6 Pollution, 269 11.6.1 Drivers, stressors and processes of pollution, 269 11.6.2 Ecological impacts and effects on ecosystem services, 271 11.6.3 Management of pollution, 273 11.7 Water quality guidelines, 274 11.8 Monitoring and assessing water quality, 275 11.8.1 Condition monitoring, 275 11.8.2 Detecting environmental impacts, 277 11.9 Multiple stressors and models of ecosystem change, 277 11.10 Synthesis, 279 12 Management issues: biodiversity conservation and climate change, 281 12.1 What is biodiversity and why does it need conservation?, 281 12.1.1 Setting priorities in biodiversity conservation, 281 12.2 Aquatic landscapes: networks and mosaics of habitats, 283 12.3 Protected areas for conserving freshwater communities, 284 12.4 Having good connections: dispersal and connectivity in conservation, 286 12.5 Protecting refuges to conserve aquatic communities, 287 12.6 Conserving aquatic species and populations, 288 12.6.1 The special challenge of conserving species with complex life histories, 288 12.6.2 The spatial extent of populations and metapopulations, 289 12.6.3 What are ‘Evolutionarily Significant Units’?, 289 12.6.4 Hidden biodiversity: cryptic species, 290 12.6.5 Endemic species and relictual faunas, 290 12.7 Threatened communities and species, 291 12.8 In the wrong place: ‘exotic aquatics’ and invasive species, 293 12.8.1 Invasive predators and competitors, 294 12.8.2 Domestic and hybridizing invasive aquatic species, 294 12.8.3 Invasive ‘ecosystem engineers’, 297 12.8.4 Potential effects of climate change on aquatic invasive species, 298 12.9 Climate change and Australian aquatic ecosystems, 299 12.9.1 Effects of increased water temperature, 300 12.9.2 Effects of changes to the hydrological cycle and water regimes, 300 12.9.3 Effects of sea-level rise, 301 12.9.4 Effects of changes to atmospheric conditions, 302 12.9.5 Effects of reduced snow cover and alpine warming, 302 12.9.6 How do these climatic changes affect freshwater species and ecosystems?, 302 12.9.7 Planned adaptation to climate change in aquatic ecosystems, 305 12.10 Synthesis, 307 13 Integrating ecology and management: a synthesis, 308 13.1 The ‘big picture’: integrating ecology and management, 308 13.2 The ‘bigger picture’: integrating social, economic and political goals, 309 13.3 Strategic adaptive management in aquatic ecology, 311 13.4 Resolving conflicts in freshwater management: a role for aquatic ecologists?, 313 13.5 Future challenges and opportunities: where to from here?, 315 13.6 Synthesis, 319 References, 321 Index, 347

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Book SynopsisTable of ContentsLIST OF CONTRIBUTORS xix PREFACE xxiii ACKNOWLEDGMENTS xxv ABOUT THE COMPANION WEBSITE xxvii SECTION I BIOENERGY FUNDAMENTALS 1 1 INTRODUCTION TO BIOENERGY 3Samir Kumar Khanal and Yebo Li 1.1 Energy 3 1.2 Non-renewable Energy 5 1.3 Renewable Energy 10 1.4 Why Renewable Energy? 11 1.5 Bioenergy 13 References 17 Exercise Problems 18 2 UNITS AND CONVERSIONS 19Samir Kumar Khanal 2.1 Introduction 19 2.2 Units of Measurement 19 2.3 Useful Units and Conversions 21 2.4 Energy and Heat 25 2.5 Volume–Mass Relationship 29 2.6 Ideal Gas Law 29 2.7 Henry’s Law 30 References and Further Reading 32 Exercise Problems 32 3 MASS AND ENERGY BALANCES 33Devin Takara and Samir Kumar Khanal 3.1 Introduction 33 3.2 Mass Balances 33 3.3 Enthalpy 35 3.4 Energy Balances 36 References and Further Reading 39 Exercise Problems 39 4 THERMODYNAMICS AND KINETICS OF BASIC CHEMICAL REACTIONS 42Devin Takara and Samir Kumar Khanal 4.1 Introduction 42 4.2 Reaction Thermodynamics 43 4.3 Reaction Kinetics 46 References and Further Reading 48 Exercise Problems 48 5 ORGANIC AND CARBOHYDRATE CHEMISTRY 50Xiaolan Luo and Yebo Li 5.1 Introduction 50 5.2 Structural Formulas and Classification of Organic Compounds 51 5.3 Aliphatic Compounds 52 5.4 Aromatic Compounds 61 5.5 Heterocyclic Compounds 62 5.6 Carbohydrates 63 5.7 Proteins and Lipids 66 References and Further Reading 69 Exercise Problems 70 6 PLANT STRUCTURAL CHEMISTRY 71Samir Kumar Khanal Saoharit Nitayavardhana and Rakshit Devappa 6.1 Introduction 71 6.2 Carbohydrates and Their Classification 72 6.3 Main Constituents of Plant Biomass 73 6.4 Plant Cell Wall Architecture 80 References 85 Exercise Problems 86 7 MICROBIAL METABOLISMS 88Arul M. Varman Lian He and Yinjie J. Tang 7.1 Introduction 88 7.2 Carbon Metabolisms 89 7.3 Metabolic Models 93 References 104 Exercise Problems 105 Appendix 7.1 Code Useful for Example 7.2 105 SECTION II BIOENERGY FEEDSTOCKS 107 8 STARCH-BASED FEEDSTOCKS 109Xumeng Ge and Yebo Li 8.1 Introduction 109 8.2 Corn 110 8.3 Sweet Potato 116 8.4 Cassava 120 8.5 Comparison of Composition Yield and Energy Potential of Corn Sweet Potato and Cassava 124 References 125 Exercise Problems 126 9 OILSEED-BASED FEEDSTOCKS 127Chengci Chen and Marisol Berti 9.1 Introduction 127 9.2 Soybean 128 9.3 Rapeseed and Canola 132 9.4 Oil Palm 135 9.5 Jatropha 136 9.6 Camelina 138 9.7 Yield and Oil Content of Major Oilseed Feedstocks 139 References 140 Exercise Problems 142 10 LIGNOCELLULOSE-BASED FEEDSTOCKS 143Sudhagar Mani 10.1 Introduction 143 10.2 Feedstock Availability and Production 144 10.3 Feedstock Logistics 151 References 167 Exercise Problems 168 11 ALGAE-BASED FEEDSTOCKS 170Xumeng Ge Johnathon P. Sheets Yebo Li and Sudhagar Mani 11.1 Introduction 170 11.2 Algae Classification Cell Structure and Characteristics 171 11.3 Mechanism of Algal Growth 172 11.4 Algal Growth Conditions 174 11.5 Steps in Algal-Biodiesel Production 176 References 195 Exercise Problems 196 SECTION III BIOLOGICAL CONVERSION TECHNOLOGIES 199 12 PRETREATMENT OF LIGNOCELLULOSIC FEEDSTOCKS 201Chang Geun Yoo and Xuejun Pan 12.1 Introduction 201 12.2 What Does Pretreatment Do? 202 12.3 Physical Pretreatment 205 12.4 Thermochemical Pretreatment 207 12.5 Other Pretreatments 216 12.6 Co-products from Lignocellulosic Feedstock Pretreatment 219 References 220 Exercise Problems 221 13 ENZYMATIC HYDROLYSIS 224David Hodge and Wei Liao 13.1 Introduction 224 13.2 Nomenclature and Classification of Hydrolases 225 13.3 Enzyme Kinetics 226 13.4 Enzymatic Hydrolysis of Carbohydrates 240 References 246 Exercise Problems 247 14 ETHANOL FERMENTATION 250Saoharit Nitayavardhana and Samir Kumar Khanal 14.1 Introduction 250 14.2 Biochemical Pathway 252 14.3 Byproducts Formation during Ethanol Fermentation 263 14.4 Microbial Cultures 264 14.5 Environmental Factors Affecting Ethanol Fermentation 267 14.6 Industrial Fuel-Grade Ethanol Production 268 References 274 Exercise Problems 275 15 BUTANOL FERMENTATION 277Victor Ujor and Thaddeus Chukwuemeka Ezeji 15.1 Introduction 277 15.2 Butanol Fermentation 279 15.3 Factors Affecting Butanol Fermentation 285 15.4 Substrates for Butanol Fermentation 287 15.5 Advanced Butanol Fermentation Techniques and Downstream Processing 288 References 292 Exercise Problems 294 16 SYNGAS FERMENTATION 296Mark R. Wilkins Hasan K. Atiyeh and Samir Kumar Khanal 16.1 Introduction 296 16.2 Stoichiometry 297 16.3 Syngas-Fermenting Bacteria 298 16.4 Factors Affecting Syngas Fermentation 303 16.5 Product Recovery 308 References 309 Exercise Problems 311 17 FUNDAMENTALS OF ANAEROBIC DIGESTION 313Samir Kumar Khanal and Yebo Li 17.1 Introduction 313 17.2 Organic Conversion in an Anaerobic Process 315 17.3 Stoichiometry of Methane Production 320 17.4 Important Considerations in Anaerobic Digestion 323 17.5 Anaerobic Digestion Model No. 1 (ADM1) 331 References 334 Exercise Problems 336 18 BIOGAS PRODUCTION AND APPLICATIONS 338Samir Kumar Khanal and Yebo Li 18.1 Introduction 338 18.2 Anaerobic Digestion Systems 338 18.3 Biogas Cleaning and Upgrading 354 18.4 Biogas Utilization 357 18.5 Digestate 358 References 358 Exercise Problems 359 19 MICROBIAL FUEL CELLS 361Hongjian Lin Hong Liu Jun Zhu and Venkataramana Gadhamshetty 19.1 Introduction 361 19.2 How Does a Microbial Fuel Cell (MFC) Work? 363 19.3 Electron Transfer Processes 365 19.4 Electrical Power and Energy Generation 370 19.5 Design and Operation of an MFC 377 References 381 Exercise Problems 382 SECTION IV THERMAL CONVERSION TECHNOLOGIES 385 20 COMBUSTION FOR HEAT AND POWER 387Sushil Adhikari Avanti Kulkarni and Nourredine Abdoulmoumine 20.1 Introduction 387 20.2 Fundamentals of Biomass Combustion 389 20.3 Biomass Properties and Preprocessing 393 20.4 Biomass Furnaces 395 20.5 Power Generation 397 20.6 Biomass Co-firing with Coal 402 20.7 Environmental Impact and Emissions of Biomass Combustion 404 References 405 Exercise Problems 405 21 GASIFICATION 407Sushil Adhikari and Nourredine Abdoulmoumine 21.1 Introduction 407 21.2 Fundamentals of Gasification 408 21.3 Gasifiers 410 21.4 Feedstock Preparation and Characterization 414 21.5 Gasification Mass and Energy Balance 416 21.6 Gas Cleanup 419 21.7 Applications of Biomass Gasification 419 References 421 Exercise Problems 421 Appendix 422 22 PYROLYSIS 423Manuel Garcia-Perez 22.1 Introduction 423 22.2 Slow vs. Fast Pyrolysis 425 22.3 Pyrolysis Reactions and Mechanisms 426 22.4 Single-Particle Models 431 22.5 Bio-Oil 432 22.6 Charcoal 434 22.7 Bio-oil Refining 434 References 437 Exercise Problems 438 SECTION V BIOBASED REFINERY 439 23 SUGAR-BASED BIOREFINERY 441Samir Kumar Khanal and Saoharit Nitayavardhana 23.1 Introduction 441 23.2 Stoichiometry 442 23.3 Sugarcane Ethanol 443 23.4 Sweet Sorghum Ethanol 446 23.5 Sugar Beet Ethanol 447 23.6 Biochemicals and Biopolymers 448 References 450 Exercise Problems 451 24 STARCH-BASED BIOREFINERY 453Samir Kumar Khanal and Saoharit Nitayavardhana 24.1 Introduction 453 24.2 Stoichiometry of Starch to Ethanol 455 24.3 Integrated Farm-Scale Biorefinery 464 References 465 Exercise Problems 466 25 LIGNOCELLULOSE-BASED BIOREFINERY 467Scott C. Geleynse Michael Paice and Xiao Zhang 25.1 Introduction 467 25.2 Cell Structure of Lignocellulosic Feedstocks 468 25.3 Stoichiometry and Energy Content 468 25.4 Lignocellulosic Biomass Conversion to Fuel 472 25.5 Co-Products from Lignocellulose-Based Biorefinery 473 25.6 Industrial Lignocellulose-Based Biorefinery 476 References 478 Exercise Problems 480 26 LIPID-BASED BIOREFINERY 481B. Brian He J. H. Van Gerpen Matthew J. Morra and Armando G. McDonald 26.1 Introduction 481 26.2 Lipid-Based Feedstocks 483 26.3 Chemical Properties of Lipids 484 26.4 Biodiesel from Lipids 491 26.5 Lipid-Based Biorefinery 498 References 501 Exercise Problems 502 SECTION VI BIOENERGY SYSTEM ANALYSIS 505 27 TECHNO-ECONOMIC ASSESSMENT 507Ganti S. Murthy 27.1 Introduction 507 27.2 What Is Techno-Economic Analysis? 508 27.3 Basic Steps in TEA 509 27.4 Tools Software and Data Sources for Performing TEA 517 References 518 Exercise Problems 518 28 LIFE-CYCLE ASSESSMENT 521Ganti S. Murthy 28.1 Introduction 521 28.2 What Is Life-Cycle Assessment (LCA)? 522 28.3 Procedure for LCA 524 28.4 Tools Available to Perform LCA 533 28.5 Advanced Topics 533 References 539 Exercise Problems 541 29 GOVERNMENT POLICY AND STANDARDS FOR BIOENERGY 544Sami Kumar Khanal Gal Hochman Ajay Shah and Jeffrey M. Bielicki 29.1 Overview of the Bioenergy Market 544 29.2 Rationale for Government Intervention 546 29.3 Government Intervention through Policy Tools 550 29.4 Biofuels Policy Implementations: Existing Policy Instruments 550 29.5 Implications of Biofuels Policies 559 References 561 Exercise Problems 561 INDEX 563

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Book Synopsis

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Book SynopsisNitrogen is arguably the most important nutrient required by plants. However, the availability of nitrogen is limited in many soils and although the earth's atmosphere consists of 78. 1% nitrogen gas (N2) plants are unable to use this form of nitrogen.Table of ContentsBiological Nitrogen Fixation VOLUME 1 Chapter 1. Introduction Frans J. de Bruijn Section 1. Focus Chapters Chapter 2. Recent advances in Understanding Nitrogenases and How They Work William Newton Chapter 3. Evolution and Taxonomy of Nitrogen-fixing Organisms with emphasis on Rhizobia Kristina Lindstrom Chapter 4. Evolution of Rhizobium Nodulation: From Nodule Specific Genes (Nodulins) to Recruitment of Common Processes Ton Bisseling Chapter 5. Bioengineering Nitrogen Acquisition in Rice: Promises for Global Food Security Herbert Kronzucker Section 2. Chemistry and Biochemistry of Nitrogenases Chapter 6. An Overview of Fe-S Protein Biogenesis from Prokaryotes to Eukaryotes Mahipal Kesawat Chapter 7. Biosynthesis of the Iron-Molybdenum Cofactor of Nitrogenase Luis Rubio Chapter 8. Distribution and Ecological Niches of Nitrogenases Alexander Glazer Section 3. Expression and Regulation of Nitrogen Fixation Genes and Nitrogenase Chapter 9. Regulation of nif Gene Expression in Azotobacter vinelandii Cesar Poza-Carrion, Luis Rubio Chapter 10. Coupling of Regulation between Nitrogen and Carbon Metabolism in Nitrogen Fixing Pseudomonas stutzeri A1501 Lin Min Chapter 11. Regulation of NItrogen Fixation and Molybdenum Transport in Rhodobacter capsulatus Bernd Masepohl Chapter 12. Metabolic Regulation of Nitrogenase Activity in Rhodospirillum rubrum: The Role of PII Proteins and Membrane Sequestration Stefan Nordlund Chapter 13. How Does the DraG-PII Complex Regulate Nitrogenase Activity in Azospirillum brasilense? Xiao-Dan Li Chapter 14. Fe Protein Over-expression Can Enhance the Nitrogenase Activity of Azotobacter vinelandii Papri Nag Chapter 15. FNR-like Proteins in Rhizobia: Past and Future Lourdes Girard Section 4. Taxonomy and Evolution of Nitrogen Fixing Organisms Chapter 16. Exploring Alternative Paths for the Evolution of Biological Nitrogen Fixation John Peters Chapter 17. Phylogeny, Diversity, Geographical Distribution and Host Range of Legume-Nodulating Betaproteobacteria: What Is the Role of Plant Taxonomy? Lionel Moulin, Euan James Chapter 18. Bradyrhizobium, The Ancestor of All Rhizobia: Phylogeny of Housekeeping and Nitrogen-fixation Genes Mariangela Hungria Chapter 19. Interaction between Host and Rhizobial Strains: Affinities and Coevolution Mario Aguilar Chapter 20. Assessment of Nitrogenase Diversity in the Environment Daniel Buckley Section 5. Genomics of Nitrogen Fixing Organisms Chapter 21. Genetic Regulation of Symbiosis Island Transfer in Mesorhizobium loti Joshua Ramsay, Clive Ronson Chapter 22. The Azotobacter vinelandii Genome: An Update Joao C. Setubal Chapter 23. The Genome Sequence of the Novel Rhizobial Species Microvirga lotononidis Strain WSM3557. Julie Ardley Chapter 24. Genome Characteristics of Frankia sp. Reflect Host Range and Host Plant Biogeography Philippe Normand, David Benson Chapter 25. Core and Accessory Henomes of The Diazotroph Azospirillum Florence Wisniewski-Dye Chapter 26. Pangenome Evolution in The Symbiotic Nitrogen Fixer Sinorhizobium meliloti Marco Galardini Chapter 27. Pangenomic Analysis of The Rhizobiales Using The GET_HOMOLOGUES Software Package Pablo Vinuesa Section 6. Physiology and Metabolism of Nitrogen Fixing Organisms Chapter 28. Metabolism of Photosynthetic Bradyrhizobia During Root and Stem Symbiosis with Aeschynomene legumes Benjamin Gourion Chapter 29. A Plethora of Terminal Oxidases and Their Biogenesis Factors in Bradyrhizobium japonicum Hauke HenneckeChapter 30. Rhizobial Extracytoplasmic Function (ECF) Factors and Their Role in Oxidative Stress Response of Bradyrhizobium japonicumHans-Martin Fischer Chapter 31. Role of the Bacterial BacA ABC-transporter in Chronic Infection of Nodule Cells by Rhizobium Peter Mergaert Chapter 32. Molecular Keys to Broad Host Range in Sinorhizobium fredii NGR234, USDA257 and HH103 Wolfgang Streit Chapter 33. Motility and Chemotaxis in the Rhizobia Michael Hynes Chapter 34. The Pts/Ntr System Globally Regulates ATP-dependent Transporters in Rhizobium leguminosarum Jurgen Prell Section 7. Nitrogen Fixing Organisms, the Plant Rhizosphere and Stress Tolerance Chapter 35. Actinorhizal Root Exudates Alter the Physiology, Surface Properties and Plant Infectivity of Frankia Louis Tisa Chapter 36. Exopolysaccharide Production in Rhizobia is Regulated by Environmental Factors Monika Janczarek Chapter 37. Regulation of Symbiotically-Important Functions by Quorum Sensing in the Sinorhizobium meliloti-Alfalfa Interaction Juan Gonzales Chapter 38. Lumichrome as a Bacterial Signal Molecule Influencing Plant Growth Felix Dakora Chapter 39. Genes Involved in Desiccation Resistance of Rhizobia and Other Bacteria Michael KahnChapter 40. The General Stress Response in Alpha-rhizobia Claude Bruand Section 8. Physiology and Regulation of Nodulation Chapter 41. The Root Hair: A Single Cell Model for Systems Biology Marc Libault Chapter 42. How Transcriptomics Revealed New Information on Actinorhizal Symbioses Establishment and Evolution Valerie Hocher Chapter 43. Molecular Biology of Infection and Nodule Development in Discaria trinervis – Frankia Actinorhizal Symbiosis Sergio Svistoonoff Chapter 44. Lotus japonicus Nodulates When It Sees Red Akihiro Suzuki Chapter 45. Out of Water of A New Model Legume: The Nod-independent Aeschynomene evenia Jean-Francois Arrighi Chapter 46. Phosphorus Use Efficiency for N2 Fixation in The Rhizobial Symbiosis with Legumes Jean –Jacques Drevon Chapter 47. Regulation of Nodule Development by Short and Long Distance Auxin Transport Ulrike Mathesius Chapter 48. Functional Analysis of Nitrogen-Fixing Root Nodule Symbioses Induced by Frankia: Transport and Metabolic Interactions Alison Berry Chapter 49. NOOT-dependent Control of Nodule Identity: Nodule Homeosis and Meristem Perturbation Pascal Ratet Volume 2 Section 9. Recognition in Nodulation Chapter 50. Roles for Flavonoids in Symbiotic Root-Rhizosphere Interactions Ulrike Mathesius Chapter 51. Nod Factor Recognition in Medicago truncatula Jean Jacques Bono Chapter 52. Role of Ectoapyrases in Nodulation Gary Stacey Chapter 53. Role of Rhizobium Cellulase CelC2 in Root Colonization and Infection Pedro Mateos Chapter 54. Nod Factor-Induced Calcium Signaling in Legumes Giles Oldroyd Chapter 55. Signalling and Communication between Actinorhizal Plants and Frankia During the Intracellular Symbiotic Process Claudine Franche Section 10. Infection and Nodule Ontogeny Chapter 56. The Role of Hormones in Rhizobial Infection Jeremy Murray Chapter 57. Nuclear Ca2+ Signaling Reveals Active Bacterial-Host Signaling throughout Rhizobial Infection in Root Hairs of Medicago truncatula David Barker Chapter 58. A Pectate Lyase Required for Plant-Cell Wall Remodelling During Infection of Legumes by Rhizobia Allan Downie Chapter 59. Dissecting The Roles in Outer and Inner Root Cell Layers of Plant Genes That Control Rhizobial Infection and Nodule Organogenesis Clare Gough Chapter 60. The Medicago truncatula NIP/LATD Transporter Is Essential for Nodulation and Appropriate Root Architecture Rebecca Dickstein Chapter 61. A MYB Coiled Coil Type Transcription Factor Interacts with NSP2 and Is Essential for Nodulation in Lotus japonicus Zhongming Zhang Chapter 62. AP2/ERF Transcription Factors and Root Nodulation Fernanda de Carvalo-Niebel Chapter 63. Identification of Medicago truncatula Genes Required for Rhizobial Invasion and Bacteroid Differentiation Peter Kalo Chapter 64. Multifacetted Roles of Nitric Oxide in Rhizobium-Legume Symbioses Eliane Meilhoc Chapter 65. Profiling Symbiotic Responses of Sinorhizobium fredii Strain NGR234 with RNA-seq Xavier Perret Chapter 66. Computational and Experimental Evidence That Auxin Accumulation in Nodule and Lateral Root Primordia Occurs by Different Mechanisms Eva Elisabeth Deinum Section 11. Transitions from the Bacterial to the Bacteroid State Chapter 67. Bacteroid Differentiation in Legume Nodules: Role of AMP-like Host Peptides in the Control of the Endosymbiont Eva Kondorosi Chapter 68. The Symbiosome Membrane Penelope Smith Section 12. Nitrogen Fixation, Assimilation and Senescence in Nodules Chapter 69. Nodulin Intrinsic Proteins: Facilitators of Water and Ammonia Transport across the Symbiosome Membrane Daniel Roberts Chapter 70. Leghemoglobins with Nitrated Hemes in Legume Root Nodule Manuel Becana Chapter 71. The Role of 1-aminocyclopropane-1-carboxylase Enzyme in Leguminous Nodule Senescence Neung Teaumroong Section 13. Microbial “Omics”Chapter 72. Pool-Seq Analysis of Microsymbiont Selection by the Legume Plant Host Juan Imperial Chapter 73. Contribution of the RNA Chaperone Hfq to Environmental Fitness and Symbiosis in Sinorhizobium meliloti José I. Jimenes-Zurdo Chapter 74. Biodiversity, Symbiotic Efficiency and Genomics of Rhizobium tropici and Related Species Mariangela Hungria Chapter 75. The Frankia alni Symbiotic Transcriptome Philippe Normand Chapter 76. A Comprehensive Survey of Soil Rhizobiales Using High-Throughput DNA Sequencing Ryan Jones Chapter 77. Gene Targeted Metagenomics of Diazotrophs in Coastal Saline Soil Bhanavath Jha Section 14. Plant “Omics” and Functional Genetics Chapter 78. The Medicago truncatula Genome Frederic Debellé Chapter 79. Leveraging Large-Scale Approaches to Dissect the Rhizobia-Legume Symbiosis Oswaldo Valdes-Lopez Chapter 80. LegumeIP: An Integrative Platform for Comparative Genomics and Transcriptomics of Model Legumes Patrick Xuechun Zhao Chapter 81. Databases of Transcription Factors in Legumes Lam-son Phan Tran Chapter 82. Functional Genomics of Symbiotic Nitrogen Fixation in Legumes with a Focus on Transcription Factors and Membrane Transporters Michael Udvardi Chapter 83. Retrotransposon (Tnt1)-insertion Mutagenesis in Medicago as a Tool for Genetic Dissection of Symbiosis in Legumes Michael Udvardi Section 15. Cyanobacteria and Archaea Chapter 84. Marine Titrogen Fixation: Organisms, Significance, Enigmas and Future Directions Jonathan Zehr Chapter 85. Requirement of Cell Wall Remodelling for Cell-Cell Communication and Cell Differentiation in Filamentous Cyanobacteria of the Order Nostocales Karl Forchhammer Chapter 86. Nitrogen Fixation in the Oxygenic Phototrophic Prokaryotes (Cyanobacteria): The Fight Against Oxygen Enrique Flores Chapter 87. Underestimation of Marine Dinitrogen Fixation: A Novel Method and Novel Diazotrophic Habitats Ruth SchmitzSection 16. Diazotrophic Plant Growth Promoting Rhizobacteria and Non-Legumes Chapter 88. One Hundred Years Discovery of Nitrogen-Fixing Rhizobacteria Claudine ElmerichChapter 89. Symbiotic Nitrogen Fixation in Legumes: Perspectives on the Diversity and Evolution of Nodulation by Rhizobium and Burkholderia Species Ann Hirsch Chapter 90. Agronomic Applications of Azospirillum and Other PGPR Yaacov Okon Chapter 91. Auxin Signaling in Azospirillum brasilense: A Proteome Analysis Stijn Spaepen Chapter 92. Genetic and Functional Characterization of Paenibacillus riograndensis: A Novel Plant Growth Promoting Bacterium Isolated from Wheat Luciane Passaglia Chapter 93. Role of Herbaspirillum seropedicae LPS in Plant Colonization Rose Adele Monteiro Chapter 94. Culture-independent Assessment of Diazotrophic Bacteria in Sugarcane and Isolation of Bradyrhizobium spp. from Field Grown Sugarcane Plants Using Legume Trap Plants Anton Hartmann Chapter 95. How Fertilization Affects the Selection of Plant Growth Promoting Rhizobacteria by Host Plants Luciane Passaglia Section 17. Field Studies, Inoculum Preparation, Applications of Nod Factors Chapter 96. Appearance of Membrane Compromised, Viable But Not Culturable and Culturable Rhizobial Cells As A Consequence of Desiccation Jan VriezenChapter 97. Making the Most of High Quality Inoculants Rosalind DeakerChapter 98. Rhizobiophages As Markers in The Selection of Symbiotically Efficient Rhizobia for Legumes Felix Dakora Chapter 99. Nitrogen Fixation with Soybean: The Perfect Symbiosis? Mariangela Hungria Chapter 100. Nodule Functioning and Symbiotic Efficiency of Cowpea and Soybean Varieties in Africa Flora Pule Meulenberg Chapter 101. Microbial Quality of Commercial Inoculants to Increase BNF and Nutrient Use Efficiency Didier Lesueur Chapter 102. Developed Fungal-Bacterial Biofilms Having Nitrogen Fixers: Universal Biofertilizers for Legumes and Non-legumes H.M. Herath Chapter 103. Phenotypic Variation in Azospirillum spp. and Other Root-Associated Bacteria Anton Hartmann Chapter 104. The physiological mechanisms of desiccation tolerance in rhizobia Andrea Casteriano Chapter 105. Food Grain Legumes: Their Contribution to Soil Fertility and Human Nutrition and Health in Africa Felix Dakora Chapter 106. Plant Breeding for Biological Nitrogen Fixation: A Review Peter KennedyChapter 107. LCO Applications Provide Improved Responses with Legumes and Non-legumes Stewart Smith Section 18 Nitrogen Fixation and Cereals Chapter 108. The Quest for Biological Nitrogen Fixation in Cereals : A Perspective and Prospective Frans J. de Bruijn Chapter 109. Environmental and Economic Impacts of Biological N2 Fixing (BNF) Cereal Crops Perrin Beatty Chapter 110. Conservation of the Symbiotic Signalling Pathway between Legumes and Cereals: Did Nodulation Constraints Drive Legume Symbiotic Genes to Become Specialised During Evolution? Charles Rosenberg Chapter 111. Occurrence and Ecophysiology of the Natural Endophytic Rhizobium-rice Association, and Translational Assessment of its Biofertilizer Performance within the Egypt Nile Delta Youssef Yanni Section 19. Concluding Chapters Chapter 112. The Relevance of N-fixation and N-recyling for Insect Biomass and N-balances of Ecosystems Martin Heil Chapter 113. Rapid Identification of Nodule Bacteria with MALDI-TOF Mass Spectrometry Xavier Perret Chapter 114. The Microbe-Free Plant: Fact or Artefact? Martin Heil

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Book SynopsisThe simplicity and lack of redundancy in their regulatory genes have made ascidians one of the most useful species in studying developmental genomics. In Developmental Genomics of Ascidians, Dr.Trade Review"In his preface, the author describes Developmental Genomics of Ascidians as his “last and largest contribution to ascidian developmental biology” (p. xi). This book is indeed a major accomplishment and a great resource for the community" (The Quarterly Review of Biology 2016)Table of ContentsPREFACE ix CHAPTER 1 A BRIEF INTRODUCTION TO ASCIDIANS 1 CHAPTER 2 THE DEVELOPMENT OF TADPOLE LARVAE AND SESSILE JUVENILES 9 CHAPTER 3 GENOMICS, TRANSCRIPTOMICS, AND PROTEOMICS 19 CHAPTER 4 RESEARCH TOOLS 31 CHAPTER 5 THE FUNCTION AND REGULATION OF MATERNAL TRANSCRIPTS 41 CHAPTER 6 LARVAL TAIL MUSCLE 53 CHAPTER 7 ENDODERM 63 CHAPTER 8 EPIDERMIS 69 CHAPTER 9 NOTOCHORD 77 CHAPTER 10 THE LARVAL AND ADULT NERVOUS SYSTEMS 89 CHAPTER 11 MESENCHYME 107 CHAPTER 12 MAKING BLUEPRINT OF CHORDATE BODY: DYNAMIC ACTIVITIES OF REGULATORY GENES 113 CHAPTER 13 DEVELOPMENT OF THE JUVENILE HEART 137 CHAPTER 14 GERM-CELL LINE, GAMETES, FERTILIZATION, AND METAMORPHOSIS 145 CHAPTER 15 INNATE IMMUNE SYSTEM AND BLOOD CELLS 159 CHAPTER 16 COLONIAL ASCIDIANS: ASEXUAL REPRODUCTION AND COLONY SPECIFICITY 167 CHAPTER 17 EVOLUTIONARY DEVELOPMENTAL GENOMICS 175 INDEX 193

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Book SynopsisAs its title suggests, this innovative book has been written for life scientists needing to analyse their data sets, and programmers, wanting a better understanding of the types of experimental images life scientists investigate on a regular basis. Each chapter presents one self-contained biomedical experiment to be analysed. Part I of the book presents its two basic ingredients: essential concepts of image analysis and Matlab. In Part II, algorithms and techniques are shown as series of recipes or solved examples that show how specific techniques are applied to a biomedical experiments like Western Blots, Histology, Scratch Wound Assays and Fluoresence. Each recipe begins with simple techniques that gradually advance in complexity. Part III presents some advanced techniques for the generation of publication quality figures. The book does not assume any computational or mathematical expertise. A practical, clearly-written introduction to biomedical image analysis that provides the tools for life scientists and engineers to use when solving problems in their own laboratories. Presents the basic concepts of MATLAB software and uses it throughout to show how it can execute flexible and powerful image analysis programs tailored to the specific needs of the problem. Within the context of four biomedical cases, it shows algorithms and techniques as series of recipes, or solved examples that show how a particular technique is applied in a specific experiment. Companion website containing example datasets, MATLAB files and figures from the book. Table of ContentsPreface vii Acknowledgements ix About the Companion Website xi 1 The Basic Ingredients 1 1.1 The Matlab Environment 1 1.2 Introduction to Matlab 3 1.3 Operations with Matrices 7 1.4 Combining Matrices 10 1.5 Addressing a Matrix 13 1.6 Mathematical Functions and Graphical Display 17 1.7 Random Numbers 23 1.8 Statistics in Matlab 26 1.9 Displaying Two-Dimensional Matrices 29 1.10 Scripts Functions and Shortcuts 37 1.11 Using Help 43 2 Introduction to Images 45 2.1 An Image as a Matrix 45 2.2 Reading Images 46 2.3 Displaying Images 49 2.4 Colormap 54 2.5 Thresholding and Manipulating Values of Images 59 2.6 Converting Images into Doubles 68 2.7 Save Your Code and Data 69 3 Introduction to Colour 71 3.1 Mixing and Displaying Colours 71 4 Western Blots 79 4.1 Recipe 1: Many Ways to Display a Western Blot 80 4.2 Recipe 2: Investigating the Numbers That Make a Western Blot 93 4.3 Recipe 3: Image Histograms 97 4.4 Recipe 4: Transforming an Image of a Western Blot 104 4.5 Recipe 5: Quantification of the Data 111 4.6 Recipe 6: Investigating Position of Bands 121 5 Scratch Wound Assays 135 5.1 Analysis of Scratch Wound Assays 135 5.2 Recipe 1: Low Pass Filtering ScratchWound Assays in the Spatial Domain 139 5.3 Recipe 2: High Pass Filtering ScratchWound Assays in the Spatial Domain 143 5.4 Recipe 3: Combining Filters and Morphological Operations 154 5.5 Recipe 4: Sensitivy to Thresholds and Hysteresis Thresholding 161 5.6 Recipe 5: Morphological Operators 167 5.7 Recipe 6: Measuring Distances Between Cellular Boundaries 178 5.8 Recipe 7: Introduction to Fourier Analysis 187 5.9 Recipe 8: Filtering Scratch Wound Assays in the Fourier Domain 201 References 213 6 Bright Field Microscopy 215 6.1 Recipe 1: Changing the Brightness and Contrast of an Image 215 6.2 Recipe 2: Shading Correction: Estimation of Shading Component as a Plane 224 6.3 Recipe 3: Estimation of Shading Component with Filters Morphological Operators and Envelopes 235 6.4 Recipe 4: Mosaicking and Stitching 247 6.5 Recipe 5: Pixel Intensity and Histograms in Immunohistochemistry 261 6.6 Recipe 6: Hue-Saturation-Value 271 6.7 Recipe 7: Multidimensional Histograms 278 Reference 289 7 Fluorescence Microscopy 291 7.1 Recipe 1: Separating and Combining Colour Channels 294 7.2 Recipe 2: Investigating the Scaling of Values 298 7.3 Recipe 3: Automatic Threshold Selection 301 7.4 Recipe 4: Measuring Absolute and Relative Areas 304 7.5 Recipe 5: Counting Nuclei 305 7.6 Recipe 6: Quantification of Region Properties Beyond the Area 308 7.7 Recipe 7: Dividing an Image into Regions 310 7.8 Recipe 8: Batch Processing and Montages 316 7.9 Recipe 9: A Myriad of Measurements 327 References 341 8 Creating Publication-Quality Figures from Matlab 343 8.1 Recipe 1: Modifying the Characteristics of the Figures 344 8.2 Recipe 2: Numerous Plots in One Figure 352 8.3 Recipe 3: Three-Dimensional Ribbons with Different Annotations 362 8.4 Recipe 4: Three-Dimensional Graphics 378 8.5 Recipe 5: Projections 388 8.6 Recipe 6: Four-Dimensional Data Set Explored 391 Index 401

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Book SynopsisIn light of the discovery of Autoimmune Syndrome Induced by Adjuvants, or ASIA, Vaccines and Autoimmunity explores the role of adjuvants specifically aluminum in different vaccines and how they can induce diverse autoimmune clinical manifestations in genetically prone individuals.Table of ContentsContributors ix Introduction 1Yehuda Shoenfeld, Nancy Agmon-Levin and Lucija Tomljenovic Part I: Mosaic of Autoimmunity 1 Role of Adjuvants in Infection and Autoimmunity 11Eitan Israeli, Miri Blank, and Yehuda Shoenfeld 2 Infections as Adjuvants for Autoimmunity: The Adjuvant Effect 25Quan M. Nhu and Noel R. Rose 3 Experimental Models of Adjuvants 35Nicola Bassi, Mariele Gatto, Anna Ghirardello, and Andrea Doria 4 Answers to Common Misconceptions Regarding the Toxicity of Aluminum Adjuvants in Vaccines 43Lucija Tomljenovic and Christopher A. Shaw 5 Allergy and Autoimmunity Caused by Metals: A Unifying Concept 57Vera Stejskal 6 Genetics and Vaccinology 65John Castiblanco and Juan-Manuel Anaya 7 Silicone and Autoimmune/Inflammatory Syndrome Induced by Adjuvants (ASIA) 79Yair Levy and Rotem Baytner-Zamir 8 Silicone Breast Implants and Autoimmune/Inflammatory Syndrome induced by Adjuvants (ASIA): A Literature Search 87Elisabetta Borella, Eitan Israeli, and Yehuda Shoenfeld 9 Autoantibodies Induced by Vaccine 93Nataša Toplak and Tadej Av¢§cin 10 The ASIA Syndrome Registry 103Ignasi Rodriguez-Pinto and Yehuda Shoenfeld 11 Vaccination in Autoimmune Diseases 107Carla Goncalves, Schahin Saad, Clovis A. Silva, and Eloisa Bonfa 12 Vaccination in Patients with Autoimmune Inflammatory Rheumatic Diseases 113Abdulla Watad, Alessandra Soriano, and Yehuda Shoenfeld Part II: Studies on Autoimmune Conditions Induced by Vaccination 13 Measles, Mumps, and Rubella Vaccine: A Triad to Autoimmunity 129Carlo Perricone, Guido Valesini, and Yehuda Shoenfeld 14 Yellow Fever Vaccine and Autoimmunity 135Roger A. Levy and Rodrigo Poubel V. Rezende 15 Antiphospholipid Syndrome and Vaccines 141Miri Blank and Paola Cruz-Tapias 16 Hepatitis B Vaccination and Autoimmunity 147Daniel S. Smyk, Lazaros I. Sakkas, Yehuda Shoenfeld, and Dimitrios P. Bogdanos 17 Adverse Reactions to Human Papillomavirus Vaccines 163Lucija Tomljenovic and Christopher A. Shaw 18 Influenza Vaccine and Autoimmune Diseases 175Luis J. Jara, Gabriela Medina, Pilar Cruz Dominguez, Olga Vera-Lastra, Miguel A. Saavedra, Monica Vazquez del Mercado, and Minoru Satoh 19 Vaccines and Autoimmunity: Meningococcal Vaccines 185Giovanna Passaro, Alessandra Soriano, and Raffaele Manna 20 Pneumococcal Vaccines and Autoimmune Phenomena 191Elisabetta Borella, Nancy Agmon-Levin, Andrea Doria, and Yehuda Shoenfeld 21 BCG and Autoimmunity 197Luigi Bernini, Carlo Umberto Manzini, and Clodoveo Ferri Part III: Autoimmune Diseases Solicited by Vaccination 22 Systemic Lupus Erythematosus Induced by Vaccines 209Nurit Katz-Agranov and Gisele Zandman-Goddard 23 Vasculitides 223Alessandra Soriano, Rotem Inbar, Giovanna Passaro, and Raffaele Manna 24 Vaccinations in Rheumatoid Arthritis 233Eitan Giat and Merav Lidar 25 Undifferentiated Connective-Tissue Diseases 247Maria Martinelli, Carlo Perricone, and Yehuda Shoenfeld 26 Vaccines, Infections, and Alopecia Areata 255Yaron Zafrir, Sharon Baum, Nancy Agmon-Levin, and Yehuda Shoenfeld 27 Aluminum Particle Biopersistence, Systemic Transport, and Long-Term Safety: Macrophagic Myofasciitis and Beyond 261Romain K. Gherardi, Josette Cadusseau, and Francois-Jerome Authier 28 Immune Thrombocytopenic Purpura: Between Infections and Vaccinations 271Carlo Perricone, Maurizio Rinaldi, Roberto Perricone, and Yehuda Shoenfeld 29 Vaccinations and Type 1 Diabetes 283Alessandro Antonelli, Silvia Martina Ferrari, Andrea Di Domenicantonio, Ele Ferrannini, and Poupak Fallahi 30 Narcolepsy and H1N1 vaccine 291María -Teresa Arango, Shaye Kivity, Nancy Agmon-Levin, Gili Givaty, Joab Chapman, and Yehuda Shoenfeld 31 Non-nutritional Environmental Factors Associated with Celiac Disease: Infections and Vaccinations 301Aaron Lerner 32 Polymyalgia Rheumatica 307Alessandra Soriano and Raffaele Manna 33 Acute Disseminated Encephalomyelitis: Idiopathic, Post-infectious, and Post-vaccination 311Dimitrios Karussis and Panayiota Petrou 34 Fibromyalgia, Chronic Fatigue, Functional Disorders, and Vaccination: Where Do We Stand? 331Jacob N. Ablin and Dan Buskila 35 Bullous Dermatoses, Infectious Agents, and Vaccines 337Yaron Zafrir, Nancy Agmon-Levin, and Sharon Baum 36 Infections, Vaccinations, and Chronic Fatigue Syndrome 345Hussein Mahagna, Naim Mahroum, and Howard Amital 37 Myositis and Vaccines 349Ignasi Rodriguez-Pinto and Yehuda Shoenfeld Index 359

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Book SynopsisNanoparticles are the building blocks for nanotechnology; they are better built, long lasting, cleaner, safer, and smarter products for use across industries, including communications, medicine, transportation, agriculture and other industries. Controlled size, shape, composition, crystallinity, and structure-dependent properties govern the unique properties of nanotechnology. Bio-Nanoparticles: Biosynthesis and Sustainable Biotechnological Implications explores both the basics of and advancements in nanoparticle biosynthesis. The text introduces the reader to a variety of microorganisms able to synthesize nanoparticles, provides an overview of the methodologies applied to biosynthesize nanoparticles for medical and commercial use, and gives an overview of regulations governing their use. Authored by leaders in the field, Bio-Nanoparticles: Biosynthesis and Sustainable Biotechnological Implications bridges the gap between biology and technology, and is an iTable of ContentsList of Contributors xv Introduction xvii 1 Diversity of Microbes in Synthesis of Metal Nanoparticles: Progress and Limitations 1Mahendra Rai, Irena Maliszewska, Avinash Ingle, Indarchand Gupta, and Alka Yadav 1.1 Introduction 1 1.2 Synthesis of Nanoparticles by Bacteria 2 1.3 Synthesis of Nanoparticles by Fungi 9 1.4 Synthesis of Nanoparticles by Algae 12 1.5 Applications of Metal Nanoparticles 16 1.5.1 Nanoparticles as Catalyst 16 1.5.2 Nanoparticles as Bio]membranes 17 1.5.3 Nanoparticles in Cancer Treatment 17 1.5.4 Nanoparticles in Drug Delivery 17 1.5.5 Nanoparticles for Detection and Destruction of Pesticides 17 1.5.6 Nanoparticles in Water Treatment 18 1.6 Limitations of Synthesis of Biogenic Nanoparticles 18 References 20 2 Role of Fungi Toward Synthesis of Nano]Oxides 31Rajesh Ramanathan and Vipul Bansal 2.1 Introduction 31 2.2 Fungus]mediated Synthesis of Nanomaterials 34 2.2.1 Biosynthesis of Binary Nano]oxides using Chemical Precursors 34 2.2.2 Biosynthesis of Complex Mixed]metal Nano]oxides using Chemical Precursors 39 2.2.3 Biosynthesis of Nano]oxides using Natural Precursors employing Bioleaching Approach 42 2.2.4 Biosynthesis of nano]oxides employing bio]milling approach 44 2.3 Outlook 46 References 47 3 Microbial Molecular Mechanisms in Biosynthesis of Nanoparticles 53Atmakuru Ramesh, Marimuthu Thiripura Sundari, and Perumal Elumalai Thirugnanam 3.1 Introduction 53 3.2 Chemical Synthesis of Metal Nanoparticles 54 3.2.1 Brust–Schiffrin Synthesis 55 3.3 Green Synthesis 57 3.4 Biosynthesis of Nanoparticles 58 3.5 Mechanisms for Formation or Synthesis of Nanoparticles 61 3.5.1 Biomineralization using Magnetotactic Bacteria (MTB) 61 3.5.2 Reduction of Tellurite using Phototroph Rhodobacter capsulatus 62 3.5.3 Formation of AgNPs using Lactic Acid and Bacteria 62 3.5.4 Microfluidic Cellular Bioreactor for the Generation of Nanoparticles 62 3.5.5 Proteins and Peptides in the Synthesis of Nanoparticles 65 3.5.6 NADH]dependent Reduction by Enzymes 65 3.5.7 Sulfate and Sulfite Reductase 66 3.5.8 Cyanobacteria 67 3.5.9 Cysteine Desulfhydrase in Rhodopseudomonas palustris 68 3.5.10 Nitrate and Nitrite reductase 68 3.6 E xtracellular Synthesis of Nanoparticles 69 3.6.1 Bacterial Excretions 69 3.6.2 Fungal Strains 71 3.6.3 Yeast: Oxido]reductase Mechanism 72 3.6.4 Plant Extracts 73 3.7 Conclusion 76 References 78 4 Biofilms in Bio]Nanotechnology: Opportunities and Challenges 83Chun Kiat Ng, Anee Mohanty, and Bin Cao 4.1 Introduction 83 4.2 Microbial Synthesis of Nanomaterials 84 4.2.1 Overview 84 4.2.2 Significance of Biofilms in Biosynthesis of Nanomaterials 89 4.2.3 Synthesis of Nanomaterials using Biofilms 90 4.3 Interaction of Microbial Biofilms with Nanomaterials 90 4.3.1 Nanomaterials as Anti]biofilm Agents 90 4.3.2 Nanomaterials as a Tool in Biofilm Studies 92 4.4 Future Perspectives 93 References 94 5 Extremophiles and Biosynthesis of Nanoparticles: Current and Future Perspectives 101Jingyi Zhang, Jetka Wanner, and Om V. Singh 5.1 Introduction 101 5.2 Synthesis of Nanoparticles 104 5.2.1 Microorganisms: An Asset in Nanoparticle Biosynthesis 104 5.2.2 E xtremophiles in Nanoparticle Biosynthesis 104 5.3 Mechanism of Nanoparticle Biosynthesis 108 5.4 Fermentative Production of Nanoparticles 111 5.5 Nanoparticle Recovery 114 5.6 Challenges and Future Perspectives 115 5.7 Conclusion 115 References 116 6 Biosynthesis of Size-Controlled Metal and Metal Oxide Nanoparticles by Bacteria 123Chung-Hao Kuo, David A. Kriz, Anton Gudz, and Steven L. Suib 6.1 Introduction 123 6.2 Intracellular Synthesis of Metal Nanoparticles by Bacteria 124 6.3 E xtracellular Synthesis of Metal Nanoparticles by Bacteria 129 6.4 Synthesis of Metal Oxide and Sulfide Nanoparticles by Bacteria 131 6.5 Conclusion 135 References 135 7 Methods of Nanoparticle Biosynthesis for Medical and Commercial Applications 141Shilpi Mishra, Saurabh Dixit, and Shivani Soni 7.1 Introduction 141 7.2 Biosynthesis of Nanoparticles using Bacteria 144 7.2.1 Synthesis of Silver Nanoparticles by Bacteria 144 7.2.2 Synthesis of Gold Nanoparticles by Bacteria 145 7.2.3 Synthesis of other Metallic Nanoparticles by Bacteria 145 7.3 Biosynthesis of Nanoparticles using Actinomycete 146 7.4 Biosynthesis of Nanoparticles using Fungi 147 7.5 Biosynthesis of Nanoparticles using Plants 148 7.6 Conclusions 149 References 149 8 Microbial Synthesis of Nanoparticles: An Overview 155Sneha Singh, Ambarish Sharan Vidyarthi, and Abhimanyu Dev 8.1 Introduction 156 8.2 Nanoparticles Synthesis Inspired by Microorganisms 157 8.2.1 Bacteria in NPs Synthesis 162 8.2.2 Fungi in NPs Synthesis 167 8.2.3 Actinomycetes in NPs Synthesis 170 8.2.4 Yeast in NPs Synthesis 171 8.2.5 Virus in NPs Synthesis 173 8.3 Mechanisms of Nanoparticles Synthesis 174 8.4 Purification and Characterization of Nanoparticles 176 8.5 Conclusion 177 References 179 9 Microbial Diversity of Nanoparticle Biosynthesis 187Raveendran Sindhu, Ashok Pandey, and Parameswaran Binod 9.1 Introduction 187 9.2 Microbial-mediated Nanoparticles 187 9.2.1 Gold 188 9.2.2 Silver 190 9.2.3 Selenium 191 9.2.4 Silica 192 9.2.5 Cadmium 192 9.2.6 Palladium 193 9.2.7 Zinc 193 9.2.8 Lead 194 9.2.9 Iron 195 9.2.10 Copper 195 9.2.11 Cerium 196 9.2.12 Microbial Quantum Dots 196 9.2.13 Cadmium Telluride 197 9.2.14 Iron Sulfide-greigite 198 9.3 Native and Engineered Microbes for Nanoparticle Synthesis 198 9.4 Commercial Aspects of Microbial Nanoparticle Synthesis 199 9.5 Conclusion 200 References 200 10 S ustainable Synthesis of Palladium(0) Nanocatalysts and their Potential for Organohalogen Compounds Detoxification 205Michael Bunge and Katrin Mackenzie 10.1 Introduction 205 10.2 Chemically Generated Palladium Nanocatalysts for Hydrodechlorination: Current Methods and Materials 206 10.2.1 Pd Catalysts 206 10.2.2 Data Analysis 207 10.2.3 Pd as Dehalogenation Catalyst 207 10.2.4 Intrinsic Potential vs. Performance 208 10.2.5 Concepts for Pd Protection 210 10.3 Bio-supported Synthesis of Palladium Nanocatalysts 211 10.3.1 Background 211 10.4 Current Approaches for Synthesis of Palladium Catalysts in the Presence of Microorganisms 212 10.4.1 Pd(II)-Tolerant Microorganisms for Future Biotechnological Approaches 213 10.4.2 Controlling Size and Morphology during Bio-Synthesis 214 10.4.3 Putative and Documented Mechanisms of Biosynthesis of Palladium Nanoparticles 215 10.4.4 Isolation of Nanocatalysts from the Cell Matrix and Stabilization 216 10.5 Bio-Palladium(0)-nanocatalyst Mediated Transformation of Organohalogen Pollutants 217 10.6 Conclusions 218 References 219 11 E nvironmental Processing of Zn Containing Wastes and Generation of Nanosized Value-Added Products 225Abhilash and B.D. Pandey 11.1 Introduction 225 11.1.1 World Status of Zinc Production 226 11.1.2 E nvironmental Impact of the Process Wastes Generated 226 11.1.3 Production Status in India 227 11.1.4 Recent Attempts at Processing Low-Grade Ores and Tailings 228 11.2 Physical/Chemical/Hydrothermal Processing 229 11.2.1 E xtraction of Pb-Zn from Tailings for Utilization and Production in China 229 11.2.2 Vegetation Program on Pb-Zn Tailings 229 11.2.3 Recovering Valuable Metals from Tailings and Residues 229 11.2.4 E xtraction of Vanadium, Lead and Zinc from Mining Dump in Zambia 230 11.2.5 Recovery of Zinc from Blast Furnace and other Dust/Secondary Resources 230 11.2.6 Treatment and Recycling of Goethite Waste 231 11.2.7 Other Hydrometallurgical Treatments of Zinc-based Industrial Wastes and Residues 231 11.3 Biohydrometallurgical Processing: International Scenario 233 11.3.1 Bioleaching of Zn from Copper Mining Residues by Aspergillus niger 233 11.3.2 Bioleaching of Zinc from Steel Plant Waste using Acidithiobacillus ferrooxidans 234 11.3.3 Bacterial Leaching of Zinc from Chat (Chert) Pile Rock and Copper from Tailings Pond Sediment 234 11.3.4 Dissolution of Zn from Zinc Mine Tailings 234 11.3.5 Microbial Diversity in Zinc Mines 234 11.3.6 Chromosomal Resistance Mechanisms of A. ferrooxidans on Zinc 235 11.3.7 Bioleaching of Zinc Sulfides by Acidithiobacillus ferrooxidans 235 11.3.8 Bioleaching of High-sphalerite Material 235 11.3.9 Bioleaching of Low-grade ZnS Concentrate and Complex Sulfides (Pb-Zn) using Thermophilic Species 236 11.3.10 Improvement of Stains for Bio-processing of Sphalerite 236 11.3.11 Tank Bioleaching of ZnS and Zn Polymetallic Concentrates 237 11.3.12 Large-Scale Development for Zinc Concentrate Bioleaching 237 11.3.13 Scale-up Studies for Bioleaching of Low-Grade Sphalerite Ore 238 11.3.14 Zinc Resistance Mechanism in Bacteria 238 11.4 Biohydrometallurgical Processing: Indian Scenario 238 11.4.1 E lectro-Bioleaching of Sphalerite Flotation Concentrate 239 11.4.2 Bioleaching of Zinc Sulfide Concentrate 239 11.4.3 Bioleaching of Moore Cake and Sphalarite Tailings 239 11.5 Synthesis of Nanoparticles 240 11.6 Applications of Zinc-based Value-added Products/Nanomaterials 244 11.6.1 Hydro-Gel for Bio-applications 244 11.6.2 Sensors 244 11.6.3 Biomedical Applications 245 11.6.4 Antibacterial Properties 245 11.6.5 Zeolites in biomedical applications 246 11.6.6 Textiles 246 11.6.7 Prospects of Zinc Recovery from Tailings and Biosynthesis of Zinc-based Nano-materials 246 11.7 Conclusions and Future Directions 247 References 248 12 Interaction Between Nanoparticles and Plants: Increasing Evidence of Phytotoxicity 255Rajeshwari Sinha and S.K. Khare 12.1 Introduction 255 12.2 Plant–Nanoparticle Interactions 256 12.3 E ffect of Nanoparticles on Plants 256 12.3.1 Monocot Plants 257 12.3.2 Dicot Plants 257 12.4 Mechanisms of Nanoparticle]induced Phytotoxicity 257 12.4.1 Endocytosis 257 12.4.2 Transfer through Ion Channels Post]ionization 262 12.4.3 Aquaporin Mediated 262 12.4.4 Carrier Proteins Mediated 262 12.4.5 Via Organic Matter 262 12.4.6 Complex Formation with Root Exudates 262 12.4.7 Foliar Uptake 263 12.5 E ffect on Physiological Parameters 263 12.5.1 Loss of Hydraulic Conductivity 263 12.5.2 Genotoxic Effects 263 12.5.3 Absorption and Accumulation 263 12.5.4 Generation of Reactive Oxygen Species (ROS) 264 12.5.5 Biotransformation of NPs 264 12.6 Genectic and Molecular Basis of NP Phytotoxicity 266 12.7 Conclusions and Future Perspectives 266 References 267 13 Cytotoxicology of Nanocomposites 273Horacio Bach 13.1 Introduction 273 13.2 Cellular Toxicity 274 13.2.1 Mechanisms of Cellular Toxicity 274 13.2.2 E ffect of Glutathione (GSH) in Oxidative Stress 276 13.2.3 Damage to Cellular Biomolecules 277 13.3 Nanoparticle Fabrication 281 13.3.1 Physico]chemical Characteristics of NPs 282 13.3.2 Cellular Uptake 284 13.3.3 Factors Affecting the Internalization of NPs 287 13.4 Immunological Response 289 13.4.1 Cytokine Production 289 13.4.2 Cytotoxicity, Necrosis, Apoptosis, and Cell Death 290 13.5 Factors to Consider to Reduce the Cytotoxic Effects of NP 292 13.6 Conclusions and Future Directions 293 References 294 14 Nanotechnology: Overview of Regulations and Implementations 303Om V. Singh and Thomas Colonna 14.1 Introduction 303 14.2 Scope of Nanotechnology 305 14.3 Safety Concerns Related to Nanotechnology 310 14.4 Barriers to the Desired Regulatory Framework 311 14.4.1 Regulatory Framework in the United States 312 14.4.2 Global Efforts toward Regulation of Nanotechnology 315 14.5 Biosynthesis of Microbial Bio]nanoparticles: An Alternative Production Method 317 14.6 Conclusion 325 References 326 Name index 331 Subject index 333

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Book SynopsisNeuroinflammation has long been studied for its connection to the development and progression of Multiple Sclerosis. In recent years, the field has expanded to look at the role of inflammatory processes in a wide range of neurological conditions and cognitive disorders including stroke, amyotrophic lateral sclerosis, and autism. Researchers have also started to note the beneficial impacts of neuroinflammation in certain diseases. Neuroinflammation: New Insights into Beneficial and Detrimental Functions provides a comprehensive view of both the detriments and benefits of neuroinflammation in human health. Neuroinflammation: New Insights into Beneficial and Detrimental Functions opens with two chapters that look at some fundamental aspects of neuroinflammation in humans and rodents. The remainder of the book is divided into two sections which examine both the detrimental and beneficial aspects of inflammation on the brain, spinal cord and peripheral nerves,Table of ContentsList of Contributors xi Preface xvii PART I Introduction 1 1 Immune Response in the Human Central Nervous System in Multiple Sclerosis and Stroke 3Hans Lassmann Introduction 3 The Concept of Neuroinflammation 3 Basic Principles of Immune Surveillance and Inflammation by Adaptive Immune Responses 4 Inflammation in the Central Nervous System of Patients with Multiple Sclerosis 7 Inflammation in Stroke Lesions 11 Microglia Activation and Macrophage Response 12 Granulocyte Infiltration 12 Conclusions 15 References 15 2 In Vivo Imaging of Glial and Immune Cell Responses in Central Nervous System Injury and Disease 21Alexandre Paré and Steve Lacroix Introduction 21 Intravital Microscopy in the CNS and Its Challenges 22 In Vivo Imaging of the CNS Following Sterile Injury 24 In Vivo Imaging of the CNS in Disorders with an Inflammatory Component 27 Conclusion 32 Acknowledgments 33 References 33 PART II Detrimental Aspects of Inflammation 39 3 Roles of CD4 and CD8 T Lymphocytes in Multiple Sclerosis and Experimental Autoimmune Encephalomyelitis 41Nathalie Arbour and Alexandre Prat Introduction 41 T Lymphocytes: Central Immune Cells 42 Autoreactive T Lymphocytes 42 From Peripheral Activation to CNS Extravasation 45 Role of CD4 T Lymphocytes in MS and EAE: Th1 versus Th17 46 Role of CD8 T Lymphocytes in MS and EAE 47 Regulatory T Lymphocytes in MS and EAE 48 Conclusions 49 Acknowledgements 49 References 49 4 Microglia and Macrophage Responses and Their Role after Spinal Cord Injury 53Antje Kroner, Andrew D. Greenhalgh, and Samuel David Introduction 53 Microglial Responses to Injury 54 Interactions between Microglia and Other Cell Types in Signaling Responses to Injury 57 Entry of Peripheral Macrophages and Differences with Microglia 59 Diverse Roles of Macrophages/Microglia in CNS Injury and Disease 60 Macrophage Polarization in SCI 61 Concluding Remarks 66 Acknowledgements 66 References 66 5 The Complexity of the Innate Immune System Activation in Stroke Pathogenesis 71María Isabel Cuartero, Ignacio Lizasoain, María Ángeles Moro, and Ivan Ballesteros Activation of the Brain Innate Immunity After Stroke 71 Myeloid Heterogeneity in Brain Ischemia 76 Concluding Remarks 81 References 81 6 Neuroinflammation in Aging 87Ashley M. Fenn, Diana M. Norden, and Jonathan P. Godbout Increased CNS Inflammation in Response to Immune Challenge is Adaptive and Beneficial 87 The CNS Microenvironment Shifts to a Proinflammatory State with Aging 88 Microglial Priming 88 Microglial Regulation 90 Immune Reactivity of Glia Contributes to Cognitive and Behavioral Deficits 97 Conclusions 100 References 100 7 Peripheral and Central Immune Mechanisms in Neuropathic Pain 107Ji Zhang Introduction 107 Inflammation in Neuropathic Pain 108 Contribution of Peripheral Immune Cells to the Pathogenesis of Neuropathic Pain 109 Critical Roles of Spinal Glial Activation in Neuropathic Pain 111 Significance of Neural Barriers in Inflammatory Response along Pain Transmission Pathway 114 Imbalance of Pro- and Anti-inflammatory Responses in Neuropathic Pain 115 Challenges in Translating Anti-inflammatory Therapeutic Strategies for the Relief of Neuropathic Pain 115 Acknowledgement 117 References 117 8 Inflammation in the Pathogenesis of Inherited Peripheral Neuropathies 123Janos Groh, Dennis Klein, Antje Kroner, and Rudolf Martini Inherited Peripheral Neuropathies 123 Subtype-Specific Molecular Patterns of CMT1 124 Molecular Commonalities of CMT1 Subtypes–a Link to Inflammation 125 The Impact of Innate Immune Reactions in Mouse Models of CMT1 126 The Impact of Adaptive Immune Reactions in Mouse Models of CMT1 129 Implications for Putative Therapeutic Approaches 130 Synopsis 132 Acknowledgements 132 References 133 9 Obesity- and Neuroinflammation-Associated Mood and Cognitive Disorders 139Nathalie Castanon, Giamal Luheshi, and Sophie Layé Introduction 139 Neuropsychiatric Comorbidity in Obesity 140 Animal Models of Obesity and MetS 140 Mechanisms Underlying the Association between Obesity/MetS and Neuropsychiatric Symptoms 142 Neuroinflammation, Sickness Behavior, and Neuropsychiatric Symptoms 143 Role of Neuroinflammation in Neuropsychiatric Symptoms Associated with Obesity and MetS 146 Conclusions 148 References 149 10 Viral Infections of the Central Nervous System: Pathogenic and Protective Effects of Neuroinflammation 155John G. Walsh and Christopher Power Introduction 155 Nervous System Infection and Inflammation 157 HIV-1 Infection: Neurological and Neuropathological Features 158 WNV Infection and Neuropathology 162 Future Perspectives 166 References 167 PART III Beneficial Aspects of Inflammation 173 11 The Interplay between the Peripheral and Local Immune Response in Recovery from Acute Central Nervous System Injuries 175Catarina Raposo and Michal Schwartz Paradigm of Protective Autoimmunity 175 Dichotomy between Microglia and Infiltrating Monocyte-Derived Macrophages 176 Infiltrating Macrophages Promote Inflammation Resolution and Axonal Regeneration 177 The Two Faces of Tregs in CNS Repair 178 Protective Autoimmunity Works at the Specialized Choroid Plexus Gate 179 Inflammation, the Old Villain in Spinal Cord Repair 181 Comprehensive View of the Protective Autoimmune Network: the Link between Autoimmune T Cells and Inflammation-Resolving Cells 181 Acknowledgments 183 References 183 12 Inflammation and Optic Nerve Regeneration 189Lukas Andereggen, Ephraim F. Trakhtenberg, Yin Yuqin, and Larry I. Benowitz Introduction 189 Background 190 Effects of inflammation on RGC survival and Optic Nerve Regeneration 192 Oncomodulin as a Key Mediator of Inflammation-Induced Regeneration 193 Synergistic Effects of Combinatorial Treatments 198 Conclusions 200 Acknowledgments 200 References 200 13 Effects of Macrophages and Monocytes in Remyelination of the CNS 205Muktha Natrajan, Bibiana Bielekova, and Robin J.M. Franklin Introduction 205 Myelin Debris Inhibits OPC Differentiation and Remyelination 207 Monocyte-Derived Macrophages are the Main Actors in Myelin Debris Phagocytosis 209 Switching from M1 to M2 Macrophages Promotes CNS Remyelination 211 Ageing Impairs Macrophage Function, Myelin Debris Clearance, and Remyelination 212 Macrophages Release Growth and Neurotrophic Factors that Promote Remyelination 213 Concluding Remarks 215 References 215 14 Microglia Involvement in Rett Syndrome 221Noël C. Derecki, James C. Cronk, and Jonathan Kipnis Introduction to Rett Syndrome and MeCP2 221 Experimental Mouse Models Used in the Study of Rett Syndrome 222 The Cellular Players in Central Nervous System Pathology of Rett Syndrome 223 Microglia: From Footnote to First-Line 224 Microglia: the Tissue-Resident Macrophages of the Brain 225 Replacement/Augmentation of MICROGLIA as A potential therapy in Rett Syndrome 228 Gene Therapy 229 Conclusions 230 References 230 15 The Role of Regulatory T Cells and Microglia in Amyotrophic Lateral Sclerosis 235David R. Beers, Weihua Zhao, Kristopher G. Hooten, and Stanley H. Appel Overview of Amyotrophic Lateral Sclerosis 235 Overview of ALS Animal Models 237 Overview of Regulatory T Cells 238 Immunologic Aspects of Microglia and Tregs in ALS 240 T Cells and ALS 242 Tregs and ALS 243 Cytokines and ALS 244 Conclusions 245 References 247 16 An Adaptive Role for TNFin Synaptic Plasticity and Neuronal Function 251Renu Heir and David Stellwagen Introduction 251 Developmental Roles of TNFα 252 TNFα in Presynaptic Function 252 TNFα effects on postsynaptic receptor trafficking 252 TNFα and Synaptic Plasticity 255 Glial Release of TNFα During Plasticity 256 TNFα-mediated homeostatic plasticity in vivo 258 TNFα-Mediated Plasticity in the Striatum 258 Implications of TNFα-Mediated Synaptic Regulation 259 References 260 17 Resolution of Inflammation in the Lesioned Central Nervous System 265Jan M. Schwab, Harald Prüss, and Charles N Serhan Introduction 265 Mechanisms of Resolution 267 Resolution Deficit Following CNS Lesions 268 Immunobiology of Resolution in CNS Lesions–Impaired Resolution Contributes to Neuropathology 269 Late Degeneration/“Tertiary” Injury and Autoimmunity as a Consequence of Failed Resolution of Inflammation in CNS Lesions? 271 Evidence for the Effectiveness of Pro-resolution Mediators in CNS Lesions 273 Conclusion 274 Acknowledgement 275 References 275 Index 281

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Book SynopsisThe Genomics Applications in Crop Improvement two volume set brings together a diverse field of international experts in plant breeding genomics to share their experiences in the field, from success stories to lessons learnt. In recent years advances in genetics and genomics have greatly enhanced our understanding of the structural and functional aspects of plant genomes. Several novel genetic and genomics approaches such as association genetics, advanced back-cross QTL analysis, allele mining, comparative and functional genomics, transcriptomics, proteomics, etc. offer unprecedented opportunities to examine crop genetic variation and utilize this variability for breeding purposes. Enhancing the prediction of the phenotype from a genotype using genomics tools is referred to as ''genomics-assisted breeding''. To date, genomics-assisted breeding has shown its potential for crop improvement in several crops, however these successes have been largely restricted to temperate cereTable of ContentsTranslational Genomics for Crop Breeding: Volume 1 - Biotic Stress Foreword vii Preface ix Chapter 1 Translational Genomics in Crop Breeding for Biotic Stress Resistance: An Introduction 1 Rajeev K. Varshney and Roberto Tuberosa Chapter 2 Bacterial Blight Resistance in Rice 11 Yanjun Kou and Shiping Wang Chapter 3 The Genetic Basis of Disease Resistance in Maize 31 Tiffany Jamann, Rebecca Nelson, and Peter Balint-Kurti Chapter 4 Genomics-Assisted Breeding for Fusarium Head Blight Resistance in Wheat 45 Hermann Buerstmayr, Maria Buerstmayr, Wolfgang Schweiger, and Barbara Steiner Chapter 5 Virus Resistance in Barley 63 Frank Ordon and Dragan Perovic Chapter 6 Molecular Breeding for Striga Resistance in Sorghum 77 Santosh P. Deshpande, Abdalla Mohamed, and Charles Thomas Hash, Jr. Chapter 7 Nematode Resistance in Soybean 95 Tri D. Vuong, Yongqing Jiao, J. Grover Shannon, and Henry T. Nguyen Chapter 8 Marker-Assisted Selection for Biotic Stress Resistance in Peanut 125 Mark D. Burow, Soraya C. M. Leal-Bertioli, Charles E. Simpson, Peggy Ozias-Akins, Ye Chu, Nicholas N. Denwar, Jennifer Chagoya, James L. Starr, M´arcio C. Moretzsohn, Manish K. Pandey, Rajeev K.Varshney, C. Corley Holbrook, and David J. Bertioli Chapter 9 Organization of Genes Conferring Resistance to Anthracnose in Common Bean 151 Juan Jose Ferreira, Ana Campa, and James D. Kelly Chapter 10 Enabling Tools for Modern Breeding of Cowpea for Biotic Stress Resistance 183 Bao-Lam Huynh, Jeffrey D. Ehlers, Timothy J. Close, Ndiaga Cisse, Issa Drabo, Ousmane Boukar, Mitchell R. Lucas, Steve Wanamaker, Marti Pottorff, and Philip A. Roberts Chapter 11 Disease Resistance in Chickpea 201 Teresa Mill´an, Eva Madrid, Muhammad Imtiaz, Mohamed Kharrat, and Weidong Chen Chapter 12 Resistance to Late Blight in Potato 221 Jadwiga Sliwka and Ewa Zimnoch-Guzowska Chapter 13 Late Blight of Tomato 241 Marcin Nowicki, Elÿzbieta U. Kozik, and Majid R. Foolad Chapter 14 Marker-Assisted Selection for Disease Resistance in Lettuce 267 I. Simko Chapter 15 Marker-Assisted Breeding for Cassava Mosaic Disease Resistance 291 E. Okogbenin, I. Moreno, J. Tomkins, C.M. Fauquet, G. Mkamilo, and M. Fregene Chapter 16 Genetics and Gene Mapping of Disease Resistance in Brassica 327 Genyi Li and Peter B.E. McVetty Appendix I – Contributors 345 Appendix II – Reviewers 351 Index 353 Color plate section can be found between pages 182 and 183. Translational Genomics for Crop Breeding: Volume 2 - Improvement for Abiotic Stress, Quality and Yield Improvement Foreword vii Preface ix Chapter 1 Translational Genomics for Crop Breeding: Abiotic Stress Tolerance, Yield, and Quality, An Introduction 1 Rajeev K. Varshney and Roberto Tuberosa Chapter 2 Applying Genomics Tools for Breeding Submergence Tolerance in Rice 9 Endang M. Septiningsih, Bertrand C. Y. Collard, Sigrid Heuer, Julia Bailey-Serres, Abdelbagi M. Ismail, and David J. Mackill Chapter 3 Genomics Applications to Salinity Tolerance Breeding in Rice 31 J. Damien Platten, Michael J. Thomson, and Abdelbagi M. Ismail Chapter 4 Marker-Assisted Introgression of Major QTLs for Grain Yield Under Drought in Rice 47 Arvind Kumar, Shalabh Dixit, and Amelia Henry Chapter 5 Molecular Breeding for Phosphorus-efficient Rice 65 Sigrid Heuer, J.H. Chin, R. Gamuyao, S.M. Haefele, and M. Wissuwa Chapter 6 Aluminum Tolerance in Sorghum and Maize 83 Jurandir V. Magalhaes, Lyza G. Maron, Miguel A. Pi˜neros, Claudia T. Guimar˜aes, and Leon V. Kochian Chapter 7 Freezing Tolerance in the Triticeae 99 Galiba Gabor, Eric J. Stockinger, Enrico Francia, Justyna Milc, Gabor Kocsy, and Nicola Pecchioni Chapter 8 Molecular Breeding for Stay-Green: Progress and Challenges in Sorghum 125 Vincent Vadez, Santosh Deshpande, Jana Kholova, Punna Ramu, and C. Tom Hash Chapter 9 Genetic Improvement of Grain Quality in Japonica Rice 143 Kiyosumi Hori and Masahiro Yano Chapter 10 Biofortified Maize – A Genetic Avenue for Nutritional Security 161 Raman Babu, Natalia Palacios, and BM Prasanna Chapter 11 Marker-Assisted Backcrossing Selection for High O/L Ratio in Cultivated Peanut 177 Padmalatha Koilkonda, Chikara Kuwata, Masanobu Fukami, Kenta Shirasawa, Koh Aoki, Satoshi Tabata, Makoto Hasegawa, Hiroyuki Kiyoshima, Shigeru Suzuki, Shigemi Sasamoto, Atsushi Kurabayashi, Hisano Tsuruoka, Tsuyuko Wada, and Sachiko Isobe Chapter 12 Genomics-Assisted Breeding for Tomato Fruit Quality in the Next-Generation Omics Age 193 Matthew P. Kinkade and Majid R. Foolad Chapter 13 Improvement of Yield per se in Sugarcane 211 M. Gouy, S. Nibouche, J.Y. Hoarau, and L. Costet Appendix I – Contributors 239 Appendix II – Reviewers 243 Index 245 Color plate section can be found between pages 82 and 83.

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Book SynopsisExplore the latest research in anthropological genetics and understand the genome's role in cultural and social development A Companion to Anthropological Genetics illustrates the role of genetic analysis in advancing the modern study of human origins, populations, evolution, and diversity. Broad in scope, this essential reference work establishes and explores the relationship between genetic research and the major questions of anthropological study. Through contributions by leading researchers, this collection explores molecular genetics and evolutionary mechanisms in the context of macro- and microevolution, paleontology, phylogeny, diet, and disease, with detailed explanations of quantitative methods, including coalescent and approximate Bayesian computation. With an emphasis on contextualizing new and developing genetic research within anthropological frameworks, this text offers critical perspective on the conditions of molecular evolution that accompany cultural and social traTable of ContentsAbout the Editor xi Notes on Contributors xiii Preface xix Part I Anthropological Genetics in Context 1 1 History and Evolution of Anthropological Genetics 3Michael H. Crawford 2 The Ethics of Genetic Ancestry Testing 17Nanibaa’ A. Garrison and Jessica D. Bardill 3 Community‐Oriented Research and the Future of Anthropological Genetics 37Ripan S. Malhi Part II Macroevolution and Phylogenetics 45 4 Calibrating the Clock 47Murray P. Cox 5 Primate Genomics and Phylogenetics 57Christopher A. Schmitt and Omer Gokcumen 6 The Neanderthal and Denisovan Genomes 69Sloan R. Williams 7 Evaluating Correspondence in Phenotypic Variation, Genetic Diversity, Geography, and Environmental Factors 89Noreen von Cramon‐Taubadel 8 Simulating Human Demographic Processes and Patterns of Genetic Variation 107Aida T. Miró‐Herrans Part III Microevolution: Colonization, Dispersal, and Differentiation 121 9 Human Population Structure and History 123John H. Relethford 10 Regional Patterns of Variation: Concepts and Applications 137Graciela S. Cabana 11 Genetic Variation and the Colonization of Eurasia 151Toomas Kivisild 12 Homo sapiens Dispersal and the Peopling of the Americas 165Rafael Bisso‐Machado and Nelson Jurandi Rosa Fagundes 13 Ancient DNA and Bioarcheology 187Jennifer A. Raff Part IV Human Adaptation: Natural Selection and Physiological Variation 199 14 Tempo of Recent Human Evolution 201Michael D. Weight and Henry C. Harpending 15 Natural Selection and Adaptation to Extreme Environments: High Latitudes and Altitudes 219Abigail W. Bigham 16 Sensory Polymorphisms and Dietary Adaptation 233Carrie C. Veilleux 17 The Evolution of the Human Pigmentation Phenotype 251Heather L. Norton 18 Anthropological Genetics and Growth and Development 267Bradford Towne, Ellen W. Demerath, and Stefan A. Czerwinski 19 Epigenetics and Human Variation 293Amy L. Non and Zaneta M. Thayer Part V Anthropology, Genetics, and the Evolution of Health and Disease 309 20 The Primate Immune System: A Survey of Innate and Acquired Immune Genes 311Leslie A. Knapp and Nicole S. Torosin 21 Genetics, Evolutionary Medicine, and the Evolution of Human Pathogens 327Amanda VanSteelandt and Anne C. Stone References 343 Index 445

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Book SynopsisDiscussing recent advances in the field of matrix metalloproteinase (MMP) research from a multidisciplinary perspective, Matrix Metalloproteinase Biologyis a collection of chapters written by leaders in the field of MMPs.Table of ContentsList of Contributors ix 1 Matrix Metalloproteinases: From Structure to Function 1Maciej J. Stawikowski and Gregg B. Fields 1.1 Introduction 1 1.2 Structures of MMPs 1 1.2.1 General MMP structure and domain organization 1 1.2.2 Catalytic domain 2 1.2.3 Catalytic mechanism 3 1.2.4 Fibronectin type II-like inserts 3 1.2.5 Linker region 4 1.2.6 Hemopexin-like domain 6 1.2.7 Transmembrane domain and cytoplasmic tail 7 1.3 Overview of MMP substrate specificity 8 1.3.1 ECM substrates 9 1.3.2 Cell surface substrates 10 1.3.3 Intracellular MMP targets 11 1.4 Selective mechanisms of action 13 1.4.1 Collagenolysis 13 1.4.2 Gelatinolysis 15 Acknowledgments 16 References 16 2 Dynamics and Mechanism of Substrate Recognition by Matrix Metalloproteases 23Ivan E. Collier and Gregory I. Goldberg 2.1 Introduction 23 2.2 Conformational flexibility of MMPs is inexorably linked to collagen proteolysis 24 2.3 Dynamics of MMP-2 and MMP-9 interaction with gelatin 26 2.4 Surface diffusion: a common mechanism for substrate interaction adapted by MMP-2 and MMP-9 26 2.5 Dynamics of MMP interaction with collagen fibrils 28 2.6 Mechanism of interaction of MMP-1, MMP-2, MMP-9, and MMP-14 with collagen substrate involves surface diffusion 28 2.7 Mechanism of MMP-1 diffusion on native collagen fibrils 30 2.8 Triple helical collagen cleavage – diffusion coupling 31 2.9 Conclusions 34 References 36 3 Matrix Metalloproteinases: From Structure to Function 41Marco Fragai and Claudio Luchinat 3.1 Introduction 41 3.2 Classification and structural features 42 3.3 Catalytic mechanism 45 3.4 Intra- and inter-domain flexibility 47 3.5 Elastin and collagen degradation 47 References 54 4 Metzincin Modulators 61Dmitry Minond 4.1 Inhibitors 61 4.1.1 Antibodies: targeting beyond the active site 61 4.1.2 Peptide-based inhibitors 65 4.1.3 Small molecules: non-zinc binding exosite inhibitors 68 4.1.4 Protein-based inhibitors 78 Summary and future directions 80 References 81 5 Therapeutics Targeting Matrix Metalloproteinases 85Jillian Cathcart, Ashleigh Pulkoski-Gross, Stanley Zucker, and Jian Cao 5.1 Introduction 85 5.2 Peptidomimetic MMP inhibitors 86 5.3 Structure-based MMPI drug design 87 5.4 Mechanism-based MMPI design 89 5.5 Allosteric MMPI design 90 5.6 Macromolecular MMP inhibitors 91 5.7 Chemically-modified tetracyclines 93 5.8 Alternative approaches 94 5.9 MMPs as anti-targets 95 5.10 Conclusions 97 References 98 6 Matrix Metalloproteinase Modification of Extracellular Matrix-Mediated Signaling 103Howard C. Crawford and Sharon M. Stack 6.1 Introduction 103 6.2 The extracellular matrix as a source for signaling ligands 104 6.3 ECM and mechanosensory signal transduction 106 6.4 Matrix remodeling and modification of mechano-sensory signaling 108 6.5 Conclusions and future directions 109 References 109 7 Meprin and ADAM Metalloproteases: Two Sides of the Same Coin? 115Christoph Becker-Pauly and Stefan Rose-John 7.1 Introduction 115 7.2 Meprin metalloproteases 116 7.3 Structure of meprin α and meprin β 116 7.4 Proteomics for the identification of meprin substrates 118 7.5 Meprins in health and disease 118 7.6 Proteolytic back-and-forth of meprins and ADAMs 119 7.7 Collagen fibril formation 119 7.8 Angiogenesis and cancer 120 7.9 Inflammation 121 7.10 ADAM Proteases 121 7.11 The ADAM family of proteases 123 7.12 Orchestration of different pathways by ADAM17 123 7.13 Regulation of ADAM17 activity 123 7.14 Role of ADAM17 in vivo 125 7.15 Role of ADAM17 in humans 125 References 126 8 Subtracting Matrix Out of the Equation: New Key Roles of Matrix Metalloproteinases in Innate Immunity and Disease 131Antoine Dufour and Christopher M. Overall 8.1 The tale of a frog’s tail 131 8.2 The MMP family 132 8.3 Making the cut as immune regulators 133 8.4 Enter the “omics” era: genomics, proteomics and degradomics 137 8.5 ECM versus non-ECM MMP substrates 138 8.6 Moonlighting protein substrates: intracellular proteins cleaved outside the cell 142 8.7 Intracellular protein substrates cleaved inside the cell by MMPs 143 8.8 Non-proteolytic roles of MMPs: missed in the myth? 145 8.9 The fairy tail of a frog has an unexpected ending 149 Acknowledgements 149 References 149 9 MMPs: From Genomics to Degradomics 153Barbara Grünwald, Pascal Schlage, Achim Krüger, and Ulrich auf dem Keller 9.1 Introduction 153 9.1.1 Genomics: general aspects 154 9.1.2 The genomics approach to MMP function in cancer 155 9.1.3 Taking first steps towards MMP inhibition in cancer therapy 156 9.1.4 Lessons from the failure of unselective MMP inhibition 157 9.1.5 Limitations of the genomic approach to MMP function 160 9.1.6 Approaching proteolysis as a system 161 9.2 Degradomics – An Overview 164 9.2.1 Global assessment of MMP expression and activity 166 9.2.2 Defining MMP active site specificity 168 9.2.3 MMP substrate degradomics 169 9.2.4 Targeted degradomics 171 9.2.5 Data integration and repositories 173 9.3 Conclusions 174 Acknowledgments 174 References 174 10 MMPs in Biology and Medicine 183Di Jia, Roopali Roy, and Marsha A. Moses 10.1 Introduction 183 10.2 Functional roles of MMPs and ADAMs 184 10.2.1 ECM remodeling 184 10.2.2 Processing of growth factors and receptors 185 10.2.3 Modulation of cell migration, invasion, proliferation, and epithelial to mesenchymal transition (EMT) 186 10.2.4 Regulation of angiogenesis 187 10.3 MMPs as diagnostic and prognostic biomarkers of cancer 187 10.3.1 Breast cancer 188 10.3.2 Prostate cancer 189 10.3.3 Lung cancer 190 10.3.4 Pancreatic cancer 191 10.3.5 Ovarian cancer 192 10.4 MMPs/ADAMs as diagnostic and prognostic biomarkers for non-neoplastic diseases 192 10.4.1 Cardiovascular diseases 193 10.4.2 Endometriosis 193 10.4.3 Preeclampsia 195 10.4.4 Arthritis 196 10.5 MMPs as biomarkers of therapeutic efficacy 197 10.6 MMP-specific molecular imaging for noninvasive disease detection 201 10.7 Conclusions 202 Acknowledgments 203 References 203 Index 215

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Book SynopsisTechnological advances have greatly increased the potential for, and practicability of, using medical neurotechnologies to revolutionize how a wide array of neurological and nervous system diseases and dysfunctions are treated.Table of Contents1. The Historical Foundation of Bionics Nick Donaldson and Giles.S. Brindley 1.1 Bionics Past & Future 1.2 History in 1973 1.2.1 Biomaterials 1.2.2 Nerve Stimulation & Recording 1.2.3 Transistors 1.2.4 Conclusion 1.3 Anaesthesia 1.4 Aseptic Surgery 1.5 Clinical Observation & Experiments 1.6 Hermetic Packages 1.6.1 Vacuum Methods 1.6.2 Welding 1.6.3 Glass 1.6.4 Glass Ceramics & Solder Glasses 1.6.5 Ceramics 1.6.6 Microcircuit Technologies 1.6.7 Leak Testing 1.7 Encapsulation (Electrical Insulation) 1.7.1 Insulation 1.7.2 Under-water insulation 1.7.3 Silicones 1.7.4 Primers 1.8 Early Implanted Devices 1.9 Afterword References 2. Development of Stable Long-Term Electrode Tissue Interfaces for Recording and Stimulation Jens Schouenborg 2.1 Introduction 2.2 Tissue responses in the brain to an implanted foreign body 2.2.1 Acute tissue responses 2.2.2 Chronic tissue responses 2.2.3 On the importance of physiological conditions 2.3 Brain Computer Interfaces (BCI) - state of the art 2.4 Biocompatibility of BCI – on the importance of mechanical compliance 2.5 Novel electrode constructs and implantation procedures 2.5.1 Methods to implant ultraflexible electrodes 2.5.2 Surface configurations 2.5.3 Matrix embedded electrodes 2.5.4 Electrode arrays encorporating drugs 2.6 Concluding remarks Acknowledgements References 3. Electrochemical Principles of Safe Charge Injection Stuart F. Cogan, David J. Garrett and Rylie A. Green 3.1 Introduction 3.2 Charge Injection Requirements 3.2.1 Stimulation Levels for Functional Responses 3.2.2 Tissue damage thresholds 3.2.3 Charge Injection Processes 3.2.4 Capacitive Charge Injection 3.2.5 Faradaic Charge Injection 3.2.6 Stimulation Waveforms 3.2.7 Voltage Transient Analysis 3.3 Electrode Materials 3.3.1 Non-noble Metal Electrodes 3.3.2 Noble metals 3.3.3 High Surface Area Capacitor Electrodes 3.3.4 Three-dimensional Noble Metal Oxide Films 3.4 Factors Influencing Electrode Reversibility 3.4.1 In vivo versus saline charge injection limits 3.4.2 Degradation Mechanisms and Irreversible Reactions 3.5 Emerging Electrode Materials 3.5.1 Intrinsically conductive polymers 3.5.2 Carbon Nanotubes and Conductive Diamond 3.6 Conclusion References 4. Principles of Recording from an Electrical Stimulation of Neural Tissue James B. Fallon and Paul M. Carter 4.1 Introduction 4.2 Anatomy and physiology of neural tissue 4.2.1 Active Neurons 4.3 Physiological principles of recording from neural tissue 4.3.1 Theory of recording 4.3.2 Recording electrodes 4.3.3 Amplification 4.3.4 Imaging 4.4 Principles of Stimulation of Neural Tissue 4.4.1 Introduction 4.4.2 Principles of Neural Stimulator Design 4.4.3 Modelling Nerve Stimulation 4.4.4 The Activating Function 4.4.5 Properties of Nerves Under Electrical Stimulation 4.5 Safety of Electrical Stimulation 4.5.1 Safe Stimulation Limits 4.5.2 Metabolic Stress 4.5.3 Electrochemical Stress 4.6 Conclusion References 5. Wireless Neurotechnology for Neural Prostheses Arto Nurmikko, David Borton and Ming Yin 5.1 Introduction 5.2 Rationale and overview of Technical Challenges Associated with Wireless Neuroelectronic Interfaces 5.3 Wireless Brain Interfaces Require Specialized Microelectronics 5.3.1 Lessons learned from Cabled Neural Interfaces 5.3.2 Special Demands for Compact Wireless Neural Interfaces 5.4 Illustrative Microsystems for High Data Rate Wireless Brain Interfaces in Primates 5.5 Power Supply and Management for Wireless Neural Interfaces 5.6 Packaging and Challenges in Hermetic Sealing 5.7 Deployment of High Data Rate Wireless Recording in Freely Moving Large Animals 5.8 Summary and Prospects for High Data Rate Brain Interfaces for Neural Prostheses Acknowledgements References 6. Preclinical Testing of Neural Prostheses Douglas McCreery 6.1 Introduction 6.2 Biocompatibility testing of neural implants 6.3 Testing for mechanical and electrical integrity 6.4 In vitro accelerated testing and accelerated aging of neural implants 6.5 In vivo testing of neural prostheses 6.6 Conclusion References 7. Auditory and Visual Neural Prostheses Robert K. Shepherd, Peter M. Seligman, Mohit N. Shivdasani 7.1 Introduction 7.2 Auditory prostheses 7.2.1 The Auditory system 7.2.2 Hearing loss 7.2.3 Cochlear implants 7.2.4 Central auditory prostheses 7.2.5 Combined electric and acoustic stimulation 7.2.6 Bilateral cochlear implants 7.2.7 Future directions 7.3 Visual prostheses 7.3.1 The Visual system 7.3.2 Vision loss 7.3.3 Retinal prostheses 7.3.4 Central visual prostheses 7.3.5 Perception through a vision prosthesis 7.3.6 Future directions 7.4 Sensory prostheses and brain plasticity 7.5 Conclusions Acknowledgments References 8. Neurobionics: Treatments for Disorders of the Central Nervous System Hugh McDermott 8.1 Introduction 8.2 Psychiatric conditions 8.2.1 Obsessive-compulsive disorder 8.2.2 Major depression 8.3 Movement disorders 8.3.1 Essential Tremor 8.3.2 Parkinson’s disease 8.3.3 Dystonia 8.3.4 Tourette syndrome 8.4 Epilepsy 8.5 Pain 8.6 Future directions Acknowledgements References 9. Brain Computer Interfaces David M. Brandman and Leigh R. Hochberg 9.1 Introduction 9.2 Motor Physiology 9.2.1 Neurons are the fundamental unit of the Brain 9.2.2 Movement occurs through coordinated activity between multiple regions of the nervous system 9.2.3 Motor Cortex: a first source for iBCI signals 9.2.4 The Parietal Cortex is implicated in spatial coordination 9.2.5 The premotor and supplementary motor cortices are engaged in movement goals 9.2.6 Functional brain organization is constantly changing 9.2.7 Section Summary 9.3 The Clinical Population for Brain Machine Interfaces 9.3.1 Paralysis may result from damage to the motor system 9.3.2 Individuals with spinal cord injuries develop motor impairments that may impact hand function 9.3.3 Individuals with LIS develop motor impairment that impacts communication 9.4 BCI Modalities 9.4.1 BCI Modalities 9.4.2 Electrodes placed in the cortex record action potentials from neurons 9.4.3 Raw voltage signals are processed into spikes 9.5 BCI Decoding and applications 9.5.1 BCI decoders convert neural information into control of devices 9.5.2 BCI decoders allow for the control of prosthetic devices 9.6 Future directions 9.6.1 Scientific and engineering directions for developing BMI technology 9.6.2 Clinical directions for development of BCI technology 9.7 Conclusion References 10. Taking a Device to Market: Regulatory and Commercial Issues John L. Parker 10.1 Introduction 10.2 Basic Research 10.3 Preclinical Development 10.4 Clinical trials and approval to sell 10.5 Building a Business not a product 10.6 Conclusions References 11. Ethical Considerations in the Development of Neural Prostheses Frank J. Lane, Kristian P. Nitsch, and Marcia Scherer 11.1 Introduction 11.2 Individuals with Disabilities & Technology Development 11.3 Ethical Principles of Biomedical Research 11.4 Conclusions References Appendix: Companies Developing and/or Marketing Bionic Devices

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Book SynopsisComputational and high-throughput methods, such as genomics, proteomics, and transcriptomics, known collectively as -omics, have been used to study plant biology for well over a decade now. This book provides an introduction to key omicsbased methods and their application in plant breeding.Trade Review“Accessible to advanced students, researchers, and professionals, Omics in Plant Breeding will be an essential entry point into this innovative and exciting field.” (Biotechnology, Agronomy, Society and Environment, 1 October 2014) Table of ContentsList of Contributors ix Foreword xiii 1 Omics: Opening up the "Black Box" of the Phenotype 1Roberto Fritsche-Neto and Aluizio Borem The Post-Genomics Era 3 The Omics in Plant Breeding 4 Genomics, Precision Genomics, and RNA Interference 5 Transcriptomics and Proteomics 8 Metabolomics and Physiognomics 8 Phenomics 9 Bioinformatics 10 Prospects 10 References 10 2 Genomics 13Antonio Costa de Oliveira, Luciano Carlos da Maia, Daniel da Rosa Farias, and Naciele Marini The Rise of Genomics 13 DNA Sequencing 13 Development of Sequence-based Markers 18 Genome Wide Selection (GWS) 25 Structural and Comparative Genomics 27 References 28 3 Transcriptomics 33Carolina Munari Rodrigues, Valeria S. Mafra, and Marcos Antonio Machado Methods of Studying the Transcriptome 34 Applications of Transcriptomics Approaches for Crop Breeding 46 Conclusions and Future Prospects 51 Acknowledgements 51 References 51 4 Proteomics 59Ilara Gabriela F. Budzinski, Thais Regiani, Monica T. Veneziano Labate, Simone Guidetti-Gonzalez, Danielle Izilda R. da Silva, Maria Juliana Calderan Rodrigues, Janaina de Santana Borges, Ivan Miletovic Mozol, and Carlos Alberto Labate History 59 Different Methods for the Extraction of Total Proteins 60 Subcellular Proteomics 64 Post-Translational Modifications 66 Quantitative Proteomics 69 Perspectives 72 References 73 5 Metabolomics 81Valdir Diola (in memoriam), Danilo de Menezes Daloso, and Werner Camargos Antunes Introduction 81 Metabolomic and Biochemical Molecules 83 Technologies for Metabolomics 83 Metabolomic Database Analysis 86 Metabolomics Applications 89 Metabolomics-assisted Plant Breeding 91 Associative Genome Mapping and mQTL Profiles 95 Large-scale Phenotyping Using Metabolomics 97 Conclusion and Outlook 98 References 99 6 Physionomics 103Frederico Almeida de Jesus, Agustin Zsogon, and Lazaro Eustaquio Pereira Peres Introduction 103 Early Studies on Plant Physiology and the Discovery of Photosynthesis 104 Biochemical Approaches to Plant Physiology and the Discovery of Plant Hormones 104 Genetic Approaches to Plant Physiology and the Discovery of Hormone Signal Transduction Pathways 106 Alternative Genetic Models for Omics Approaches in Plant Physiology 112 "Physionomics" as an Integrator of Various Omics for Functional Studies and Plant Breeding 117 Acknowledgements 121 References 121 7 Phenomics 127Roberto Fritsche-Neto, Aluizio Borem, and Joshua N. Cobb Introduction 127 Examples of Large-scale Phenotyping 128 Important Aspects for Phenomics Implementation 134 Main Breeding Applications 141 Final Considerations 144 References 144 8 Electrophoresis, Chromatography, and Mass Spectrometry 147Thais Regiani, Ilara Gabriela F. Budzinski, Simone Guidetti-Gonzalez, Monica T. Veneziano Labate, Fernando Cotinguiba, Felipe G. Marques, Fabricio E. Moraes, and Carlos Alberto Labate Introduction 147 Two-dimensional Electrophoresis (2DE) 148 Chromatography 150 Mass Spectrometry 155 Data Analysis 161 References 164 9 Bioinformatics 167J. Miguel Ortega and Fabricio R. Santos Introduction 167 The "Omics" Megadata and Bioinformatics 167 Hardware for Modern Bioinformatics 169 Software for Genomic Sequencing 170 Software for Contig Assembling 172 Assembly Using the Graph Theory 173 New Approaches in Bioinformatics for DNA and RNA Sequencing 174 Databases, Identification of Homologous Sequences and Functional Annotation 175 Annotation of a Complete Genome 179 Computational System with Chained Tasks Manager (Workflow) 181 Applications for Studies in Plants 182 Final Considerations 183 References 184 10 Precision Genetic Engineering 187Thiago J. Nakayama, Aluizio Borem, Lucimara Chiari, Hugo Bruno Correa Molinari, and Alexandre Lima Nepomuceno Introduction 187 Zinc Finger Nucleases (ZFNs) 190 Transcription Activator-like Effector Nucleases (TALENs) 193 Meganucleases (LHEs: LAGLIDADG Homing Endonucleases) 194 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) 195 Implications and Perspectives of the use of PGE in Plant Breeding 197 References 202 11 RNA Interference 207Francisco J.L. Aragao, Abdulrazak B. Ibrahim, and Maria Laine P. Tinoco Introduction 207 Discovery of RNAi 208 Mechanism of RNA Interference 209 Applications in Plant Breeding: Naturally Occurring Gene Silencing and Modification by Genetic Engineering 211 Resistance to Viruses 215 Host-induced Gene Silencing 218 Insect and Disease Control 218 Improving Nutritional Values 219 Secondary Metabolites 220 Perspectives 220 References 222 Index 229

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

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Book SynopsisDiet and exercise have long been recognized as important components of a healthy lifestyle, as they have a great impact on improving cardiovascular and cerebrovascular functions, lowering the risk of metabolic disorders, and contributing to healthy aging. As a greater proportion of the world's population is living longer, there has been increased interest in understanding the role of nutrition and exercise in long-term neurological health and cognitive function. Diet and Exercise in Cognitive Function and Neurological Diseases discusses the role and impact that nutrition and activity have on cognitive function and neurological health. The book is divided into two sections. The first section focuses on diet and its impact on neurobiological processes. Chapters focus on the impacts of specific diets, such as the Mediterranean, ketogenic and vegan diets, as well as the role of specific nutrients, fats, fatty acids, and calorie restriction on neurological health and cogniTable of ContentsContributors xi Foreword Kirk I. Erickson xv Foreword Shin Murakami xvii Preface xixTahira Farooqui and Akhlaq A. Farooqui Acknowledgments xxi 1 Nutrition, Genes, and Neuroscience: Implications for Development, Health, and Disease 1Margaret Joy Dauncey 2 Neurochemical Effects of Western Diet Consumption on Human Brain 15Akhlaq A. Farooqui and Tahira Farooqui 3 Effect of Mediterranean Diet on Human Health in Seniors: Relationship with Telomers 29Virginia Boccardi and Giuseppe Paolisso 4 Effect of a Mediterranean Diet on Mental and Physical Quality of Life 39Marialaura Bonaccio, Giovanni de Gaetano, and Licia Iacoviello 5 Ketogenic Diets for the Treatment of Neurologic Disease 47Christa W. Habela and Eric H. Kossoff 6 Levels of n‐3 Fatty Acids and their Metabolites in the Brain: Their Impact on Brain Function and Neurological Disorders 59Akhlaq A. Farooqui and Tahira Farooqui 7 Homocysteine Levels in Neurological Disorders 73Ahmed A. Moustafa, Doaa H. Hewedi, Abeer M. Eissa, Dorota Frydecka, and Błażej Misiak 8 Table Salt and Dementia 83Surender R. Neravetla and Shantanu R. Neravetla 9 Contribution of Diet and Exercise in the Pathogenesis of Major Depression 93Adrian L. Lopresti 10 Role of Diet and Exercise in Diabetic Retinopathy 105Mohammad Shamsul Ola, Haseeb A. Khan, and Abdullah S. Alhomida 11 The Effect of Western Diet on Cognition in Humans 111Heather M. Francis and Richard J. Stevenson 12 Role of Diet and Exercise in Intervention of Age‐Induced Impairments 123Kanti Bhooshan Pandey and Syed Ibrahim Rizvi 13 Hormesis and Cognitive Function: An Evolutionary/Adaptive Arabesque Leading to Longevity 133Alistair V.W. Nunn, Geoffrey W. Guy, and Jimmy D. Bell 14 Polyphenols and Cognitive Function 143Edwin D. Lephart 15 Prevention of Dementia Through Modifiable Risk Factors 163Patsri Srisuwan 16 Physical Exercise Improves Cognition in Brain Disorders: Alzheimer’s Disease 175Trevor Archer and Danilo Garcia 17 Molecular, Biochemical, and Physiological Basis of Beneficial Actions of Exercise 183Undurti N. Das 18 Beneficial Effects of Exercise and Cognitive Training on Cognitive Functions in Older Adults: Introduction of Smart Aging Studies 205Rui Nouchi and Ryuta Kawashima 19 Exercise and Cognitive Functions 213Bijli Nanda and S. Manjunatha 20 Role of Sleep in Cognition, Immunity, and Disease and Its Interaction with Exercise 225Mark R. Zielinski and Dmitry Gerashchenko 21 Effect of Forced and Voluntary Exercise on Neural Plasticity Mediated by Astrocytes 241Caren Bernardi, Mario Roberto Generosi Brauner, and Carlos Alberto Goncalves 22 Effect of Exercise on the Aging Brain 253Bonita L. Marks 23 The Effects of Exercise on Neuronal Survival 267Michael J. Chen 24 Exercise and Cognitive Function in Older Adults 279Nicola J. Gates and Maria Fiatarone Singh 25 Research Issues and Clinical Implications of Exercise Effects in the Treatment of Depressive and Anxiety Disorders 295A. Garrett Hazelton, Richard Bloch, and Sy Saeed 26 Exercise‐Induced Protection Against Aging and Neurodegenerative Diseases: Role of Redox‐ and Mitochondrial‐Based Alterations 309Ines Marques‐Aleixo, Estela Santos‐Alves, Paula I. Moreira, Paulo J. Oliveira, Jose Magalhaes, and Antonio Ascensao 27 Exercise, Neuroplasticity, and Growth Factors in Adolescence 323Helios Pareja‐Galeano, Sara Mayero, and Fabian Sanchis‐Gomar 28 Summary, Perspective, and Direction for Future Studies 339Tahira Farooqui and Akhlaq A. Farooqui Index 349

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Book SynopsisIn vitro fertilization (IVF) and other assisted reproductive technologies (ART) have become a significant part of human reproduction, with already one in 50 children worldwide being born through ART and the demand steadily increasing. To accommodate the various kinds of infertility problems, new methods have been developed to increase IVF and ART success rates and it has also become possible to treat sperm, eggs, and embryos in culture to improve reproductive success, to increase the health state of an embryo, and to prevent disease in the developing child. Human Reproduction: Updates and New Horizons focuses on recent developments and new approaches to study egg and sperm cells and embryo development, as well as addressing the increasing demand for IVF and ART to overcome infertility problems of various kinds that are encountered by an increasing number of couples worldwide. The book includes 10 chapters written by experts in their specific fields to provide informatiTable of ContentsList of Contributors xv 1 Sperm Selection Techniques and their Relevance to ART 1Luke Simon, Monis B. Shamsi, and Douglas T. Carrell 1.1 Introduction 1 1.2 Need of Sperm Selection in ART 2 1.3 Methodology of Sperm Selection 3 1.4 Electrophoretic Sperm Separation 14 1.5 Zeta Test 18 1.6 Microelectrophoresis Sperm Selection 21 1.7 Raman Spectroscopy 24 1.8 Hyaluronic Acid Binding Assay 27 1.9 Future Perspective 30 References 31 2 In Vitro Maturation of Human Oocytes: Current Practices and Future Promises 45Catherine M.H. Combelles 2.1 Introduction 45 2.2 Clinical Indications for IVM 46 2.3 Ovarian Stimulation Approaches for the Retrieval of Immature Oocytes 51 2.4 Maternal Conditions that may Influence IVM 54 2.5 Follicular Origins of Immature Oocytes for IVM 55 2.6 Clinical Safety of IVM 57 2.7 Concluding Remarks towards the Optimization of IVM 58 References 61 3 Molecular Biology of Endometriosis 71Jayasree Sengupta, G. Anupa, Muzaffer Ahmed Bhat, and Debabrata Ghosh 3.1 Introduction 71 3.2 Brief Background 71 3.3 Genetic Basis of Endometriosis 76 3.4 Molecular Mechanisms of Endometriosis 77 3.5 Molecular Etiopathological Basis of Endometriosis: Leads in Genomics Era 83 3.6 Molecular Etiopathological Basis of Endometriosis: Leads in the Post-Genomics Era 99 3.7 Future Targets 113 Acknowledgments 115 Conflicts of Interest 116 References 116 4 Novel Immunological Aspects for the Treatment of Age-induced Ovarian and Testicular Infertility, Other Functional Diseases, and Early and Advanced Cancer Immunotherapy 143Antonin Bukovsky 4.1 Introduction 143 4.2 Ovarian Infertility 145 4.3 Novel In Vitro Proposals for Ovarian Infertility Treatment 163 4.4 Novel In Vivo Proposal for Ovarian and Testicular Infertility Treatment 170 4.5 Systemic Treatment of Other Functional Diseases by Tissue Rejuvenation 174 4.6 Advantages of Local and Systemic Use of Honey Bee Propolis and Cayenne Pepper 175 4.7 The Promise of Pyramid Healing Systems 180 4.8 Raw Shiitake Causes Early Neoplasia Regression and Malignancy Recurrence Prevention 180 4.9 Immune Modulation for the Treatment of an Advanced Cancer 182 4.10 Advanced Ovarian Cancer Regression Case Report 184 4.11 Discussion 187 4.12 Conclusions 192 Abbreviations 193 Competing Interests 193 Author Contribution 193 References 194 5 Mitochondrial Manipulation for Infertility Treatment and Disease Prevention 205Tetsuya Ishii 5.1 Introduction 205 5.2 The Roles of Mitochondria in Fertilization, Embryonic Development, and Disease 206 5.3 The Genetics of Mitochondria and Mitochondrial Diseases 209 5.4 Ooplasmic Transfer to Treat Infertility 210 5.5 Pronuclear Transfer to Achieve Pregnancy 214 5.6 Germinal Vesicle Transfer to Restore the Viability of Oocytes 216 5.7 Mitochondrial Diseases and Prevention of their Inheritance 217 5.8 Mitochondrial Replacement by Transferring Pronuclei and MII Spindle 218 5.9 Discussion 220 Acknowledgments 222 References 223 6 Novel Imaging Techniques to Assess Gametes and Preimplantation Embryos 231Jason E. Swain 6.1 Introduction 231 6.2 Light and Impact on Mammalian Gametes and Embryos 232 6.3 Novel Imaging Approaches for Gametes and Embryos 233 6.4 Conclusion 255 References 256 7 Clinical Application of Methods to Select In Vitro Fertilized Embryos 267Kirstine Kirkegaard, Thomas F. Dyrlund, and Hans Jakob Ingerslev 7.1 Introduction 267 7.2 Morphological Assessment 268 7.3 Genomic and Transcriptomic Analysis 279 7.4 Analysis of Conditioned Culture Medium 285 7.5 Summary 294 References 295 8 New Horizons/Developments in Time-Lapse Morphokinetic Analysis of Mammalian Embryos 313Munevver Serdarogullari, Necati Findikli, and Mustafa Bahcecî 8.1 Introduction 313 8.2 Utilization of Time-Lapse Morphokinetics in Mammalian Embryos: A Historical Perspective 314 8.3 What is TLM? 315 8.4 What are the Benefits of TLM? 316 8.5 Application of TLM in Human ART Practice 318 8.6 The Possible Utilization of TLM Analysis in Aneuploidy Detection 324 8.7 Expected Contributions of TLM Technology in the Future of Mammalian Embryology 327 References 328 9 The Non-Human Primate Model for Early Human Development 339Stuart Meyers and Renee Riejo-Pera 9.1 Introduction 339 9.2 Why Primate Models Are Critical to Understanding Human Development and Subfertility 340 9.3 NHP Model of Assisted Reproductive Technology (ART) 342 9.4 NHP Model of Early Embryo Development 343 9.5 Research Perspective on NHP Embryo Development 345 9.6 Summary 347 References 348 10 Cytoskeletal Functions, Defects, and Dysfunctions Affecting Human Fertilization and Embryo Development 355Heide Schatten and Qing-Yuan Sun 10.1 Introduction 355 10.2 Components of the Cytoskeleton and their Important Functions in Reproductive Biology 356 10.3 The Role of the Cytoskeleton in Oocyte Maturation 360 10.4 Maturation Failures and Oocyte Aging 369 10.5 Fertilization and First Mitosis/Cell Division 371 10.6 Cellular Differentiation/Polarization During Pre-Implantation Embryo Development/Compaction Stage 374 10.7 Perspectives and Future Directions 380 References 381 Index 399

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Book SynopsisTechnology Platforms for 3D Cell Culture: A Users Guide points to the options available to perform 3D culture, shows where such technology is available, explains how it works, and reveals how it can be used by scientists working in their own labs.Table of ContentsList of contributors, vii Preface, xi List of abbreviations, xiv 1 An introduction to the third dimension for routine cell culture, 1Antonio Romo‐Morales and Stefan Przyborski Part I: Aggregate‐based technologies 2 Gravity‐enforced microtissue engineering, 23Randy Strube, Johannes Haugstetter, Markus Furter, Andreia Fernandez, David Fluri and Jens M. Kelm 3 Physiologically relevant spheroid models for three‐dimensionalcell culture, 50Nicole A. Slawny and MaryAnn Labant 4 NanoCulture Plate: A scaffold‐based high‐throughput three‐dimensional cell culture system suitable for live imaging and co‐culture, 74Manabu Itoh, Kazuya Arai, Hiromi Miura and M. Mamunur Rahman 5 Micro‐moulded non‐adhesive hydrogels to form multicellular microtissues – the 3D Petri Dish®, 97Elizabeth Leary, Sean Curran, Michael Susienka, Kali L. Manning, Andrew M. Blakely and Jeffrey R. Morgan 6 Organotypic microtissues on an air‐liquid interface, 123Lars E. Sundstrom, Igor Charvet and Luc Stoppini Part II: Hydrogels 7 Materials and assay systems used for three‐dimensional cell culture, 145Suparna Sanyal and Marshall Kosovsky 8 HyStem®, a customisable hyaluronan‐based hydrogel matrix for 3D cell culture, 173T. I. Zarembinski, B. J. Engel, N. J. Doty, P. E. Constantinou, M. V. Onorato, I. E. Erickson, E. L. S. Fong, M. Martinez, R. L. Milton, B. P. Danysh, N. A. Delk, D. A. Harrington, M. C. Farach‐Carson and D. D. Carson 9 3‐D Life biomimetic hydrogels: A modular system for cell environment design, 197Brigitte M. Angres and Helmut Wurst Part III: Scaffolds 10 Alvetex®, a highly porous polystyrene scaffold for routine three‐dimensional cell culture, 225Antonio Romo‐Morales, Eleanor Knight and Stefan Przyborski 11 CelluSponge™ and Go Matrix as innovative three‐dimensional cell culture platforms, 250Bramasta Nugraha 12 Mimetix® electrospun scaffold: An easy‐to‐use tool for 3D cell culture in drug discovery and regenerative medicine, 284Robert J. McKean and Elena Heister Part IV: 3D bioreactor technologies 13 Quasi Vivo® bioreactor technology, 305J. Malcolm Wilkinson 14 Three‐dimensional cell‐based assays in hollow fibre bioreactors, 327John J. S. Cadwell and William G. Whitford 15 Three‐dimensional engineered tissues for high‐throughput compound screening: Mechanical properties of skin and ageing, 351Michael Conway, Ayla Annac and Tetsuro Wakatsuki 16 Three‐dimensional cell culture in the Rotary Cell Culture System™, 370Stephen S. Navran Glossary, 386 Index, 393

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Book SynopsisA multi-disciplinary look at the current state of knowledge regarding motor control and movementfrom molecular biology to robotics The last two decades have seen a dramatic increase in the number of sophisticated tools and methodologies for exploring motor control and movement. Multi-unit recordings, molecular neurogenetics, computer simulation, and new scientific approaches for studying how muscles and body anatomy transform motor neuron activity into movement have helped revolutionize the field.Neurobiology of Motor Controlbrings together contributions from an interdisciplinary group of experts to provide a review of the current state of knowledge about the initiation and execution of movement, as well as the latest methods and tools for investigating them. The book ranges from the findings of basic scientists studying model organisms such as mollusks andDrosophila, to biomedical researchers investigating vertebrate motor production to neuroengiTable of ContentsList of Contributors xiii About the Cover xvii 1 Introduction 1Ansgar Büschges and Scott L. Hooper References 5 2 Electrophysiological Recording Techniques 7Scott L. Hooper and Joachim Schmidt 2.1 Introduction 7 2.2 Terminology 8 2.3 Intracellular and Patch Clamp Recording 9 2.3.1 Recording Electrodes 9 2.3.2 Current-Clamp:Measuring Transmembrane Potential 12 2.3.3 Voltage Clamp: Measuring Transmembrane Current 15 2.3.3.1 Voltage Clamp with Transmembrane Potential as Reference 15 2.3.3.2 Voltage Clamp with Preparation (Bath) Ground as Reference 16 2.4 Extracellular Recording and Stimulation 17 2.5 A Brief History of Electrophysiological Recording 21 2.6 Concepts Important to Understanding Neuron Recording Techniques 27 2.6.1 Membrane Properties 27 2.6.2 Intracellular Recording 29 2.6.3 Extracellular Recording 32 2.6.3.1 Intracellular Action Potential Shape 33 2.6.3.2 Axon Embedded in Uniform, Infinite Volume Conductor 33 2.6.3.3 Variations in Extracellular Action Potential Shape Induced by Non-Uniform, Non-Infinite Volume Conductors 42 2.6.3.4 Bipolar Recording 44 2.6.3.5 Extracellular Action Potential Summary 46 Acknowledgements 47 References 47 3 Multi-Unit Recording 55Arthur Leblois and Christophe Pouzat 3.1 Introduction 55 3.2 Chapter Organization and Expository Choices 56 3.3 Hardware 57 3.4 Spike Sorting Methods 60 Endnotes 69 References 70 4 The “New Math” of Neuroscience: Genetic Tools for Accessing and Electively Manipulating Neurons 75Andreas Schoofs,Michael J. Pankratz, and Martyn Goulding 4.1 Introduction 75 4.2 Restricting Gene Expression to Specific Neurons 76 4.2.1 Promoter Bashing, Enhancer Trapping: Binary Systems for Targeted Gene Expression 77 4.2.2 Intersectional Strategies 81 4.2.3 Temporally Inducible Systems 82 4.3 Tracing, Manipulating, and Monitoring Neurons 84 4.3.1 Tracing Neuronal Projections and Connections with Fluorescent Reporters 84 4.3.2 Viral Tracers for Mapping Neural Connections 85 4.3.3 Manipulating Neuronal Function 87 4.3.4 Monitoring Neuronal Activity 90 4.4 Case Studies 92 4.5 Future Perspective 98 References 98 5 Computer Simulation—Power and Peril 107Astrid A. Prinz and Scott L. Hooper 5.1 Introduction 107 5.2 Why Model? 107 5.3 Modeling Approaches 110 5.4 Model Optimization and Validation 118 5.5 Beyond Purely ComputationalModels 120 5.6 Fundamental Concepts and Frequently Used Models in Motor Control 121 5.6.1 How to Predict the Future 121 5.6.2 Neuron Models 123 5.6.3 Synapse Models 127 5.6.4 Muscle Models 128 5.6.5 Biomechanical Models 128 5.7 The Future 129 Acknowledgements 130 References 130 6 Evolution of Motor Systems 135Paul S. Katz and Melina E. Hale 6.1 Introduction 135 6.2 Phylogenetics 136 6.3 Homology and Homoplasy 138 6.4 Levels of Biological Organization 139 6.5 Homologous Neurons 139 6.6 Deep Homology 142 6.7 Homoplasy 145 6.8 Convergence in Central Pattern Generators 150 6.9 Evolutionary Loss 152 6.10 Evolution of Novel Motor Behaviors 152 6.11 Three Scenarios for the Evolution of Novel Behavior 154 6.11.1 Generalist Neural Circuitry 154 6.11.2 Rewired Circuitry 157 6.11.3 Functional Rewiring with Neuromodulation 159 6.12 Motor System Evolvability 161 6.13 Neuron Duplication and Parcellation 162 6.14 Divergence of Neural Circuitry 164 6.15 Summary and Conclusions 165 Acknowledgements 165 References 165 7 Motor Pattern Selection 177 7.1 Introduction to Motor Pattern Selection in Vertebrates and Invertebrates 178Hans-Joachim Pflüger and Sten Grillner References 179 7.2 Selection of Action—A Vertebrate Perspective 181 Sten Grillner and Brita Robertson 7.2.1 Introduction 181 7.2.2 Control of Locomotory Outputs 182 7.2.3 The Organization and Role of the Basal Ganglia 184 7.2.4 ConceptualModel of the Organization Underlying Selection of Behavior 187 7.2.5 The Organization of Motor Control From Cortex (Pallium in Lower Vertebrates) 189 7.2.6 The Relative Role of Different Forebrain Structures for Selection of Behavior 189 Acknowledgements 190 References 191 7.3 Motor Pattern Selection and Initiation in Invertebrates with an Emphasis on Insects 195Hans-Joachim Pflüger 7.3.1 Introduction 195 7.3.2 Organization Principles of Relevant Sensory Systems 196 7.3.3 Movement-Generating Neural Networks in Invertebrates 196 7.3.4 Motor Pattern Selection in Invertebrates 197 7.3.4.1 Probabilistic “Selection”: Intrinsically Variable CPGs in Mollusk Feeding 197 7.3.4.2 Selection via CPG Coordination 198 7.3.4.3 Selection by Neuromodulators or Neurohormones 198 7.3.4.4 Selection by Command Neurons Not in the Brain 201 7.3.4.5 The Brain is Crucial in the Motor Selection Process 202 7.3.5 Two Case Studies 207 7.3.6 Concluding Remarks on Invertebrates 213 7.3.7 Are There Common Themes between Motor Pattern Selection in Invertebrates and Vertebrates? 213 References 216 8 Neural Networks for the Generation of RhythmicMotor Behaviors 225Ronald M. Harris-Warrick and Jan-Marino Ramirez 8.1 Introduction 225 8.2 Concept of the Central Pattern Generator 225 8.3 Overall Organization of Rhythmic Motor Networks 227 8.4 Identification of CPG Neurons and Synapses: The “Wiring Diagram” 234 8.5 Cellular PropertiesThat Shape Network Output: Building Blocks for Network Operation 238 8.6 Combined Neural Mechanisms for Rhythmogenesis 240 8.7 Ionic Currents Shaping CPG Network Neuron Intrinsic Firing Properties 241 8.7.1 Role of Outward Currents in Regulating Pacemaker and Network Activity 241 8.7.2 Role of Inward Currents in the Generation of Pacemaker and Network Activity 243 8.7.3 Interaction of Inward and Outward Currents in the Generation of Pacemaker Activity 245 8.7.4 Homeostatic Plasticity and the Balance between Different Ion Channel Types 245 8.7.5 Rapid Changes in Extracellular Ion Concentrations during Rhythmic Network Function 246 8.8 Role of Network Synaptic Properties in Organizing Rhythmic Behaviors 246 8.9 Variable Output from Motor Networks 249 8.10 Conclusions 252 Acknowledgements 253 References 253 9 Sensory Feedback in the Control of Posture and Locomotion 263Donald H. Edwards and Boris I. Prilutsky 9.1 Introduction 263 9.2 History and Background of Feedback Control 264 9.3 Classical Control Theory 264 9.4 Nervous System Implementation in the Control of Posture and Limb Movements 267 9.5 Organization and Function in Arthropods 274 9.5.1 Locomotory System Gross Anatomy 274 9.5.2 Proprioceptors and Exteroceptors 274 9.5.3 Arthropod Nervous Systems 275 9.5.4 Postures and Movement Commands 275 9.5.5 Sensory Feedback in the Maintenance of Posture 275 9.5.6 Sensory Feedback in Movement andWalking 276 9.6 Organization and Function in Vertebrates 282 9.6.1 Sensory Feedback in the Maintenance of Posture 282 9.6.2 Sensory Feedback and its Integration with Motor Commands in Movement 285 9.7 Conclusions 293 Acknowledgements 294 Endnote 294 References 294 10 Coordination of Rhythmic Movements 305Jean-Patrick Le Gal, Réjean Dubuc, and Carmen Smarandache-Wellmann 10.1 Introduction 305 10.2 Overview of Invertebrate CPGs 306 10.2.1 Stomatogastric Nervous System: Feeding Circuits in Decapod Crustacea 308 10.2.2 Leech Locomotion 315 10.2.3 Crayfish Swimmeret System 317 10.2.4 Insect Locomotion 319 10.2.5 MultipleMechanisms Mediate Coordination in Invertebrate Systems 321 10.3 Overview of Vertebrate CPGs 321 10.3.1 General Characteristic of Vertebrate CPGs 322 10.3.1.1 Locomotor CPGs 322 10.3.1.2 Respiratory CPGs 323 10.3.1.3 Feeding CPGs 324 10.3.2 CPG Interactions within One Motor Function 324 10.3.2.1 Unit Generators in Limbless Swimming Vertebrates 324 10.3.2.2 Unit Generators in Mammalian Limbs 325 10.3.3 CPGs Interactions for Different Motor Functions 327 10.3.3.1 Coordination of Respiration and Swallowing 327 10.3.3.2 Coordination of Locomotion and Respiration 328 10.4 Conclusion 331 References 332 11 Prehensile Movements 341Till Bockemühl 11.1 Introduction: Prehension as Goal-Directed Behavior 341 11.2 The Redundancy Problem in Motor Control 343 11.3 Redundancy Occurs on Multiple Levels of the Motor System 346 11.4 Overcoming the Redundancy Problem 349 11.4.1 InvariantMovement Features 350 11.4.2 Increasing the Number of Task Conditions 352 11.4.3 Reducing the Number of DOFs 357 References 361 12 Muscle, Biomechanics, and Implications for Neural Control 365Lena H. Ting and Hillel J. Chiel 12.1 Introduction 365 12.2 Behavioral Context Determines How Motorneuron Activity Is Transformed into Muscle Force and Power 366 12.2.1 The Neuromuscular Transform Is History-Dependent 367 12.2.1.1 Motorneurons Are Subject to Neuromodulation and History-Dependence That Can Significantly Alter Their Output 368 12.2.1.2 Presynaptic Neurotransmitter Release at the Neuromuscular Junction Is History-Dependent 368 12.2.1.3 Post-SynapticMuscle Excitation Is History-Dependent and Subject to Modulation 368 12.2.1.4 Contractile Dynamics of Cross-Bridge Interactions Are History Dependent 369 12.2.1.5 The Molecular Motors of Muscles Give Rise to the Functional and History-Dependent Properties of Muscle Force Generation 369 12.2.2 Muscle Power Depends on Behavioral Context 371 12.2.3 Muscle Specialization Reflects Behavioral Repertoire 373 12.3 Organismal Structures Transform Muscle Force into Behavior 374 12.3.1 Effects of Muscle Force Depend on the Properties of the Body and the Environment 375 12.3.1.1 The Relative Importance of Inertial, Viscous, and Spring-Like Forces Affect the Role of Muscle Force 375 12.3.1.2 Muscle Function Depends on Behavioral Context and Environmental Forces 377 12.3.1.3 Biomechanical Affordances and Constraints of Body Structures Affect Muscle Functions 377 12.3.2 Muscles Are Multi-Functional 381 12.3.3 Specialization of Biomechanical Structures Reflect Behavioral Repertoire 385 12.4 Biomechanics Defines Meaningful Patterns of Neural Activity 387 12.4.1 Organismal Structures Are Multi-Functional 389 12.4.2 Many Functionally-Equivalent Solutions Exist for Sensorimotor Tasks 392 12.4.3 Structure and Variability in Motor Patterns Reflect Biomechanics 394 12.4.4 Specialization of Neuromechanical Systems Reflect Behavioral Repertoire 399 12.5 Conclusions 401 Acknowledgements 402 References 402 13 Plasticity and Learning in Motor Control Networks 417John Simmers and Keith T. Sillar 13.1 Introduction 417 13.2 Homeostatic Motor Network Assembly 418 13.3 Short-Term Motor Learning Conferred by Sodium Pumps 420 13.3.1 Swimming CPG Network Plasticity in Xenopus Frog Tadpoles 420 13.3.2 Comparative Aspects of Na+ Pump Contribution to Neural Network Function 425 13.4 CPG Network Plasticity and Motor Learning Conferred by Operant Conditioning 426 13.5 Discussion and Conclusions 432 References 436 14 Bio-inspired Robot Locomotion 443Thomas Buschmann and Barry Trimmer 14.1 Introduction 443 14.2 Mechanical Engineering Background and a Biological Example 444 14.3 Legged Robots with Skeletal Structures 446 14.3.1 Mechanism Design, Sensing, and Actuation 446 14.3.2 Basic Dynamics of Legged Locomotion 447 14.3.3 Trajectory-OrientedWalking Control 448 14.3.4 Limit CycleWalkers 450 14.3.5 CPG-Based Control and Step-Phase Control 451 14.4 Soft Robots 452 14.4.1 Limitations and Advantages of Soft Materials 452 14.4.2 The Challenges 453 14.4.2.1 Actuators 453 14.4.2.2 Sensors 455 14.4.2.3 Control of Soft Robots 456 14.4.3 Bioinspired Locomotion in Soft Robots 459 14.5 Conclusion and Outlook 463 References 463 Index 473

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Book SynopsisProfessor Gerald Esch has already published two books in what is becoming an informal series of essays exploring the way that discoveries about the biology of parasites have influenced ecological and evolutionary theories over a career that has spanned nearly 50 years. This book will be the third set of essays and will focus on key moments of discovery and explore how these achievements were due to collaboration, mentoring, and community building within the field of ecological parasitology. The book will not only describe case studies, pure science and biology but also act as a career guide for early-career ecologists emphasizing the importance of collaboration in the advancement of science.Table of ContentsPreface viii Acknowledgments xi The Players xii 1 The Beginning 1 2 The End of the Beginning 18 3 Gull Lake and the W.K. Kellogg Biological Station 28 4 Gull Lake and the Connection with the Savannah River Ecology Laboratory 40 5 Development of Some Conceptual Notions 52 6 The Pond: Part I 62 7 The Pond: Part II 79 8 The Big Lake 92 9 The Strigeids 104 10 Some Small Streams and Small Ponds 112 11 Red Sore Disease 121 12 The End, Almost 131 13 The Catastrophic Collapse of the Larval Trematode Component Community in Charlie’s Pond (North Carolina) 144 14 An Epilogue: What’s Involved with Graduate School? 155

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Book SynopsisThis book combines recent information and discoveries in the field of human molecular biology and human molecular evolution. It provides an interdisciplinary approach drawing together data from various diverse disciplines to address both the more classical anthropological content and the current more contemporary molecular focus of courses. Chapters include a history of human evolutionary genetics; the human genome structure and function; population structure and variability; gene and genomic dynamics; culture; health and disease; bioethics; future.Table of ContentsPreface, ix 1 The history of human evolutionary genetics, 1 World views, 1 Science and philosophy, 1 The biology of mankind: anatomy and physiology in a historical context (up to the 16th century), 3 Beginnings of the present scientific model, 4 Biological evolution and genetic foundations: the brilliant quartet, 5 Nineteenth century: cytology, embryology, and reproduction, 9 Twentieth century, the century of genetics, 10 The synthetic theory of evolution, 11 Bacterial and molecular genetics, 11 Parallel developments: paleoanthropology, 12 Technical and methodological developments, 13 Conclusions, 14 Review questions and exercises, 14 References, 14 2 The human genome: structure, function, and variation, 16 Science, politics, and ethics, 16 Structural aspects, 17 Normal and abnormal phenotype distribution, 19 Function, 21 Sex chromosomes, 23 Paleogenomics, 25 Variability: mtDNA, 28 Nuclear variability, 28 Exomes and proteomes, 30 Selection or drift? History, 31 Selection or drift? Methods, 32 Selection or drift? Analyses, 34 Nervous system and culture, 37 Conclusions, 37 Review questions and exercises, 37 References, 38 3 Population structure, 42 DNA-based marker systems, 42 SNPs, STRs, and Indels as DNA markers, 45 Population genetic tools for analyzing population structure, 49 Forces affecting population dynamics, structure, and evolution, 55 Applications of population genetics, 60 From populations to races and species, 62 Review questions and exercises, 64 References, 65 4 Genetic variability, 68 On the nature of variability, 68 Mechanisms responsible for generating genetic variability, 69 Randomness of mutations, 71 Inheritance and environment, 75 Selection works on the phenotype, 76 The impact of selection, 77 Cultural expressions as markers of ancestry, 79 Congruency among marker systems, 80 Does junk DNA exist?, 80 How genetic diversity is studied?, 82 Epigenetic diversity, 84 Review questions and exercises, 85 References, 86 5 Gene and genomic dynamics, 87 Molecular evidence for punctuated equilibrium and gradualism, 88 Next-generation sequencing, 90 Genetic variation, 92 Variation, population structure, and effective population size, 94 Recombination and its effect on variation, 94 Linkage equilibrium and disequilibrium, 95 Forces leading to linkage disequilibrium, 98 Linkage disequilibrium and SNP haplotypes, 99 Linkage disequilibrium in humans, 100 Genome structural variations, 102 CNV classifications and formation mechanisms, 102 Methods used to detect CNVs, 103 CNVs associated with human phenotypes, 105 CNVs and evolution, 106 CNV in primates, 107 Chromosome rearrangements and selfish genetic elements, 108 Transposable elements, 109 Population dynamics of transposable elements, 110 Transposons in human evolution, 111 Selfish genetic elements in evolution, 113 Genome-wide association studies, 113 Concerns over the effective use of GWAS, 117 Conclusions, 117 Review questions and exercises, 118 References, 119 6 Human origins and early diasporas, 124 The on switch to humanity, 124 Early hominins, 128 Emerging themes and variations in hominin evolution, 130 The first hominin migrants, 134 The emergence of modern humans, 135 The Saharan pump, 135 Early migrations, 136 Neanderthals prevailed, 136 Review questions and exercises, 138 References, 139 7 Culture, 141 Concept, 141 Origin and development, 141 Factors that could condition cultural evolution, 142 Biology–culture interaction, 145 Language, 146 Domestication, 148 Art, 151 Free will, morality, and religion, 153 Conclusions, 155 Review questions and exercises, 155 References, 155 8 Health and disease, 158 Hopes and reality, 158 Concept of health and methods of study, 158 Darwinian medicine, 160 Parent–offspring conflict, 161 Pathogen history, 161 Evolution of infectious diseases, 162 DNA damage, mutagenesis, and teratogenesis, 163 What is better, more or less gene product?, 165 Genetic manipulation of animals to study health and disease, 166 Reproductive fitness and health, 167 Consanguinity, 168 Violence, 168 Cancer, 171 Degenerative diseases, 172 Ecogenetics, pharmacogenetics, and pharmacogenomics, 174 Detection of genetic diseases, 176 Genetic counseling, 176 Treatment, 178 Conclusions, 179 Review questions and exercises, 179 References, 180 9 Recent human evolution: an integrative approach, 182 Recent human evolution, 182 Out of Africa, 184 Back to Africa, 188 Beyond Arabia, 190 The Asian agricultural revolution and the Austronesian expansion, 194 Evidence from plants and animals, 198 Contacts between South America and Polynesia, 200 Review questions and exercises, 202 References, 203 10 Bioethics: consequences and implications of genetic technology on human evolution, 206 Social and biological evolution, 207 Overview of ethics and philosophical influences on Western ethics, 207 Evolution of ethics and morality, 212 The history and beginning of modern-day bioethics, 213 Reproductive technologies and the new eugenics: unnatural selection?, 216 Enhancement through IVF, PGD, and CRISPR, 219 Ethical issues associated with medical technology, 220 Gene therapy, 220 Stem cell therapy, 222 Biosimilars, 222 Genetic privacy, 222 Genetic testing, 223 DNA profiling, 224 Conclusions, 227 Review questions and exercises, 227 References, 228 11 Future of human evolution, 230 Gene and culture coevolution, 231 Life expectancy and population growth: past, present, and future, 231 Mutation rates and future evolution, 232 The evolution of new genes, 234 Climate change, 234 Diet, 235 Sex selection, 236 Artificial selection, 236 Transhumanism and artificial intelligence, 237 Conclusions, 238 Review questions and exercises, 239 References, 239 Appendix, 241 Index, 249

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Book SynopsisShort, compelling, but mostly thought-provoking essysthatencompass many of the central issues shaping ecology and conservation in the changing world Collected essays from one of the best known ecologists and conservationists in the world Includes all issues at the cutting edge of the interface between ecology and conservation Attractive to a broad audience of ecologists, conservationists, natural resource managers, policy makers, and naturalists Table of ContentsPreamble: Why this book? Acknowledgments xiii Essay 1 How did I get here? 1 Essay 2 Found! The survivor in the swamps (2005) 4 Essay 3 In defense of footnotes (2014) 7 Part I: Change, the challenge Chapter 1 Conservation and change 13 Chapter 2 A digression on paradigms 18 Essay 4 The power of paradigms (2014) 23 Essay 5 Patterns, paradigms, and preconceptions (2013) 29 Essay 6 Fat times, lean times, and competition among predators (1993) 33 Chapter 3 Equilibrium, stability, and change 39 Essay 7 From our southern correspondent(s) (2011) 44 Essay 8 Boom and bust: lessons from the outback (2014) 51 Chapter 4 A digression on disturbance 57 Essay 9 Oil, oil, everywhere…(2010) 60 Part II: The forces of change Chapter 5 Climate change and sea-level rise 71 Essay 10 Polar bears, golden toads, and conservation futures (2008) 76 Chapter 6 Land-use change 79 Essay 11 Will land-use change erode our conservation gains? (2007) 85 Essay 12 Landscape ecology: the science and the action (1999) 88 Chapter 7 Distributional changes: invasive species 91 Chapter 8 Societal, cultural, and political change 96 Essay 13 Wildlife, people, and water: who wins? (2012) 100 Chapter 9 Population growth 105 Chapter 10 Linkages among changes 109 Part III: Conservation conundrums Chapter 11 Variation and history 117 Essay 14 The eclipse of history? (2008) 122 Essay 15 From our southern correspondent(s): which history? (2013) 125 Chapter 12 A digression on baselines and targets 129 Essay 16 Shooting at a moving target (2011) 133 Chapter 13 Ecological thresholds 138 Essay 17 Tipping points in the balance of nature (2010) 144 Chapter 14 Ecological resilience 149 Chapter 15 Dealing with novelty 154 Essay 18 Black swans and outliers (2012) 160 Essay 19 Moving outside the box (2009) 164 Chapter 16 Uncertainty: a boon or a bane? 167 Essay 20 Taking risks with the environment (2012) 172 Essay 21 Uncertainty and the relevance of ecology (2008) 176 Chapter 17 Prioritization and triage 180 Essay 22 Talking about triage in conservation (2015) 188 Chapter 18 Protected areas: where the wild things are 191 Essay 23 Build it and they will come (2013) 197 Essay 24 The dangers of black-and-white conservation (2007) 203 Chapter 19 Ecosystem services and the value of nature 206 Essay 25 What’s so new about ecosystem services? (2007) 211 Part IV: Doing conservation Chapter 20 What is it we are trying to conserve? 217 Essay 26 Be careful what you wish for (2014) 222 Essay 27 Concluding comments: Are bird communities real? (1980) 227 Essay 28 A metaphor meets an abstraction: the issue of "Healthy Ecosystems" (2015) 230 Chapter 21 Numbers, numbers, numbers 237 Essay 29 Is "monitoring" a dirty word? (2009) 241 Essay 30 The place of long-term studies in ornithology (1984) 244 Essay 31 What use is small data in a big data world? (2013) 247 Chapter 22 A digression on words 251 Essay 32 Word processing versus writing (1983, 2011) 254 Chapter 23 Debates in ecology and conservation 257 Essay 33 On skepticism and criticism in ornithology (1981) 264 Essay 34 The demise of wildness? (2007) 267 Chapter 24 What lies behind the debates? Philosophy, values, and ethics 270 Chapter 25 A digression on advocacy in conservation 275 Essay 35 Scientific responsibility and responsible ecology (1997) 280 Part V: Concluding comments Chapter 26 Whither ecology and conservation in a changing world? 287 Essay 36 "It was the best of times, it was the worst of times…" (2009) 292 Essay 37 Being green isn’t easy (2010) 295 Essay 38 Stewart Udall and the future of conservation (2010) 298 References 301 Scientific names of species mentioned in the text 319 Index 323

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Book SynopsisThe third edition of this best-selling book continues to offer a user-friendly, step-by-step introduction to all the key processes involved in bringing a drug to the market, including the performance of pre-clinical studies, the conduct of human clinical trials, regulatory controls, and even the manufacturing processes for pharmaceutical products. Concise and easy to read, Drugs: From Discovery to Approval, Third Edition quickly introduces basic concepts, then moves on to discuss target selection and the drug discovery process for both small and large molecular drugs. The third edition incorporates the latest developments and updates in the pharmaceutical community, provides more comprehensive coverage of topics, and includes more materials and case studies suited to college and university use. Biotechnology is a dynamic field with changes across R&D, clinical trials, manufacturing and regulatory processes, and the third edition of the text provides timely updates for thoTable of ContentsPreface xv 1 Introduction 1 1.1 Aim of this Book 1 1.2 An Overview of the Drug Discovery to Approval Process 2 1.3 The Pharmaceutical Industry 6 1.4 Economics of Drug Discovery and Development 11 1.5 Trends in Drug Discovery and Development 13 1.6 Case Study #1.1 15 1.7 Case Study #1.2 17 1.8 Summary of Important Points 20 1.9 Review Questions 20 1.10 Brief Answers and Explanations 21 1.11 Further Reading 22 2 Drug Discovery: Targets and Receptors 23 2.1 Drug Discovery Processes 23 2.2 Medical Needs 24 2.3 Target Identification 26content 2.4 Target Validation 33 2.5 Drug Interactions with Targets or Receptors 36 2.6 Enzymes 40 2.7 Receptors and Signal Transduction 42 2.8 Assay Development 52 2.9 Case Study #2.1 52 2.10 Case Study #2.2 53 2.11 Summary of Important Points 57 2.12 Review Questions 57 2.13 Brief Answers and Explanations 58 2.14 Further Reading 58 3 Drug Discovery: Small Molecule Drugs 61 3.1 Introduction 61 3.2 Irrational Approach 62 3.3 Rational Approach 67 3.4 Antisense Approach 85 3.5 RNA Interference Approach 88 3.6 Chiral Drugs 91 3.7 Closing Remarks 92 3.8 Case Study #3.1 94 3.9 Case Study #3.2 96 3.10 Summary of Important Points 98 3.11 Review Questions 99 3.12 Brief Answers and Explanations 99 3.13 Further Reading 100 4 Drug Discovery: Large Molecule Drugs 103 4.1 Introduction 103 4.2 Vaccines 105 4.3 Antibodies 117 4.4 Cytokines 128 4.5 Hormones 134 4.6 Gene Therapy 137 4.7 Stem Cells and Cell Therapy 139 4.8 Case Study #4.1 141 4.9 Case Study #4.2 144 4.10 Summary of Important Points 146 4.11 Review Questions 147 4.12 Brief Answers and Explanations 148 4.13 Further Reading 148 5 Drug Development and Preclinical Studies 151 5.1 Introduction 151 5.2 Pharmacodynamics 154 5.3 Pharmacokinetics 158 5.4 Toxicology 168 5.5 Animal Tests, In Vitro Assays, and In Silico Methods 172 5.6 Formulations and Delivery Systems 175 5.7 Nanotechnology 183 5.8 Case Study #5.1 184 5.9 Case Study #5.2 185 5.10 Summary of Important Points 187 5.11 Review Questions 188 5.12 Brief Answers and Explanations 188 5.13 Further Reading 189 6 Clinical Trials 191 6.1 Definition of Clinical Trial 191 6.2 Ethical Considerations 192 6.3 Clinical Trials 195 6.4 Regulatory Requirements for Clinical Trials 204 6.5 Clinical Data Management 215 6.6 Role of Regulatory Authorities 218 6.7 Gene Therapy Clinical Trial 218 6.8 Adaptive Clinical Trial 220 6.9 Meta-Analysis 221 6.10 Case Study #6.1 222 6.11 Case Study #6.2 226 6.12 Summary of Important Points 227 6.13 Review Questions 228 6.14 Brief Answers and Explanations 228 6.15 Further Reading 229 7 Regulatory Authorities 231 7.1 Role of Regulatory Authorities 231 7.2 US Food and Drug Administration 233 7.3 European Medicines Agency 236 7.4 Japan’s Pharmaceuticals and Medical Devices Agency (PMDA) 238 7.5 China Food and Drug Administration 240 7.6 India’s Central Drugs Standard Control Organization 240 7.7 Australia’s Therapeutic Goods Administration 241 7.8 Canada’s Health Canada 243 7.9 Other Regulatory Authorities 243 7.10 Authorities other than Drug Regulatory Agencies 243 7.11 International Conference on Harmonization 244 7.12 World Health Organization 245 7.13 Pharmaceutical Inspection Cooperation Scheme 246 7.14 Case Study # 7.1 246 7.15 Case Study # 7.2 249 7.16 Summary of Important Points 250 7.17 Review Questions 251 7.18 Brief Answers and Explanations 251 7.19 Further Reading 252 8 Regulatory Applications 253 8.1 Introduction 253 8.2 United States 254 8.3 European Union 272 8.4 Japan 280 8.5 China 282 8.6 India 287 8.7 Australia 287 8.8 Canada 287 8.9 Case Study #8.1 290 8.10 Case Study #8.2 292 8.11 Summary of Important Points 294 8.12 Review Questions 299 8.13 Brief Answers and Explanations 299 8.14 Further Reading 300 9 Good Manufacturing Practice: Regulatory Requirements 301 9.1 Introduction 301 9.2 United States 302 9.3 Europe 308 9.4 International Conference on Harmonization (ICH) 309 9.5 Pharmaceutical Inspection Cooperation Scheme (PIC/S) 311 9.6 Selected Core Elements of GMP 312 9.7 Selected GMP Systems 335 9.8 New cGMP Initiatives 350 9.9 Case Study #9.1 352 9.10 Case Study #9.2 358 9.11 Summary of Important Points 362 9.12 Review Questions 363 9.13 Brief Answers and Explanations 363 9.14 Further Reading 364 10 Good Manufacturing Practice: Drug Manufacturing 367 10.1 Introduction 367 10.2 GMP Manufacturing 371 10.3 GMP Inspection 372 10.4 Manufacture of Small Molecule APIs (Chemical Synthesis Methods) 379 10.5 Manufacture of Large Molecule APIs (Recombinant DNA Methods) 385 10.6 Finished Dosage Forms 394 10.7 Product Quality Review 398 10.8 Manufacturing Variations 399 10.9 Case Study #10.1 400 10.10 Case Study #10.2 404 10.11 Summary of Important Points 407 10.12 Review Questions 408 10.13 Brief Answers and Explanations 408 10.14 Further Reading 408 11 Future Perspectives 411 11.1 Past Advances and Future Challenges 411 11.2 Small Molecule Pharmaceutical Drugs 412 11.3 Large Molecule Biopharmaceutical Drugs 414 11.4 Traditional Medicine 414 11.5 Personalized Medicine 419 11.6 Gene Therapy 420 11.7 Cloning and Stem Cells 420 11.8 Old Age Diseases and Aging 423 11.9 Lifestyle Drugs 423 11.10 Performance-Enhancing Drugs 428 11.11 Chemical and Biological Terrorism 428 11.12 Transgenic Animals and Plants 432 11.13 Antibiotics Drug Resistance 433 11.14 Regulatory Issues 435 11.15 Intellectual Property Rights and Marketing Exclusivities 437 11.16 Bioethics 440 11.17 Concluding Remarks 442 11.18 Case Study #11.1 445 11.19 Case Study #11.2 447 11.20 Further Reading 449 Appendix 1 History of Drug Discovery and Development 451 A1.1 Early History of Medicine 451 A1.2 Drug Discovery and Development in the Middle Ages 453 A1.3 Foundation of Current Drug Discovery and Development 454 A1.4 Beginnings of Modern Pharmaceutical Industry 454 A1.5 Evolution of Drug Products 455 A1.6 Further Reading 456 Appendix 2 Cells, Nucleic Acids, Genes, and Proteins 457 A2.1 Cells 457 A2.2 Nucleic Acids 460 A2.3 Genes and Proteins 462 A2.4 Further Reading 468 Appendix 3 Selected Drugs and Their Mechanisms Of Action 469 Appendix 4 A DHFR Plasmid Vector 481 Appendix 5 Vaccine Production Methods 483 Appendix 6 Vaccines Approved By FDA 485 Appendix 7 Pharmacology/Toxicology Review Format 489 Appendix 8 Examples of General Biomarkers 495 Appendix 9 Toxicity Grading 499 Appendix 10 Health Systems in Selected Countries 505 Acronyms 509 Glossary 515 Index 519

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Book SynopsisFor nearly a decade, scientists, educators and policy makers have issued a call to college biology professors to transform undergraduate life sciences education. As a gateway science for many undergraduate students, biology courses are crucial to addressing many of the challenges we face, such as climate change, sustainable food supply and fresh water and emerging public health issues. While canned laboratories and cook-book approaches to college science education do teach students to operate equipment, make accurate measurements and work well with numbers, they do not teach students how to take a scientific approach to an area of interest about the natural world. Science is more than just techniques, measurements and facts; science is critical thinking and interpretation, which are essential to scientific research. Discovery-Based Learning in the Life Sciences presents a different way of organizing and developing biology teaching laboratories, to promote both dTable of ContentsAcknowledgments xiii 1 The New Life Sciences 1 The Challenges We Face in Teaching the New Biology 2 Visions of Change 5 Need for Structural Change 6 Conceptual Organization of Introductory Biology 8 Learning and Mastering 10 Further Reading 13 2 Changing Goals and Outcomes in Introductory Life Science Course Laboratories 15 The Introductory Science Course Experience That We Have 15 How Science is Actually Done 15 Challenges to Successful Science Teaching 18 Pre-College Preparation Disparities 18 Avoiding the Textbook as the Organizer of Your Course 18 Weaning Away from Content-Heavy Lectures 20 The Elements of Successful Science Learning 21 Student Autonomy 21 Relevance 21 Student Investment 21 Sustained Engagement 22 Understanding Through Teaching 23 Two Re-organizational Schemes for an Introductory Biology Course 23 Re-organizational Scheme 1: Putting the Classroom First 23 Re-organizational Scheme 2: Putting the Laboratory First 26 Example Topic: Biological Arms Races (Conceptual Areas: Structure and Function, Information Storage and Transfer, Evolution, Systems) 27 What Do These Scenarios have in Common? What is Going on? 28 Classroom Support for the Laboratory Work 29 Summary 30 Further Reading 31 3 Incorporating Discovery-Based Laboratory Experiences at the Introductory Level 33 The Reality of Introductory Biology Laboratories 37 Converting the Survey Approach to Biology Techniques into Discovery-Based Experiences that Emphasize Concepts 38 Module I: What are the Effects of Different Aspects of Climate Change or Other Anthropogenic Changes on Plant Primary Productivity? 41 Weeks 1 and 2: Observing Plant Cells and Measuring Plant Primary Productivity –Two Laboratory Weeks 42 Simple Assays of Photosynthesis/Primary Productivity 44 Week 3: Designing Independent Experiments to Explore the Effects of Climate Change on Primary Productivity in Green Plants 46 Week 4 and 5: Student-designed Discovery-based Experiments and Data Analysis 46 Week 6: Field Observations of Plant Communities in Areas Exposed to Fertilizer Run-off or Other Human Activity such as Road Salt Application in the Winter 47 Assessments 47 Module 2: How Does Antibiotic Resistance Develop? 48 Week 1: Observing cell division; Measuring bacterial Growth and Introduction to Sterile Techniques 49 Week 2: Plate Assay or Turbidity Measurements to Examine Antibiotic Resistance, Design of Selection Experiments 50 Weeks 3–5: Independent Experiments Examining Antibiotic Resistance 52 Week 6–7: Continued Experiments if Time Permits 54 Assessments 54 Module 3: Self-Discovery Explorations of Human Diseases Caused by Single Nucleotide Polymorphisms 54 Week 1: Student Investigation Specific Aims and Goals –Use of Bioinformatics to Explore Genetic Diseases Associated with SNPs 56 Weeks 2 and 3: SNP Analysis for TASR 38 or cdk3 Using Polymerase Chain Reaction 58 Assessment Ideas 58 Summary 60 Further Reading 60 4 The Constraints and Realities of Discovery-Based Laboratories 63 Instructor Expertise 63 Time 65 Preparation Time 66 Student Time In and Out of the Laboratory 66 Time for Class and Laboratory –the Schedule of Classes 68 Time of Academic Year 69 The Physical Arrangement of the Teaching Laboratory 70 Class Size 71 Number of Laboratory Sections 72 Resources for Discovery-Based Laboratories 72 Organisms 73 Equipment 76 Safety Considerations for Independent Projects 76 Transportation for Field-Based Studies 76 Preparatory Staff 77 Student Interns/TAs 78 Summary 78 Further Reading 78 5 A Model Introductory Biology Course 81 Instructor Group Meetings 81 Shared Course Materials 82 Flexible Design Allows for the Introduction of New Modules 82 Overall Conceptual Organization 83 Laboratory Modules for the First Edition of “Introduction to Biological Investigation” 84 Module 1: Caenorhabditis elegans: From Genes to Behavior 84 Module 2: Cyanogenic Clover: Genetic Variation and Natural Selection 89 Module 3: Biodiversity and Soil Microbial Ecology 93 Additional Laboratory Modules 95 Module 4: Personal Genomics: Understanding Individual Genetic Variation 96 Module 5: Behavioral Variations Within a Species 97 Assessment of Learning of Core Concepts and Skills 99 Student Evaluation of the Course 99 Faculty Concerns and Discomforts 100 Further Reading 101 6 Two Model Scenarios for an Intermediate-Level Life Science Course 103 Model 1: Exploration of Gerontogenes and Behavior 105 Assessment of Skills and Student Learning 107 Model 2: How do Common Lawn Chemicals Affect the Behavior and the Nervous System of C. elegans? 107 Summary of the Format 110 Assessment of Student Learning 110 Goal 1: Achieve a Solid Foundation in the Experimental Approaches to a Variety of Current Research Questions in Neuroscience and Behavior 111 Goal 2: Achieve a Sophisticated Ability to Read and Interpret the Primary Experimental Literature 111 Goal 3: Formulate a Hypothesis, Design and Conduct a Multilevel Experimental Project Over SeveralWeeks to Discover New Information About the Relationship Between Genes and Behavior 111 Goal 4: Perform and Understand Appropriate Statistical Analysis of Behavioral Data, Gain Confidence in the Use and Limitations of Model Organisms, Computational and Bioinformatics Approaches to Examining Complex Relationships Between Genes and Behavior 112 Goal 5: Become Facile in the “Language” of Neuroscience and Behavior, with a Thorough Mastery of our Chosen Subtopics, asWell as a Keen Ability to Speak and Write on the Discipline 112 Further Reading 113 7 Assessments and Why They Are Important 115 What is Assessment? 115 Student Learning Assessments 116 Course-Based Assessments 120 Example 1: Assessment of Discovery-Based Introductory Biology Course 122 Example 2: Assessment of a Redesigned Introductory Cell Biology Course Using Pretesting and Post-Testing 124 Instructor Quality Assessments 126 Interpreting the Data 127 What to do with the Data? 128 Further Reading 129 8 Fully Incorporating Vision and Change 131 The Anthropocene and the Importance of Biology Literacy 131 Limited Resources Constrain the Discovery Laboratory for All 132 Alternative Approaches 133 Envisioning Introductory Biology for the Science-Literate Citizen 134 Introductory Life Sciences: The Discovery-Based Classroom 135 Organizing the Discovery-Based Classroom: An Introductory Life Science Course for All Students 137 Unit One: Food and Energy 137 Unit Two: Climate Change and Other Human Impacts 140 Unit Three: Health and Disease 142 Summary of This Chapter 143 Combining Science Literacy Training with Science Career Training 144 Concluding Thoughts 145 Further Reading 146 Appendix A: Laboratory Instructions for Behavioral Experiments Using Caenorhabditis elegans 149 Learning Goals and Expectations 150 Part 1: Initial Behavioral Observations ofWild-Type and MutantWorms 150 Workshop 1A: Mechanosensory Behavior Experiments and Statistical Analysis 150 Workshop 1B: Chemosensory Behavioral Experiment and Statistical Analysis 153 Appendix B: Instructions for Microscopy Workshop 157 Assignment forWorkshop 2 158 Procedure for Preparing Wet Mounts of C. elegans 158 Index 161

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Book SynopsisA thought-provoking exploration of deleterious mutations in the human genome and their effects on human health and wellbeing Despite all of the elaborate mechanisms that a cell employs to handle its DNA with the utmost care, a newborn human carries about 100 new mutations, originated in their parents, about 10 of which are deleterious. A mutation replacing just one of the more than three billion nucleotides in the human genome may lead to synthesis of a dysfunctional protein, and this can be inconsistent with life or cause a tragic disease. Several percent of even young people suffer from diseases that are caused, exclusively or primarily, by pre]existing and new mutations in their genomes, including both a wide variety of genetically simple Mendelian diseases and diverse complex diseases such as birth anomalies, diabetes, and schizophrenia. Milder, but still substantial, negative effects of mutations are even more pervasive. As of now, we possess no means of reducing Table of ContentsPreface ix 1 Genotypes and Phenotypes 1 1.1 DNA is a Text 1 1.2 Genomes Small and Large 6 1.3 Genes and Intergenic Regions 7 1.4 Cells, Mitosis, and Meiosis 14 1.5 From Genotype to Phenotype 17 Further Reading 21 2 Mendelian Inheritance and Population Genetics 23 2.1 Inheritance is Discrete 23 2.2 Populations are Genetically Variable 27 2.3 Loci and Genes 33 2.4 Effects of Alleles on Phenotypes 37 2.5 Mendelian Traits and Diseases 43 Further Reading 46 3 Complex Traits and Their Inheritance 49 3.1 Complex Inheritance of Phenotypes 49 3.2 Properties of a Complex Trait 52 3.3 Complex Traits in Populations 55 3.4 Effects of Heredity and Environment on Complex Traits 60 3.5 Polymorphic Loci Behind Complex Variation 64 Further Reading 68 4 Unavoidable Mutation 71 4.1 Phenomenon of Mutation 71 4.2 Kinds of Mutations 73 4.3 Spontaneous Mutation 75 4.4 Evolution of Mutation Rates 77 4.5 Artificial Mutagenesis and Antimutagenesis 79 Further Reading 81 5 Struggle for Fidelity 83 5.1 Fidelity of DNA Replication 83 5.2 Cleaning Up After the Replisome 88 5.3 Dealing with DNA Damages 91 5.4 Harms of Broken Maintenance 96 5.5 Mechanisms of Mutation 100 Further Reading 104 6 Mutation Rates 107 6.1 Measuring Mutation Rates 107 6.2 Data on Mutation Rates 109 6.3 Guilty Older Men 112 6.4 Rates of Phenotypically Drastic Mutations 114 6.5 Mild Mutations and Mutational Pressures 118 Further Reading 121 7 Natural Selection 123 7.1 Vulnerable Adaptations and Their Evolutionary Origin 123 7.2 Two Basic Characteristics of Selection 127 7.3 Measuring Natural Selection 129 7.4 Selection at a Polymorphic Locus 132 7.5 Selection on a Quantitative Trait 135 Further Reading 138 8 Functioning DNA and Junk DNA 141 8.1 Selective Neutrality and Random Drift 141 8.2 Effective Population Size 144 8.3 Junk DNA Provides the Simplest Evidence for Evolution 144 8.4 Finding Functioning Genome Segments 145 8.5 The Genomic Rate of Deleterious Mutations 147 Further Reading 148 9 It Takes All the Running You Can Do 149 9.1 Middle Class Neighborhood for Drosophila 149 9.2 Selection Against Deleterious Alleles 153 9.3 Mutation–Selection Equilibrium 155 9.4 Inbreeding Depression 158 9.5 Dangerous Slightly Deleterious Alleles 160 Further Reading 162 10 Phenomenon of Imperfection 165 10.1 Phenotypic and Genotypic Imperfection 165 10.2 Five Evolutionary Causes of Imperfection 168 10.3 Weakly Perfect Human Genotypes and Phenotypes 171 10.4 Native, Novel, and Optimal Environments 173 10.5 Factors, Exacerbating Mutation Imperfection 175 Further Reading 176 11 Our Imperfect Fitness 177 11.1 Properties of an Allele 177 11.2 Human Derived Alleles 180 11.3 Average Imperfection of a Genotype 186 11.4 Variation Among Genotypes 190 11.5 Selection in Modern Human Populations 192 Further Reading 197 12 Our Imperfect Wellness 199 12.1 Qualitative Characteristics of Wellness 199 12.2 Quantitative Traits 206 12.3 Contributions of Heredity and Environment 208 12.4 Wellness‐impairing Alleles 211 12.5 Genetic Architecture of Wellness 215 Further Reading 217 13 Mutational Pressure on Our Species 219 13.1 Mutational Pressure on Diseases 219 13.2 Mutational Pressure on Quantitative Traits 225 13.3 Possible Increase of the Mutational Pressure 226 13.4 De Novo Mutations and Human Wellness 228 13.5 Optimistic and Pessimistic Scenarios 230 Further Reading 231 14 Ethical Issues 233 14.1 Lessons from History 233 14.2 Modern Practices 237 14.3 Humanist Ethics and the Main Concern 241 14.4 The Main Concern and Ethical Dilemmas 244 14.5 Role of Scientists 247 Further Reading 250 15 What to Do? 253 15.1 Conditionally Beneficial or Unconditionally Deleterious? 253 15.2 Mutationless Utopia: What Could It Be? 257 15.3 Mutationless Utopia: Is It Ever Going to Happen? 261 15.4 What Can I Do Without Germline Genotype Modification? 265 15.5 Prognosis 268 Further Reading 269 Index 271

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Book SynopsisAn authoritative overview of the ecological activities of microbes in the biosphere Environmental Microbiology and Microbial Ecologypresents a broad overview of microbial activity and microbes' interactions with their environments and communities. Adopting an integrative approach, this text covers both conventional ecological issues as well as cross-disciplinary investigations that combine facets of microbiology, ecology, environmental science and engineering, molecular biology, and biochemistry. Focusing primarily on single-cell forms of prokaryotes and cellular forms of algae, fungi, and protozoans this book enables readers to gain insight into the fundamental methodologies for the characterization of microorganisms in the biosphere. The authors draw from decades of experience to examine the environmental processes mediated by microorganisms and explore the interactions between microorganisms and higher life forms. Highly relevant to modern readers, this book examines topics incTable of ContentsPreface xv 1 Introduction to Microorganisms and Their Activities 1 1.1 Central Themes of Environmental Microbiology and Microbial Ecology 1 1.2 Are the Terms Prokaryotes or Eukaryotes Relevant? 1 1.2.1 Intracellular Membranes in Prokaryotes 2 1.2.2 Compartmentalized Heterotrophic Bacterial Cells 3 1.2.3 The Universal Tree of Life: Rooted or Unrooted 4 1.2.4 What About the Giant Viruses? 4 1.3 Major Approach to Study Microorganisms 5 1.3.1 Application of Genomics, Metagenomics, and Proteomics 6 1.3.2 Biochemical and Physiological Analysis 7 1.4 The Impact of Horizontal Gene Transfer Between Microorganisms 7 1.4.1 Genetic Islands 9 1.4.2 Risks from Genetically Modified Organisms 10 1.4.3 Microbial Viruses and Gene Transfer Agents 10 1.5 What Determines Which Microorganisms are Present? 12 1.5.1 Metabolism as a Basis of Selection 13 1.5.2 Is Persistence of Microorganisms Dependent Only on Spore Production? 14 1.6 Is the Size and Shape of a Prokaryotic Cell Important? 19 1.6.1 Nanobacteria 19 1.6.2 Ultramicroscopic Bacteria 21 1.6.3 Very Large Bacteria 21 1.6.4 Influence of Diffusion on Bacterial Cell Form 22 1.6.5 Features of a Specific Cell Form 22 1.6.5.1 Coccus Form 22 1.6.5.2 Rod Form 22 1.6.5.3 Curved Rod or Spirochete Form 23 1.6.5.4 Unusual Forms 23 1.7 Microbial Predation 23 1.7.1 Bacteria as Prey 23 1.7.2 Bacteria as Trackers and Predators 24 1.8 Summary 25 Discussion Questions 25 References 26 Further Reading 31 2 Microbes in the Biosphere: Examination, Cultivation, and Communities 33 2.1 Overview and Focus 33 2.2 Microscopy to Study Environmental Microbes 33 2.2.1 Light Supported Microscopy 34 2.2.2 Fluorescence Microscopy 35 2.2.3 Scanning Confocal Laser Microscopy 37 2.2.4 High Resolution by Electron Microscopy 37 2.3 Internal Structures in Prokaryotes 41 2.3.1 Gas Vacuoles 41 2.3.2 Sulfur Globules 41 2.3.3 Polymeric Carbon Reserves 42 2.3.4 Polyphosphate Granules 43 2.3.5 Metallic Nanoparticles 43 2.4 Strategies for Culturing Microorganisms 44 2.4.1 Overview 44 2.4.2 Approaches for Isolation of Microorganisms 45 2.4.3 Establishing Microbial Communities 45 2.4.4 The iChip and Growing Uncultured Bacteria 46 2.5 Molecular Detection 49 2.5.1 Characterization of Microorganisms Using Genomics and Metagenomics 49 2.5.2 Physiological Analysis Using Metatranscriptomics and Metaproteomics 53 2.5.3 Lipid Biomarker Profiles 54 2.6 Examining Bacteria that Do Not Grow as Pure Cultures in the Laboratory 56 2.6.1 Host‐dependent Microorganisms 56 2.6.1.1 Bacteria as Obligate Pathogens 56 2.6.1.2 Bacteria as Endosymbionts 57 2.6.1.3 The Nanoarchaeum–Ignicoccus Relationship 58 2.6.2 Molecular Analysis of Uncultivable Bacteria 58 2.7 Microbial Community Structures 59 2.7.1 Primary Production and Microbial Communities 59 2.7.2 Biofilms 62 2.7.3 Role of Quorum Sensing 64 2.8 Summary 67 Discussion Questions 68 References 68 Further Reading 75 3 Terrestrial Systems: Soil and Subsurface Environments 77 3.1 Overview and Focus 77 3.2 Soil: An Environment for Microorganisms 77 3.2.1 Soil Horizons 78 3.2.2 Soil Organic Matter (SOM) 78 3.3 Soil Microbiology 80 3.3.1 Soil Prokaryotes 80 3.3.2 Soil Fungi 82 3.3.3 Soil Crusts 83 3.3.4 Soil Invertebrates and Burrowing Animals 83 3.3.5 The Rhizosphere and Associated Bacteria 83 3.4 Understanding Soil Ecosystems 85 3.4.1 The Carbon : Nitrogen Ratio 85 3.4.2 The Fungi : Bacteria Ratio 85 3.4.3 SOM and Soil Food Webs 86 3.4.4 Influence of Agricultural Management on the Soil Microbe Community 89 3.4.5 Impact of Viruses on the Soil Microbiota 90 3.5 Subsurface Microbiology 90 3.5.1 Groundwater 90 3.5.2 Cave Water 92 3.5.3 Deep Subsurface Aquifers 92 3.5.3.1 Aquifer in a Coal‐bearing Basin 92 3.5.3.2 Deep Granitic Aquifer 93 3.5.3.3 Anaerobic, Alkaline Aquifer 94 3.5.3.4 Saline Hydrothermal Aquifer 94 3.6 Deep Subsurface Microbiology 95 3.6.1 Marine Sediment Microbiology 96 3.6.2 Deep Mines and Boreholes 97 3.6.3 Deep Subsea Floor 98 3.6.4 Deep Subsurface Storage Sites 98 3.6.4.1 Storage of Nuclear Fuel Waste 98 3.6.4.2 Underground Storage for H 2 and CH 4 100 3.6.4.3 Underground Storage for CO 2 101 3.6.4.4 Geothermal Energy Production 102 3.6.5 Endolithic Microorganisms 102 3.7 Life in Deep Subsurfaces 103 3.7.1 Adjusting to a Subsurface Diet 103 3.7.2 Energy Sources in the Deep Biosphere 103 3.7.3 The Benefit of Living Together 105 3.8 Geomicrobiology 106 3.8.1 Rock and Mineral Weathering 106 3.8.2 Mineral Transformations 107 3.8.3 Microbial Metal Binding 109 3.8.4 Microbiota of Subsurface Crystals 109 3.9 Summary 110 Discussion Questions 111 References 111 Further Reading 116 4 Aquatic Surface Environments: Freshwater, Marine, and Wastewater 117 4.1 Overview and Focus 117 4.2 Water as Relevant to Microbial Growth 117 4.2.1 Water Activity 118 4.3 Marine Environments and Associated Microbiomes 119 4.3.1 Marine Primary Productivity 120 4.3.2 Marine Heterotrophs 122 4.3.3 Bacterial Symbionts and Marine Hosts 123 4.3.4 Microbial EPSs, Marine Snow, and Marine Gel Particles 125 4.3.5 Brackish Water and Intertidal Zones 127 4.3.6 Coral Reefs 128 4.4 Freshwater Environments and Associated Microbiomes 131 4.4.1 Lakes and Rivers 132 4.4.2 Wetlands 137 4.4.3 The Snow and Glacier Ice Ecosystems 139 4.4.4 Microbiota of Cold and Hot Springs 140 4.4.5 Microbial Mats 142 4.5 Maintaining Populations in Low Nutrient Environments 144 4.6 Aquaculture Wastewater 148 4.7 Hormone Degradation in Fresh Water 149 4.8 Human Activities and Influence on Microbial Ecology 150 4.9 Drinking Water 151 4.10 Municipal Water Treatment 151 4.11 Wastewater Treatment Systems 152 4.11.1 Septic Tanks 152 4.11.2 Municipal Wastewater Treatment 152 4.11.2.1 Primary Treatment 153 4.11.2.2 Secondary Treatment 153 4.12 Alternative Approaches for Wastewater Treatment 154 4.13 Coliforms and Other Indicator Organisms 155 4.14 Viruses in Aquatic Environments: Diversity and Activity 156 4.15 Summary 158 Discussion Questions 159 References 159 Further Reading 166 5 Life in Extreme Environments 167 5.1 Overview 167 5.2 Sampling in Extreme Environments 168 5.3 Extreme Temperature Environments 173 5.3.1 Psychrophiles 174 5.3.2 Thermophiles 176 5.3.2.1 Alpine Environment – Yellowstone National Park 176 5.3.2.2 Hydrothermal Vent Communities 179 5.3.2.3 The Guaymas Basin 180 5.4 Xerophiles 180 5.5 Piezophiles 182 5.6 Acidophiles 183 5.7 Alkaliphiles 187 5.8 Halophiles and Chaophiles 189 5.9 Radioresistant Microorganisms 194 5.10 Membrane Adaptations to Extreme Conditions 195 5.10.1 Low Temperatures 195 5.10.2 High Temperatures 196 5.10.3 pH Extremes: Low and High 196 5.11 Astrobiology 197 5.12 Nutrient Limited Environments 198 5.13 Volcanic Surfaces 200 5.14 Summary 202 Discussion Questions 202 References 202 Further Reading 209 6 Mutualism: Microorganisms and Terrestrial Plants 211 6.1 Overview and Focus 211 6.2 Cyanobacteria and the Chloroplast Ancestor 211 6.3 Lichens: Cyanobacteria/Algae–Fungi Mutualism 217 6.3.1 Distribution and Organization 217 6.3.2 Natural Products of Lichens 219 6.4 Mutualisms with Cyanobacteria as Intracellular or Epiphytic Organisms 220 6.4.1 Bryophytes 220 6.4.2 Mosses 221 6.4.3 Azolla 221 6.4.4 Gunnera 222 6.4.5 Cycads 222 6.4.6 Geosiphon 222 6.4.7 Diatoms 224 6.5 Rhizobia–Legume Symbiosis 224 6.5.1 Bacterial Species Involved 224 6.5.2 Rhizospheric Rhizobia 225 6.5.3 The Root Nodulation Process 226 6.5.4 Nodules on Plant Stems 230 6.6 Frankia and the Non‐legume Nitrogen‐fixing Nodule 231 6.7 Mycorrhizae 233 6.7.1 Arbuscular Mycorrhizae (AM) 235 6.7.2 Ectomycorrhiza (EcM) 236 6.8 Patterns of Regulation for Plant–Microbe Mutualism 237 6.9 Bacterial‐Fungal Interactions 238 6.9.1 Direct Effects 238 6.9.2 Plant Growth‐promoting Bacteria 239 6.9.3 Systemic Induction of Plant Immunity 239 6.10 Endophytic Microorganisms 240 6.11 Microbiology of the Phyllosphere 241 6.12 Summary 242 Discussion Questions 243 References 243 Further Reading 247 7 Mutualism: Microorganisms and Animals 249 7.1 Overview and Focus 249 7.2 Building a Microbial Community – The Role of the Host 249 7.2.1 Microbiology and Innate Immunity 249 7.2.2 Microbiology and Adaptive Immunity 250 7.3 Host Models to Study Parasite Relationships 251 7.3.1 Germ‐free Animals 251 7.3.2 Caenorhabditis elegans 251 7.3.3 Drosophila melanogaster 252 7.3.4 Galleria mellonella 252 7.4 Digestive Tract Environment 252 7.4.1 Omnivores 253 7.4.2 Carnivores 254 7.4.3 Herbivores 255 7.4.3.1 Bacteria and Archaea 257 7.4.3.2 Anaerobic Protozoa 257 7.4.3.3 Anaerobic Fungi 258 7.4.3.4 Probiotics and Methane Mitigation Strategies 260 7.5 The Human Microbiome 260 7.5.1 Skin 260 7.5.2 Oral Microorganisms 261 7.5.3 Intestinal Microbiome 263 7.5.3.1 Establishment of Intestinal Flora 263 7.5.3.2 The Healthy Gut 264 7.5.3.3 Influence of the Intestine on Human Health 265 7.5.3.4 Obesity, Diabetes, and Health Issues 266 7.5.3.5 Probiotics 269 7.6 Gut Microbiota across the Animal World 269 7.6.1 Systems of Maternal Transmission 270 7.6.2 Microbiota of Ruminates and Hindgut Fermenters 270 7.6.3 Gut Microbiota of Bears 275 7.6.4 Microbiota of Birds 275 7.6.5 Intestinal Bacteria of Fish 278 7.7 Insect–Fungus Symbiosis 279 7.7.1 Scale Insects and Septobasidium 279 7.7.2 Attine Ant–Fungus Symbiosis 279 7.7.3 Woodwasp–Fungus Symbiosis 280 7.7.4 Ambrosia Beetles–Fungus 281 7.7.5 Termite–Fungus 281 7.8 Mutualisms Involving Insects and Bacteria 282 7.8.1 Aphids–Buchnera and Endosymbionts 282 7.8.2 Wolbachia–Insects 283 7.8.3 Mealybug–Bacteria 283 7.8.4 Termite Gut–Bacteria 284 7.9 Mutualisms Involving Invertebrates 285 7.9.1 Microbiome of Marine Worms 285 7.9.2 Squid (Euprymna)–Vibrio fischeri Symbiosis 286 7.9.3 Medicinal Leech–Aeromonas sp. and Rikenella‐like Bacteria 287 7.9.4 Nematode–Bacteria 288 7.10 Summary 288 Discussion Questions 289 References 290 Further Reading 295 8 Microbes Driving the Nutrient Cycles 297 8.1 Overview and Focus 297 8.2 Nutrient Cycles and What Drives Them 297 8.3 The Aerobic Environment 299 8.3.1 The “Great Oxidation Event” 299 8.3.2 Oxygen Cycle 300 8.3.3 Hydrogen Peroxide and ROS 303 8.4 Carbon – A Renewable Resource 304 8.4.1 Carbon Dioxide Fixation and Carbonate Reduction 305 8.4.2 Methanogenesis, Methanotrophy, and Methylotrophy 306 8.4.3 Mineralization of Carbon Compounds 308 8.4.4 Production and Utilization of CO 311 8.4.5 Production and Utilization of Hydrogen Cyanide 312 8.5 Nitrogen for Biosynthesis and Energy 312 8.5.1 Nitrification 314 8.5.2 Denitrification 314 8.5.3 Nitrate Reduction 315 8.5.4 Nitrite Reductase 316 8.5.5 Metabolism of NO and N 2 O 316 8.5.6 Production of NO by NOS 317 8.5.7 Respiratory Ammonification 317 8.5.8 Anammox Reaction 318 8.5.9 Assimilation of Nitrogen 318 8.5.10 Dinitrogen Fixation 318 8.6 Sulfur Cycling 319 8.6.1 Oxidation of Hydrogen Sulfide 320 8.6.2 Oxidation of Elemental Sulfur 321 8.6.3 Dissimilative S 0 Reduction 321 8.6.4 Dissimilative Sulfate Reduction 322 8.6.5 Assimilatory Sulfate Reduction 322 8.6.6 Production of H 2 S and Dimethyl Sulfide 322 8.6.6.1 Hydrogen Sulfide 322 8.6.6.2 Dimethyl Sulfide 323 8.7 Cycling of Trace Elements 324 8.7.1 Iron 324 8.7.2 Manganese 326 8.8 Phosphorus Cycling 328 8.9 Selenium Cycling 330 8.10 Cycling Toxic Elements 331 8.10.1 Mercury 331 8.10.2 Arsenic 332 8.11 Summary 335 Discussion Questions 335 References 336 Further Reading 340 9 Bioremediation Using Microorganisms 341 9.1 Overview and Focus 341 9.2 Microbial Bioremediation: Strategies and Applications 341 9.2.1 Biostimulation 343 9.2.2 Bioaugmentation 344 9.2.2.1 Indigenous Bacteria 344 9.2.2.2 Genetically Modified Organisms 344 9.2.3 Intrinsic Bioremediation 345 9.2.4 Microbial Consortium 345 9.2.5 Co‐metabolism 346 9.3 Organic Compounds and Xenobiotics Degraded 347 9.3.1 Pesticides 347 9.3.2 Chlorinated Organic Compounds 348 9.3.2.1 Chloroethylenes 349 9.3.2.2 Chloromethanes 350 9.3.2.3 Polychlorinated Biphenyl Compounds 351 9.3.3 Population Dynamics in Degradation of Hydrocarbons 352 9.3.3.1 Oil Spills 352 9.3.3.2 Fuel Hydrocarbons 353 9.3.3.3 Polyaromatic Hydrocarbons 355 9.3.3.4 Azo Dyes 357 9.3.4 Explosives 357 9.3.4.1 Trinitrotoluene 357 9.3.4.2 RDX and HMX 359 9.3.4.3 Perchlorate 359 9.3.5 Bioremediation and Detoxification of Metal(loid)s 359 9.3.5.1 Dissimilatory Metal(loid) Reduction 360 9.3.5.2 Methylation Reactions 361 9.4 Design of Systems for Bioremediation 362 9.4.1 In Situ vs Ex Situ 362 9.4.2 Bioreactors 363 9.4.3 Biofarming 363 9.4.4 Permeable Reactive Barriers 363 9.4.5 Groundwater and Lagoon Treatment 363 9.4.6 Bioventing 364 9.5 Summary 364 Discussion Questions 364 References 365 Further Reading 370 10 Biocorrosion and Geomicrobiology 371 10.1 Overview and Focus 371 10.2 Microbially Influenced Corrosion (MIC) of Ferrous Metals 371 10.2.1 Current Theories of Biocorrosion 371 10.2.1.1 Emic 373 10.2.1.2 Cmic 374 10.2.1.3 Iron Sulfide Crusts 374 10.2.1.4 Biofilms and Extracellular Matrix 374 10.2.2 Biocorrosion of Nonferrous Materials 375 10.2.3 Control of Biocorrosion 376 10.3 Bioalteration of Rocks, Monuments, and Other Surfaces 376 10.3.1 Biofilms on Rocks and Buildings 376 10.3.2 Biodegradation of Art Objects 377 10.3.2.1 Marble Statues in Italy 377 10.3.2.2 Paintings in the Lascaux Cave in France 377 10.3.2.3 Mogao Grottoes in China 378 10.3.2.4 Damage to Frescoes 378 10.3.3 Biotechnology for Restoration of Artworks and Historic Stones 378 10.4 Biodeterioration of Concrete 380 10.5 Mineral Interaction and Biomineralization 382 10.5.1 Iron Hydroxides 382 10.5.2 Magnetic Mineral Crystals 383 10.5.3 Manganese Oxides 383 10.5.4 Carbonates 384 10.5.5 Phosphates 384 10.5.6 Sulfates 385 10.5.7 Sulfides 385 10.5.8 Clays 385 10.5.9 Uranium Precipitate and Crystals 386 10.5.10 Gold Grains 386 10.6 Interactions with Transition and Rare Earth Elements 387 10.6.1 Transition Elements 387 10.6.2 Rare Earth Elements 388 10.7 Toxic Elements 389 10.7.1 Mercury 389 10.7.2 Chromium 389 10.7.3 Arsenic 390 10.7.4 Selenium 390 10.8 Metallic and Metalloid Nanoparticles of Microbial Origin 391 10.9 Summary 393 Discussion Questions 393 References 394 Further Reading 398 11 Microbial Communities and Metabolic Networks 399 11.1 Overview and Focus 399 11.2 Examples of Succession of Populations 399 11.2.1 Development of Coral Black Band Disease 400 11.2.2 Population Succession in Production of Dairy Products 400 11.2.3 Population Dynamics in Fermentation of Non‐dairy Foods 401 11.2.3.1 Kimchi 401 11.2.3.2 Coffee 401 11.2.3.3 Cocoa 402 11.2.3.4 Chinese Soy Sauce 402 11.2.4 Composting Plant Material 403 11.3 Impact of Climate Change on Microorganisms 403 11.3.1 Marine Environment 403 11.3.2 Soil Environment 404 11.4 Syntrophy and Co‐metabolism 406 11.5 Ecosystem Created by Hydraulic Fracturing in Shale 408 11.6 Extracellular Electron Transport 408 11.6.1 Membrane‐bound Proteins 409 11.6.2 Electron Shuttling 409 11.6.3 Nanowires 410 11.6.4 Extracellular Electron Movement in Biofilms 410 11.7 Cross‐talk: Interkingdom Signaling 410 11.7.1 Microbial Endocrinology 411 11.7.2 Cross‐signaling in Nonhuman Systems 412 11.8 Evolving Systems of Interest 412 11.8.1 Polyploidy in Bacteria 412 11.8.2 Impact of Viruses and CRISPR‐cas Systems 414 11.8.3 Impact of Outer Membrane Vesicles 416 11.8.4 Atmospheric Microbiology 420 11.8.5 Long‐distance Electron Transfer 423 11.9 Summary 424 Discussion Questions 425 References 425 Further Reading 433 Index 435

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Book SynopsisPublished with the New York Academy of Sciences A timely, broad-ranging exploration of the neurobiological basis and molecular mechanisms of migraines Migraines impact the lives of a significant portion of the world's population, afflicting sufferers with severe pain, nausea, and often visual impairment.Table of ContentsList of Contributors xv Foreword xxi Part I Anatomy and physiology 1 1 Functional anatomy of trigeminovascular pain 3Karl Messlinger and Mária Dux 1.1 Anatomy of the trigeminovascular system 3 1.2 Trigeminal ganglion 9 1.3 Trigeminal brainstem nuclear complex 12 2 Physiology of the meningeal sensory pathway 31Andrew Strassman and Agustin Melo-Carrillo 2.1 Anatomy of the trigeminovascular system 31 2.2 Nociceptive response properties of peripheral and central neurons in the meningeal sensory pathway 32 2.3 Activity of neurons in the meningeal sensory pathway under conditions associated with headache: CSD and nitroglycerin 36 2.4 Role of blood vessels in activation of the meningeal sensory pathway 38 2.5 Unique neuronal properties of the meningeal sensory pathway 39 2.6 Intracranial vs extracranial mechanisms of migraine: new findings 40 References 41 3 Meningeal afferent ion channels and their role in migraine 49Gregory Dussor PhD 3.1 Meningeal afferents and migraine pain 49 3.2 Transient receptor potential (TRP) channels and headache 49 3.3 Acid-sensing ion channels 54 3.4 Glutamate-gated channels 55 3.5 ATP-gated channels 55 3.6 K+ channels 56 3.7 Other ion channels that may contribute to dural afferent signaling 57 3.8 Conclusions 57 3.9 Acknowledgements 58 References 58 4 Functional architecture of central pain pathways: focus on the trigeminovascular system 69Rodrigo Noseda and Luis Villanueva 4.1 Introduction 69 4.2 Ascending trigeminal nociceptive pathways 69 4.3 Trigeminovascular pain is subject to descending control 77 4.4 Conclusions 82 References 83 Part II Special features of migraine pain 91 5 Visceral pain 93Michael S. Gold and G.F. Gebhart 5.1 Organization of innervation 93 5.2 Common features of visceral pain and headache 96 5.3 Summary and conclusions 101 5.4 Acknowledgement 101 References 102 6 Meningeal neurogenic inflammation and dural mast cells in migraine pain 107Dan Levy PhD 6.1 Introduction 107 6.2 The neurogenic inflammation hypothesis of migraine 108 6.3 Meningeal neurogenic plasma protein extravasation and migraine 108 6.4 Meningeal neurogenic vasodilatation and migraine 110 6.5 Neurogenic mast cell activation in migraine 111 6.6 Endogenous events that could promote meningeal NI in migraine 113 6.7 Anti-migraine drugs and meningeal NI 113 6.8 Is meningeal NI a pro-nociceptive event in migraine? 114 6.9 Conclusions 115 References 116 7 Sensitization and photophobia in migraine 125Aaron Schain and Rami Burstein 7.1 Introduction 125 7.2 Experimental activation of trigeminovascular pathways 125 7.3 Peripheral sensitization 127 7.4 Central sensitization: medullary dorsal horn 127 7.5 Central sensitization: thalamus 129 7.6 Temporal aspects of sensitization and their implications to triptan therapy 129 7.7 Modulation of central sensitization 131 7.8 Neural substrate of migraine-type photophobia 133 References 135 8 Central circuits promoting chronification of migraine 139Christopher W. Atcherley, Kelsey Nation, Milena De Felice, Jennifer Y. Xie, Michael H. Ossipov, David W. Dodick and Frank Porreca 8.1 Introduction 139 8.2 Pharmacotherapy of migraine 140 8.3 Medication overuse headache (MOH) and migraine chronification 141 8.4 Central circuits modulating pain 143 8.5 Evaluation of descending modulation: diffuse noxious inhibitory controls and conditioned pain modulation 145 8.6 Conclusions 148 References 149 9 Triptans to calcitonin gene-related peptide modulators – small molecules to antibodies – the evolution of a new migraine drug class 157Richard J Hargreaves 9.1 Introduction 157 9.2 Trigeminovascular system – migraine physiology and pharmacology 157 9.3 Small molecule CGRP receptor antagonists 159 9.4 Current status of small molecule CGRP receptor antagonist programs 161 9.5 Unraveling the site of action of small molecule CGRP receptor antagonists using clinical pharmacology and brain imaging 162 9.6 Biologic approaches to CGRP modulation 163 9.7 Summary and conclusion 167 References 168 10 Lessons learned from CGRP mutant mice 175Levi P. Sowers, Annie E. Tye and Andrew F. Russo 10.1 Introduction 175 10.2 Modeling migraine 175 10.3 Calcitonin gene-related peptide (CGRP) in migraine 176 10.4 What has CGRP manipulation in mice taught us about migraine? 177 10.5 Conclusions 183 References 183 Part III Clinical characteristics of migraine 189 11 The clinical characteristics of migraine 191F. Michael Cutrer MD, Ryan Smith MD and David W. Dodick MD 11.1 Overview of migraine 191 11.2 Migraine prodrome 191 11.3 The migraine headache is the centerpiece of the syndrome 192 11.4 Migraine aura 194 11.5 Proposed aura types 197 11.6 Postdrome 198 11.7 Status migrainosus 199 Summary 199 References 199 12 The premonitory phase of migraine 201Michele Viana and Peter J. Goadsby 12.1 What is the premonitory phase? Towards a definition 201 12.2 How common are premonitory symptoms? 202 12.3 Do premonitory symptoms reliably predict a migraine attack? 202 12.4 Premonitory symptoms in individuals 203 12.5 Intra-patient variability of the premonitory phase 203 12.6 Difference between patients with and without premonitory symptoms 204 12.7 Premonitory symptoms in children 204 12.8 Premonitory symptoms and migraine triggers 204 12.9 Premonitory symptoms and pathophysiological studies 205 12.10 Treatment during the premonitory phase 206 12.11 Conclusion 206 References 207 Part IV Migraine genetics and CSD 209 13 The genetic borderland of migraine and epilepsy 211Isamu Aiba and Jeffrey Noebels 13.1 Introduction 211 13.2 Gene-linked comorbidity 211 13.3 The challenge of dissecting seizure and aura excitability defects 212 13.4 Clinical overlap of migraine with aura and epilepsy phenotypes 214 13.5 Acquired and genetic etiologies of migraine with aura and epilepsies 216 13.6 Migraine aura is linked to specific genes with locus and allelic heterogeneity 218 13.7 Correspondence of regional brain susceptibility for migraine in genetic epilepsy syndromes 219 13.8 Are SD thresholds progressive? 220 13.9 Spreading depolarization in cardiorespiratory brainstem regions, a candidate mechanism of SUDEP 221 13.10 Brainstem SD is a “second hit” leading to SUDEP 222 13.11 Tau ablation prevents seizures, SUDEP and brainstem SD threshold in models of SUDEP 223 13.12 Conclusion 223 13.13 Acknowledgements 223 References 223 14 Genetics of monogenic and complex migraine 233Else A. Tolner, Else Eising, Gisela M. Terwindt, Michel D. Ferrari and Arn M.J.M. van den Maagdenberg 14.1 Migraine is a genetic disease 233 14.2 How to identify genes for migraine? 234 14.3 Gene identification in monogenic Familial Hemiplegic Migraine 234 14.4 Functional studies of gene mutations in monogenic familial hemiplegic migraine 236 14.5 Genetic studies in monogenic disorders in which migraine is a prominent part of the clinical phenotype 239 14.6 Genome-wide association studies in common polygenic migraine 240 14.7 Future directions in genetic migraine research 241 References 243 15 Lessons from familial hemiplegic migraine and cortical spreading depression 251Daniela Pietrobon 15.1 Introduction 251 15.2 FHM genes and functional consequences of FHM mutations 252 15.3 Insights into the mechanisms underlying susceptibility to cortical spreading depression and initiation of migraine attacks from the functional analysis of FHM mouse models 255 15.4 Acknowledgements 260 References 260 16 From cortical spreading depression to trigeminovascular activation in migraine 267Turgay Dalkara and Michael A. Moskowitz 16.1 CSD causes the visual aura 267 16.2 SD may underlie transient neurological dysfunctions preceding attacks 269 16.3 Does SD cause headache? 270 16.4 Human data supporting the parenchymal inflammatory signaling 274 16.5 Meningeal neurogenic inflammation amplifies the parenchymal signal 275 16.6 Understanding human CSD and migraine without aura 276 16.7 Potential of CSD models to understand migraine and drug development 278 References 278 Part V Modeling and imaging in migraine 285 17 Mathematical modeling of human cortical spreading depression 287Markus A. Dahlem 17.1 Introduction 287 17.2 Microscopic models: cellular and cytoarchitectonic detail 288 17.3 Computational models 291 17.4 Macroscopic models: large scale spatiotemporal phenomenology 292 References 301 18 Tools for high-resolution in vivo imaging of cellular and molecular mechanisms in cortical spreading depression and spreading depolarization 307K;;v;;lc;;m K;;l;;ç, Hana Uhlirova, Peifang Tian, Payam A. Saisan, Mohammad Abbas Yaseen, Jonghwan Lee, Sergei A. Vinogradov, David A. Boas, Sava Sakadžic and Anna Devor ´ 18.1 Introduction 307 18.2 Large-scale imaging of vascular dynamics with microscopic resolution 308 18.3 Combining measurements of single-vessel diameter with imaging and quantification of intracellular Ca2+ in neurons and astrocytes 309 18.4 NADH autofluorescence: an endogenous marker of energy metabolism 311 18.5 Direct imaging of molecular O2 in blood and tissue 312 18.6 Employing optogenetics to study inter-cellular communication 314 18.7 Conclusions and outlook 314 References 315 19 Animal models of migraine aura 321Shih-Pin Chen, Jeremy Theriot, Cenk Ayata and KC Brennan 19.1 Introduction: spreading depression and migraine 321 19.2 In vivo and in vitro models of SD susceptibility 322 19.3 Experimental preparations 324 19.4 Methods to trigger SD 327 19.5 Methods to detect CSD 329 19.6 SD susceptibility attributes 331 19.7 Recommended quality measures for experimental models of migraine aura 333 19.8 Future directions 334 References 335 20 Human models of migraine 347Jakob Møller Hansen MD, PhD and Messoud Ashina MD, PhD, DMSc 20.1 Introduction 347 20.2 The first steps: GTN and the NO-hypothesis 347 20.3 Calcitonin gene-related peptide (CGRP) 351 20.4 Vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase activating polypeptide (PACAP) 353 20.5 Can we gain from the use of experimental models to study functional consequences of migraine mutations? 354 20.6 Conclusion 355 References 355 21 Imaging pain and headache 363Duncan J. Hodkinson, Sophie L. Wilcox and David Borsook 21.1 Introduction 363 21.2 Functional brain changes in migraine 363 21.3 Structural brain changes in migraine 367 21.4 Insights from orofacial pain 370 21.5 Conclusions 371 References 372 Index 377

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Book SynopsisThrough eight successful editions, and over nearly 40 years, Biogeography: An Ecological and Evolutionary Approach has provided a thorough and comprehensive exploration of the varied scientific disciplines and research that are essential to understanding the subject. The text has been praised for its solid background in historical biogeography and basic biology, that is enhanced and illuminated by discussions of current research. This new edition incorporates the exciting changes of the recent years, and presents a thoughtful exploration of the research and controversies that have transformed our understanding of the biogeography of the world. It also clearly identifies the three quite different arenas of biogeographical research: continental biogeography, island biogeography and marine biogeography. It is the only current textbook with full coverage of marine biogeography. It reveals how the patterns of life that we see today have been created by the twoTable of ContentsPreface xi Acknowledgements xiii 1 The History of Biogeography 1 Lessons from the Past 1 Ecological versus Historical Biogeography, and Plants versus Animals 3 Biogeography and Creation 4 The Distribution of Life Today 5 Evolution – a Flawed and Dangerous Idea! 7 Enter Darwin – and Wallace 8 World Maps: Biogeographical Regions of Plants and Animals 10 Getting around the World 12 The Origins of Modern Historical Biogeography 16 The Development of Ecological Biogeography 19 Living Together 20 Marine Biogeography 23 Island Biogeography 24 Biogeography Today 26 SECTION I: The Challenge of Existing 31 2 Patterns of Distribution: Finding a Home 33 Limits of Distribution 37 The Niche 38 Overcoming the Barriers 39 Climatic Limits: The Palms 41 A Successful Family: The Daisies (Asteraceae) 42 Patterns among Plovers 46 Magnolias: Evolutionary Relicts 49 The Strange Case of the Testate Amoeba 50 Climatic Relicts 52 Topographical Limits and Endemism 59 Physical Limits 60 Species Interaction: A Case of the Blues 66 Competition 69 Reducing Competition 71 Predators and Prey, Parasites and Hosts 73 Migration 76 Invasion 79 3 Communities and Ecosystems: Living Together 89 The Community 89 The Ecosystem 92 Ecosystems and Species Diversity 95 Biotic Assemblages on a Global Scale 98 Mountain Biomes 103 Global Patterns of Climate 106 Climate Diagrams 109 Modelling Biomes and Climate 112 4 Patterns of Biodiversity 117 How Many Species are There? 118 Latitudinal Gradients of Diversity 123 Is Evolution Faster in the Tropics? 131 The Legacy of Glaciation 132 Latitude and Species Ranges 133 Diversity and Altitude 134 Biodiversity Hotspots 136 Diversity in Space and Time 139 Intermediate Disturbance Hypothesis 141 Dynamic Biodiversity and Neutral Theory 142 SECTION II: THE ENGINES OF THE PLANET 147 5 Plate Tectonics 149 The Evidence for Plate Tectonics 149 Changing Patterns of Continents 154 How Plate Tectonics affects the Living World, Part I: Events on Land 154 How Plate Tectonics affects the Living World, Part II: Events in the Oceans 156 Islands and Plate Tectonics 162 Terranes 164 6 Evolution, the Source of Novelty 169 The Mechanism of Evolution: The Genetic System 172 From Populations to Species 173 Sympatry versus Allopatry 176 Defining the Species 179 A Case Study: Darwin’s Finches 180 Controversies and Evolution 183 Charting the Course of Evolution 188 SECTION III: ISLAND BIOGEOGRAPHY 193 7 Life, Death and Evolution on Islands 195 Types of Island 196 Getting There: The Challenges of Arriving 196 Dying There: Problems of Survival 197 Adapting and Evolving 199 The Hawaiian Islands 201 Integrating the Data: The Theory of Island Biogeography 208 Modifying the Theory 212 The General Dynamic Model for Oceanic Island Biogeography 214 Nestedness 216 Living Together: Incidence and Assembly Rules 216 Building an Ecosystem: The History of Rakata 218 SECTION IV: PATTERNS OF LIFE 229 8 From Evolution to Patterns of Life 231 Dispersal, Vicariance and Endemism 231 Methods of Analysis 232 Event]Based Biogeography 236 Reticulate Patterns 239 The Molecular Approach to Historical Biogeography 245 Molecules and the More Distant Past 250 9 Patterns in the Oceans 255 Zones in the Ocean and on the Seafloor 257 Basic Biogeography of the Seas 260 The Open]Sea Environment 261 The Ocean Floor 268 The Shallow]Sea Environment 273 10 Patterns in the Past 291 Early Land Life on the Moving Continents 292 One World – for a While 295 Biogeography of the Earliest Mammals 298 Early History of the Flowering Plants 303 Reconstructing Early Biomes 305 11 Setting the Scene for Today 315 The Biogeographical Regions Today 315 The Basis of Mammal Biogeography 317 Patterns of Distribution Today, I: The Mammals 319 Patterns of Distribution Today, II: The Flowering Plants 322 History of Today’s Biogeographical Regions 323 The Old World Tropics: Africa, India and South]East Asia 324 Australia 331 New Caledonia 334 New Zealand 335 The West Indies 336 South America 341 The Northern Hemisphere: Holarctic Mammals and Boreal Plants 346 12 Ice and Change 353 Climatic Wiggles 354 Interglacials and Interstadials 356 Biological Changes in the Pleistocene 358 The Last Glacial 361 Causes of Glaciation 370 The Current Interglacial: A False Start 375 Forests on the Move 377 The Dry Lands 381 Changing Sea Levels 383 A Time of Warmth 384 Climatic Cooling 386 Recorded History 388 Atmosphere and Oceans: Short]Term Climate Change 388 The Future 390 SECTION V: PEOPLE AND PROBLEMS 397 13 The Human Intrusion 399 The Emergence of Humans 399 Modern Humans and the Megafaunal Extinctions 406 Plant Domestication and Agriculture 409 Animal Domestication 414 Diversification of Homo sapiens 415 The Biogeography of Human Parasitic Diseases 417 Environmental Impact of Early Human Cultures 420 14 Conservation Biogeography 425 Welcome to the Anthropocene 425 Less, and Less Interesting 429 What is behind the Biodiversity Crisis? 430 Crisis Management: Responding to Biodiversity Loss 435 The Birth of Conservation Biogeography 437 The Scope of Conservation Biogeography 438 Conservation Biogeography in Action 443 The Future is Digital 446 Conclusions 449 Glossary 455 Index 469 Colour plates between pages 146 and 147

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Book SynopsisThrough eight successful editions, and over nearly 40 years, Biogeography: An Ecological and Evolutionary Approach has provided a thorough and comprehensive exploration of the varied scientific disciplines and research that are essential to understanding the subject.Table of ContentsPreface xi Acknowledgements xiii 1 The History of Biogeography 1 Lessons from the Past 1 Ecological versus Historical Biogeography, and Plants versus Animals 3 Biogeography and Creation 4 The Distribution of Life Today 5 Evolution – a Flawed and Dangerous Idea! 7 Enter Darwin – and Wallace 8 World Maps: Biogeographical Regions of Plants and Animals 10 Getting around the World 12 The Origins of Modern Historical Biogeography 16 The Development of Ecological Biogeography 19 Living Together 20 Marine Biogeography 23 Island Biogeography 24 Biogeography Today 26 SECTION I: THE CHALLENGE OF EXISTING 31 2 Patterns of Distribution: Finding a Home 33 Limits of Distribution 37 The Niche 38 Overcoming the Barriers 39 Climatic Limits: The Palms 41 A Successful Family: The Daisies (Asteraceae) 42 Patterns among Plovers 46 Magnolias: Evolutionary Relicts 49 The Strange Case of the Testate Amoeba 50 Climatic Relicts 52 Topographical Limits and Endemism 59 Physical Limits 60 Species Interaction: A Case of the Blues 66 Competition 69 Reducing Competition 71 Predators and Prey, Parasites and Hosts 73 Migration 76 Invasion 79 3 Communities and Ecosystems: Living Together 89 The Community 89 The Ecosystem 92 Ecosystems and Species Diversity 95 Biotic Assemblages on a Global Scale 98 Mountain Biomes 103 Global Patterns of Climate 106 Climate Diagrams 109 Modelling Biomes and Climate 112 4 Patterns of Biodiversity 117 How Many Species are There? 118 Latitudinal Gradients of Diversity 123 Is Evolution Faster in the Tropics? 131 The Legacy of Glaciation 132 Latitude and Species Ranges 133 Diversity and Altitude 134 Biodiversity Hotspots 136 Diversity in Space and Time 139 Intermediate Disturbance Hypothesis 141 Dynamic Biodiversity and Neutral Theory 142 SECTION II: THE ENGINES OF THE PLANET 147 5 Plate Tectonics 149 The Evidence for Plate Tectonics 149 Changing Patterns of Continents 154 How Plate Tectonics affects the Living World, Part I: Events on Land 154 How Plate Tectonics affects the Living World, Part II: Events in the Oceans 156 Islands and Plate Tectonics 162 Terranes 164 6 Evolution, the Source of Novelty 169 The Mechanism of Evolution: The Genetic System 172 From Populations to Species 173 Sympatry versus Allopatry 176 Defining the Species 179 A Case Study: Darwin’s Finches 180 Controversies and Evolution 183 Charting the Course of Evolution 188 SECTION III: ISLAND BIOGEOGRAPHY 193 7 Life, Death and Evolution on Islands 195 Types of Island 196 Getting There: The Challenges of Arriving 196 Dying There: Problems of Survival 197 Adapting and Evolving 199 The Hawaiian Islands 201 Integrating the Data: The Theory of Island Biogeography 208 Modifying the Theory 212 The General Dynamic Model for Oceanic Island Biogeography 214 Nestedness 216 Living Together: Incidence and Assembly Rules 216 Building an Ecosystem: The History of Rakata 218 SECTION IV: PATTERNS OF LIFE 229 8 From Evolution to Patterns of Life 231 Dispersal, Vicariance and Endemism 231 Methods of Analysis 232 Event‐Based Biogeography 236 Reticulate Patterns 239 The Molecular Approach to Historical Biogeography 245 Molecules and the More Distant Past 250 9 Patterns in the Oceans 255 Zones in the Ocean and on the Seafloor 257 Basic Biogeography of the Seas 260 The Open‐Sea Environment 261 The Ocean Floor 268 The Shallow‐Sea Environment 273 10 Patterns in the Past 291 Early Land Life on the Moving Continents 292 One World – for a While 295 Biogeography of the Earliest Mammals 298 Early History of the Flowering Plants 303 Reconstructing Early Biomes 305 11 Setting the Scene for Today 315 The Biogeographical Regions Today 315 The Basis of Mammal Biogeography 317 Patterns of Distribution Today, I: The Mammals 319 Patterns of Distribution Today, II: The Flowering Plants 322 History of Today’s Biogeographical Regions 323 The Old World Tropics: Africa, India and South‐East Asia 324 Australia 331 New Caledonia 334 New Zealand 335 The West Indies 336 South America 341 The Northern Hemisphere: Holarctic Mammals and Boreal Plants 346 12 Ice and Change 353 Climatic Wiggles 354 Interglacials and Interstadials 356 Biological Changes in the Pleistocene 358 The Last Glacial 361 Causes of Glaciation 370 The Current Interglacial: A False Start 375 Forests on the Move 377 The Dry Lands 381 Changing Sea Levels 383 A Time of Warmth 384 Climatic Cooling 386 Recorded History 388 Atmosphere and Oceans: Short‐Term Climate Change 388 The Future 390 SECTION V: PEOPLE AND PROBLEMS 397 13 The Human Intrusion 399 The Emergence of Humans 399 Modern Humans and the Megafaunal Extinctions 406 Plant Domestication and Agriculture 409 Animal Domestication 414 Diversification of Homo sapiens 415 The Biogeography of Human Parasitic Diseases 417 Environmental Impact of Early Human Cultures 420 14 Conservation Biogeography 425 Welcome to the Anthropocene 425 Less, and Less Interesting 429 What is behind the Biodiversity Crisis? 430 Crisis Management: Responding to Biodiversity Loss 435 The Birth of Conservation Biogeography 437 The Scope of Conservation Biogeography 438 Conservation Biogeography in Action 443 The Future is Digital 446 Conclusions 449 Glossary 455 Index 469 Colour plates between pages 146 and 147

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Book SynopsisNorth America contains an incredibly diverse array of natural environments, each supporting unique systems of plant and animal life. These systems, the largest of which are biomes, form intricate webs of life that have taken millennia to evolve. This richly illustrated book introduces readers to this extraordinary array of natural communities and their subtle biological and geological interactions. Completely revised and updated throughout, the second edition of this successful text takes a qualitative, intuitive approach to the subject, beginning with an overview of essential ecological terms and concepts, such as competitive exclusion, taxa, niches, and succession. It then goes on to describe the major biomes and communities that characterize the rich biota of the continent, starting with the Tundra and continuing with Boreal Forest, Deciduous Forest, Grasslands, Deserts, Montane Forests, and Temperature Rain Forest, among others. Coastal environments, including the Laguna Trade Review"The disciplines of ecology and biogeography are so closely intertwined that many scholars of theserespective fields are, by necessity and shared interest, well versed in both (Jenkins and Ricklefs2011). This overlap is evident in the layout of Ecology of North America. With a scalable subject suchas ecosystems, the authors could have approached the discussion of their material from various angles. Their decision to employ a biomestructured theme to describe the assemblage of North American ecosystems is both logical and practical. This approach is certain to be appealing to biogeographers who use the textbook. In fact, this book could be used as a supplementary textbookin a biogeography class. Ecology of North America will serve as a good introductory text for students interested in the ecology of the continent. The book begins with an overview chapter of basic ecological principles and terms, including sound explanations of succession, biodiversity, and biogeography. Subsequent chapters are individually devoted to various North American ecosystems/biomes. These chapters define the unique attributes of each biome and fluidly address the important abiotic and biotic components of each, along with representative plant and animal assemblages, interactions, andadaptations, as well as characteristic biome-level disturbances and ecological challenges. Both authorsare wildlife ecology experts, yet their knowledge and understanding of plant ecology and their success in balancing the text between floral and faunal ecological discussions are both refreshing and impressive.....The inclusion of “infoboxes” is a meaningful addition; this type of aside succeeds in adding interest and depth to textbooks. Comprehensive bibliographies are included after each chapter,and the division of each one by chapter subheadings is helpful......The new edition of Ecology of NorthAmerica is a welcome addition to contemporary ecology textbook offerings. The authors have updateda good introductory text that is highly approachable and readable. It offers a worthy additionto textbook options in the discipline, and I recommend it as an essential resource for studentsand teachers of North American ecosystems" (Frontiers of Biogeography- December 2016)Table of ContentsForeword viii Preface ix Acknowledgments xi 1 Introduction 1 A brief overview of ecology 1 The ecosystem 2 Abiotic limits 3 Climate and topography 4 Soils and soil profiles 4 Biotic community 6 Community succession 6 Plant succession: from pioneer to climax 6 Primary and secondary succession 6 Succession and species abundance 7 The biome concept 7 Biodiversity 7 The “species richness gradient” 8 Biodiversity “hotspots” 8 Patterns of distribution 9 Continental patterns 9 Geographical and ecological distribution 10 Some ecological concepts 10 Niches 10 Ecological equivalents 12 Bergmann’s rule 12 Allen’s rule 13 Readings and references 14 2 Tundra 17 Climatic and glacial influences 17 Soils and geological influences 17 Permafrost 18 Patterned ground 18 Eskers and tundra wildlife 20 Glacial refugia 21 Features and adaptations 21 Plant adaptations to harsh conditions 21 Plant growth and reproduction 22 Decomposition and soil nutrients 23 Some animal adaptations 23 Major vegetative communities 24 Shrub tundra 25 Dwarf birch heath 25 Cottongrass heath 25 Fellfields 25 Invertebrates and tundra ecology 25 Selected tundra mammals 26 Lemmings 26 Arctic ground squirrels 27 Arctic foxes 28 Barren]ground caribou 28 Selected tundra birds 29 Gyrfalcons 29 Snowy owl 30 Ross goose 30 Highlights 31 Absentees: amphibians and reptiles 31 Lichens and “reindeer moss” 31 Snow goose “eat outs” 32 Alpine Tundra 33 Fragile Tundra 34 Impacts of human activity 34 Global warming 35 Readings and references 36 3 Boreal Forest 41 Climatic boundaries and soils 41 Features and adaptations 42 Plant adaptations 42 Animal adaptations 42 Frequent fires 42 Niches in the Boreal Forest 43 Selected biotic communities 44 Tree line and forest tundra 44 Muskeg 46 Coniferous swamps 46 Comparative ecology of lakes 46 Appalachian Extension 48 Mountain balds 48 Highlights 49 The 10]year cycle 49 Wolves and moose 50 A wealth of salamanders 52 Red squirrels 53 Ecological challenges 54 Acid rain 54 Spruce budworm and DDT 55 Balsam woolly adelgid 55 The Boreal Forest Agreement 56 Readings and references 57 4 Eastern Deciduous Forest 61 Climatic boundaries and soils 61 Features and adaptations 61 The forest primeval 63 The layered forest 63 Autumn leaves 64 Ground and leaf litter 64 Mast 65 Biotic associations 66 Northern hardwoods conifer forests 66 Beech–Maple–Basswood 67 Mesophytic forest 68 Oak–Hickory 69 Mississippi alluvial plain 70 Southern Mixed Forest 70 Some associated communities 71 Longleaf pine forests 71 New Jersey Pine Barrens 73 Carolina bays 74 Highlights 75 Acorns and blue jays 75 Deer yards 75 Kirtland’s warblers and fire 76 Franklin’s lost tree 77 Cicadas: buzz in the forest 77 Ecological challenges 78 Declines of neotropical migrants 78 Forest destruction by exotic organisms 80 Reintroduction of red wolves 81 Readings and references 82 5 Grasslands: Plains and Prairies 89 Major associations 89 Tallgrass prairie 89 Midgrass prairie 90 Shortgrass prairie 90 Transition zones 93 Aspen parklands 93 Cross Timbers 96 Western transition 96 Features and adaptations 97 Seasonal grasses 97 Soils 99 Role of fire 101 Prairie streams 101 Prairie wetlands and waterfowl 102 Pleistocene extinctions 103 Selected prairie mammals 104 Bison 104 Prairie dogs 104 Pronghorns 106 Selected prairie birds 106 Burrowing owls 106 Prairie chickens 107 Highlights 108 Riparian forests 108 The Platte River 108 Nebraska Sandhills 109 Ants 109 Isolation and contact on the plains 110 Grassland settlement 110 Prairie preservation 111 Readings and references 113 6 Regional Grasslands and Related Areas 120 Regional associations 120 Palouse prairie 120 California Annual Grasslands 122 Southwestern desert grasslands 124 Edwards Plateau 126 Tamaulipan Mezquital 127 Highlights 129 Rodents and vegetation 129 Channeled Scablands 130 Snake River Birds of Prey Conservation Area 130 Mima mounds 131 Desertification 132 Readings and references 132 7 Deserts 136 Physical geography 136 Why deserts are dry 136 Desert mountains and bajadas 138 Ancient lakes 138 Features and adaptations 139 Desert soils and surfaces 139 Plant adaptations 140 Animal adaptations 141 The major deserts 144 Chihuahuan Desert 144 Sonoran Desert 145 Mojave Desert 147 Great Basin Desert 149 Highlights 150 Nurse trees 150 “Trees” for desert woodpeckers 151 Boojums and elephants: unique trees 153 Yucca moths 154 Desert fishes 154 Realm of reptiles 155 Of soils and mice 156 Deserts and predators 157 Pygmies of the sagebrush steppe 158 Desert quail rainfall and vitamin A 159 Sailing stones 159 Wheeled threats to deserts 159 Readings and references 160 8 Chaparral and Pinyon]Juniper Woodlands 167 Features and adaptations of chaparral 168 Coastal (California) chaparral 171 Chamise chaparral 171 Manzanita chaparral 171 Ceanothus chaparral 171 Other chaparral communities 171 Interior (Arizona) chaparral 172 Pinyon]juniper woodlands 172 Distribution and ecology 172 Human uses 173 Chaparral and fire 173 Water]repellant soils 173 Post]fire vegetation 174 Wildlife and chaparral fires 174 Highlights 174 Allelopathy in chaparral 174 Animal associates in coastal chaparral 175 Lizards and burned chaparral 175 Pinyon jays 176 Human influences 176 Readings and references 176 9 Montane Forests 180 Features and adaptations 180 Montane Forest zones 181 Lower montane zone 181 Upper montane zone 181 Subalpine zone 182 Associated habitats 183 Mountain parks and meadows 183 Black Hills 185 Redwoods and sequoias 186 Bristlecone pine forest 188 Fire in montane forests 190 Highlights 192 Western chipmunks and competitive exclusion 192 Squirrels bears and pine cones 194 Sky islands in Arizona 195 Monarchs in winter 196 Bears and moths 196 Readings and references 198 10 Temperate Rain Forest 203 What is old]growth forest? 203 Features and adaptations 204 Valleys of rain forest 204 Epiphytes canopy roots and “scuzz” 206 More about logs 207 Succession on glacial till 208 Highlights 209 Bears salmon and forest enrichment 209 A seabird in the forest 212 Some small mammals and their ecology 213 Banana slugs 213 Pacific yew 214 Giant salamanders and other amphibians 214 Mount St Helens 215 Ecological controversy 217 Readings and references 218 11 Coastal Environments 223 Currents and climates 223 Features and adaptations 224 Rocky seashores and tidal pools 224 Sandy seashores 225 Chesapeake Bay 227 Mother Lagoon 228 Submergent communities 230 Seagrass meadows 230 Forests in the ocean 232 Oyster reefs 233 Emergent communities 235 Atlantic tidal marshes 235 Marshes of the Gulf Coast 236 Mangrove islands and thickets 238 Some associated communities 239 Barrier islands 239 Coral reefs 241 Maritime forests 243 Highlights 243 Synchrony at Delaware Bay 243 Waterbird colonies 245 A whale of a success 247 Ecological challenges 248 Natural disturbances 248 Sea]level rise 250 Readings and references 251 12 A Selection of Special Environments 259 The Grand Canyon 259 Caves 262 Arctic ice cap 265 Niagara Escarpment 267 The “Father of Waters” 268 The Everglades 271 Fossil Lagerstätten: Windows into North America’s ecological past 275 Burgess Shale 275 La Brea tar pits 277 The Florida Keys 278 The Great Lakes 280 Habitat highlights 282 Rivers of ice 282 Hot springs and geysers 283 Forest in the clouds 284 Granite outcrops and inselbergs 285 Palm forest 285 Mineral licks 286 Bogs and their carnivorous plants 287 Readings and references 288 Appendix 296 Glossary 309 Index 321

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Book SynopsisThe comprehensive and authoritative guide to clinical reproductive science The field of clinical reproductive science continues to evolve; this important resource offers the basics of reproductive biology as well as the most recent advance in clinical embryology. The author - a noted expert in the field - focuses on the discipline and covers all aspects of this field. The text explores causes of male and female infertility and includes information on patient consultation and assessment, gamete retrieval and preparation, embryo culture, embryo transfer and cryopreservation. Comprehensive in scope, the text contains an introduction to the field of clinical reproductive science and a review of assisted reproductive technology. The author includes information on a wide range of topics such as gonadal development, the regulation of meiotic cell cycle, the biology of sperm and spermatogenesis, in vitro culture, embryo transfer techniques, fundamentals of fertilisation, oocyte activation aTable of ContentsList of Contributors xi About the Editor xv Preface xvii Acknowledgements xix About the Companion Website xxi Section One Reproductive Science: Fundamentals of Human Reproductive Biology 1 1 Sexual Differentiation, Gonadal Development, and Development of the External Genitalia: A Review of The Regulation of Sexual Differentiation 3Rebecca M. Perrett 2 Male and Female Reproductive Anatomy 35Sara Sulaiman and James Coey 3 Fundamentals of Reproductive Endocrinology 45Derrick Ebot, Haider Hilal, Michael Carroll, and James Coey 4 The Ovaries, Oocytes, and Folliculogenesis 57Jacques Gilloteaux and James Coey 5 The Human Spermatozoa 65Allan Pacey and Katrina Williams 6 The Biology of Fertilization 75Michael Carroll 7 Human Embryo Development: From Zygote Stage to Peri‐Implantation Blastocyst 93Stéphane Berneau and Michael Carroll 8 The Female Reproductive Tract and Early Embryo Development: A Question of Supply and Demand 99Henry J. Leese and Daniel R. Brison Section Two Clinical Reproductive Science: Causes of Male and Female Infertility 109 9 Disorders of Male Reproductive Endocrinology 111Michael Carroll 10 Disorders of Female Reproductive Endocrinology 125Mahshid Nickkho‐Amiry and Cheryl T. Fitzgerald 11 Oocyte Aneuploidy and the Maternal Age Effect 133Mary Herbert 12 Female Reproductive Pathology: Peritoneal, Uterine, and Fallopian Tube Pathologies 147Kenneth Ma Kin Yue, Rosa Trigas, and Edmond Edi‐Osagie 13 Pathologies of the Male Reproductive Tract 159Aarush Sajjad, Muhammad A. Akhtar, and Yasmin Sajjad 14 The Impact of Infections on Reproduction and Fertility 177Val Edwards Jones 15 Nutrition, Fetal Health, and Pregnancy 189Emma Derbyshire 16 The Embryonic Environment and Developmental Origins of Health 195Tom P. Fleming and Congshan Sun 17 Lifestyle and Environmental Impacts on Fertility 205Ana‐Maria Tomova and Michael Carroll Section Three Clinical Reproductive Science In Practice: IVF and Assisted Reproductive Technologies 215 18 Assessing the Infertile Couple 217Narmada Katakam, Ruth Arnesen, Caroline Watkins, Bert Stewart, and Luciano G. Nardo 19 Ovarian Stimulation Protocols 231Nikolaos Tsampras and Cheryl T. Fitzgerald 20 Oocyte Retrieval Techniques and Culture of Oocytes 241Dawn Yell 21 Sperm Preparation: Strategy and Methodology 251Stephen Harbottle 22 Diagnostic Semen Analysis: Uncertainty, Clinical Value, and Recent Advances 265Mathew Tomlinson 23 Surgical Sperm Retrieval 279Muhammad A. Akhtar, Elizabeth Hester, Solmaz Gul Sajjad, and Yasmin Sajjad 24 In Vitro Fertilization and Intracytoplasmic Sperm Injection 291Bryan Woodward 25 Morphological Assessment of Embryos in Culture 303J. Diane Critchlow 26 In Vitro Culture of Gametes and Embryos – The Culture Medium 317Robbie Kerr 27 Incubators in the Assisted Reproductive Technology Laboratory 333Louise Hyslop 28 Embryo Transfer Techniques and Improving Embryo Implantation Rates 341Rachel Cutting 29 Cryopreservation of Gametes and Embryos 351Tope Adeniyi 30 Preimplantation Genetic Diagnosis and Screening 371Colleen Lynch and Brendan Ball 31 Long‐Term Follow‐Up of Children Conceived Through In Vitro Fertilization 385Omar Abdel‐Mannan and Alastair G. Sutcliffe Index 393

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Book SynopsisHarmful Algal Blooms: A Compendium Desk Referenceprovides basic information on harmful algal blooms (HAB) and references for individuals in need of technical information when faced with unexpected or unknown harmful algal events. Chapters in this volume will provide readers with information on causes ofHAB, successful management and monitoring programs, control, prevention, and mitigation strategies, economic consequences of HAB, associated risks to human health, impacts of HAB onfood webs and ecosystems, and detailed information on the most common HAB species. Harmful Algal Blooms: A Compendium Desk Reference will be an invaluable resource to managers, newcomers to the field, those who do not have easy or affordable access to scientific literature, and individuals who simply do not know where to begin searching for the information needed, especially when faced with novel and unexpected HAB events. Edited by three of the world''s leading harmful algal bloTable of ContentsList of Contributors xvii Acknowledgments xxi Introduction xxiii 1 Causes of Harmful Algal Blooms 1Patricia M. Glibert and JoAnn M. Burkholder 1.1 Introduction 1 1.2 “Getting There”: The Classic Perspective on Introduced Species and Links to Cultural Eutrophication 2 1.2.1 Introduced Species 2 1.2.2 Anthropogenically Introduced Nutrients 3 1.3 “Being There”: Blooms and Why They Succeed 5 1.3.1 Nutrient-Related HAB 5 1.3.2 Resource Ratios, Nutrient Stoichiometry, and Optimal Nutrient Ratios 6 1.3.3 Diversity in Use of Forms of Nitrogen 9 1.3.4 Toxicity 10 1.3.5 Mixotrophy: Use of “Packaged” and Dissolved Particulate Nutrients 12 1.3.6 Other Adaptations 13 1.4 “Staying There”: Links to Physical Structure and Climate 14 1.4.1 Physical Structure: Large-Scale and Small-Scale Natural Hydrological Features 14 1.4.2 Physical Dynamics: Anthropogenic Hydrological Changes 15 1.4.3 Reinforcing Feedbacks 16 1.4.3.1 Trophic Disruptions 16 1.4.3.2 Biogeochemical Alterations 17 1.4.4 Climate Change 18 1.5 Conclusions 20 Acknowledgments 21 References 21 2 Detection and Surveillance of Harmful Algal Bloom Species and Toxins 39Gregory J. Doucette, Linda K. Medlin, Pearse McCarron, and Philipp Hess 2.1 Introduction 39 2.2 Organism Detection 41 2.2.1 Visual/Optical 41 2.2.1.1 Light Microscopy (LM)/Utermöhl’s 41 2.2.1.2 Light Microscopy/Flow Cytometry 41 2.2.1.3 In Vivo Fluorometry 42 2.2.1.4 Spectral Absorbance/Spectroradiometry 43 2.2.2 Molecular 43 2.2.2.1 Whole Cell Format 44 2.2.2.2 Cell-Free Format 47 2.3 Toxin Detection 51 2.3.1 In Vivo Assays 53 2.3.1.1 Rat Bioassay 58 2.3.1.2 Mouse Bioassay 58 2.3.2 In Vitro Assays 59 2.3.2.1 Functional Assays 60 2.3.2.2 Structural Assays 66 2.3.2.3 Biosensors 71 2.3.3 Analytical Techniques 72 2.3.3.1 High-Performance Liquid Chromatography with Optical Detection (UV or FLD) 73 2.3.3.2 Liquid Chromatography–Mass Spectrometry (LC-MS) and Liquid Chromatography–Tandem Mass Spectrometry (LC-MS/MS) 75 2.3.3.3 Other Analytical Methods: Capillary Electrophoresis (CE), Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF), and Laser Ablation Electrospray Ionization (LAESI) 78 2.3.3.4 Perspectives 79 2.4 Autonomous, In Situ Technologies 80 2.4.1 Environmental Sample Processor (McLane Research Laboratories) 81 2.4.2 Imaging Flow Cytobot (McLane Research Laboratories) 83 2.4.3 Optical Phytoplankton Discriminator (aka BreveBuster; Mote Marine Laboratory) 84 2.4.4 CytoBuoy (CytoBuoy b.v.) 85 2.4.5 SPATT Passive Samplers 86 2.5 Conclusions and Future Prospects 87 Disclaimer 89 References and Further Reading 89 3 Modeling Marine Harmful Algal Blooms: Current Status and Future Prospects 115Kevin J. Flynn and Dennis J. McGillicuddy, Jr. 3.1 Introduction 115 3.2 Building Models to Describe Ecological Events 117 3.3 Limitations to What Models Can Do, and Why 119 3.3.1 Building Models 119 3.3.2 Model Complexity 119 3.3.3 The Need for Data 120 3.3.4 Validating Models 121 3.4 Modeling T-HAB and ED-HAB Events 121 3.5 How Good Are Current HAB Models? 122 3.6 Future Modeling of T-HAB and ED-HAB: Managing Expectations 128 3.7 Improving Our Capabilities 129 3.7.1 Changes in the Biological–Modeling Interface 129 Acknowledgments 130 References 130 4 Harmful Algal Blooms and Shellfish 135Leila Basti, Hélène Hégaret, and Sandra E. Shumway 4.1 Introduction 135 4.2 Major Shellfish Poisonings 136 4.2.1 Paralytic Shellfish Poisoning (PSP) 136 4.2.2 Diarrheic Shellfish Poisoning (DSP) 137 4.2.3 Neurotoxic Shellfish Poisoning (NSP) 138 4.2.4 Amnesic Shellfish Poisoning (ASP) 139 4.2.5 Azaspiracid Shellfish Poisoning (AZP) 139 4.3 Other Toxins: Pectenotoxins (PTX) and Yessotoxins (YTX) 140 4.4 Emerging Shellfish Poisonings 141 4.5 Toxin Uptake, Accumulation, and Depuration 142 4.6 Shellfish Contamination in North America 143 4.6.1 Bivalves 143 4.6.1.1 Paralytic Shellfish Contamination 143 4.6.1.2 Diarrheic Shellfish Contamination 149 4.6.1.3 Neurotoxic Shellfish Contamination 150 4.6.1.4 Amnesic Shellfish Contamination 151 4.6.2 Gastropods 154 4.6.3 Crustaceans 162 4.7 Impacts on Shellfish 163 4.8 Conclusions and Perspectives 164 References and Further Reading 167 5 Vulnerabilities of Marine Mammals to Harmful Algal Blooms 191Margaret H. Broadwater, Frances M. Van Dolah, and Spencer E. Fire 5.1 Introduction 191 5.2 Overview of Algal Toxins 192 5.2.1 Brevetoxins 193 5.2.2 Ciguatoxins 199 5.2.3 Diarrhetic Shellfish Poisoning Toxins 200 5.2.4 Domoic Acid 201 5.2.5 Paralytic Shellfish Toxins 206 5.2.6 Other Algal and Cyanobacterial Toxins 209 5.3 Impacts of Algal Toxins Specific to Marine Mammals 210 5.3.1 The Effects of Toxin Exposure Depend on Animal Physiology and Behavior 210 5.3.2 Emerging Issues: Non-acute and Multiple Toxin Exposure 211 5.3.3 Prospects for Managing Impacts of HAB 211 5.4 Considerations for the Evaluation of HAB Toxins in Marine Mammals 212 5.4.1 Sampling Marine Mammals for HAB Toxin Analysis 213 5.4.2 Priority Needs for Investigating HAB Toxin Involvement in Marine Mammal Morbidity and Mortality 214 Abbreviations 214 References and Further Reading 215 6 Interactions between Seabirds and Harmful Algal Blooms 223Corinne M. Gibble and Brian A. Hoover 6.1 Introduction 223 6.2 Historical Interactions between HAB and Seabirds 224 6.2.1 Paralytic Shellfish Poisoning (PSP) 224 6.2.2 Neurotoxic Shellfish Poisoning (NSP) 227 6.2.3 Amnesic Shellfish Poisoning 228 6.2.4 Akashiwo sanguinea 228 6.2.5 Diarrheic Shellfish Poisoning (DSP) 229 6.2.6 CyanoHAB 230 6.3 Improved Monitoring and Establishment of Causality 231 6.3.1 Coordinating Monitoring and Pathology to Confirm Relationships between HAB and Seabird Mortality 231 6.3.2 Seabirds as Biological Indicators 233 6.4 Implications for Conservation 234 References 235 7 Food Web and Ecosystem Impacts of Harmful Algae 243JoAnn M. Burkholder, Sandra E. Shumway, and Patricia M. Glibert 7.1 Introduction 243 7.2 Approaches, Pitfalls, Progress, and Goals 277 7.3 High-Biomass Algal Blooms 279 7.4 Emerging Recognition of the Roles of Allelochemicals 282 7.4.1 Microalgae 283 7.4.2 Thalloid Macroalgae 285 7.4.3 Filamentous Mat-Forming Macroalgae 287 7.5 Toxigenic Algae in Aquatic Food Webs 287 7.5.1 Toxic Microcystis aeruginosa Blooms across North America 289 7.5.2 Toxic Prymnesium parvum Blooms and Fish Communities in Two Texas Rivers 290 7.5.3 Toxic Pseudo-nitzschia Blooms in Coastal Upwelling Areas 292 7.5.4 Toxic Alexandrium Blooms in the Northeast 292 7.5.5 Toxic Karenia brevis Blooms along the Florida Coast 293 7.6 Ecosystem-Disruptive Algal Blooms 294 7.7 Future Directions 295 Appendix A: Scientific Names for Organisms Listed by Common Name in This Chapter, Also Indicating Species Affected by Karenia brevis (Kb) 297 References and Further Reading 301 8 Assessing the Economic Consequences of Harmful Algal Blooms: A Summary of Existing Literature, Research Methods, Data, and Information Gaps 337Charles M. Adams, Sherry L. Larkin, Porter Hoagland, and Brian Sancewich 8.1 Introduction 337 8.2 Overview 338 8.3 Research Methodologies 338 8.4 Sources and Types of Data 347 8.5 Spatial and Temporal Scopes 348 8.6 Nature of the Hazard 349 8.7 Current Research Gaps 350 8.8 Conclusion 351 Acknowledgments 351 References and Further Reading 351 9 Public Health and Epidemiology 355Lynn M. Grattan, Joe Schumacker, Andrew Reich, and Sailor Holobaugh 9.1 Introduction 355 9.2 What Is Public Health and Epidemiology? 355 9.3 HAB and Human Illness 356 9.3.1 Paralytic Shellfish Poisoning (PSP) 357 9.3.1.1 Exposure 357 9.3.1.2 Clinical Symptoms 361 9.3.1.3 Treatment 361 9.3.2 Amnesic Shellfish Poisoning (ASP) 361 9.3.2.1 Exposure 361 9.3.2.2 Clinical Syndrome 361 9.3.2.3 Treatment 362 9.3.3 Neurotoxic Shellfish Poisoning (NSP) 362 9.3.3.1 Exposure 362 9.3.3.2 Clinical Illness 363 9.3.3.3 Treatment 363 9.3.4 Brevetoxin Inhalation Syndrome (BIS) 363 9.3.4.1 Exposure 363 9.3.4.2 Clinical Illness 363 9.3.4.3 Treatment 363 9.3.5 Diarrhetic Shellfish Poisoning (DSP) 363 9.3.5.1 Exposure 363 9.3.5.2 Clinical Syndrome 364 9.3.5.3 Treatment 364 9.3.6 Ciguatera Fish Poisoning (CFP) 364 9.3.6.1 Exposure 364 9.3.6.2 Clinical Illness 364 9.3.6.3 Treatment 365 9.3.7 Azaspiracid Shellfish Poisoning (AZP) 365 9.3.7.1 Exposure 365 9.3.7.2 Clinical Syndrome 366 9.3.7.3 Treatment 366 9.3.8 Toxic Cyanobacteria 366 9.3.8.1 Exposure 366 9.3.8.2 Clinical Syndromes 366 9.3.8.3 Treatment 366 9.4 The HAB Manager’s Role in Preventing HAB-Related Illnesses 367 9.4.1 HAB Management Exemplars 367 9.4.2 The Native American Perspective from Washington State, USA: Domoic Acid and Paralytic Shellfish Toxins 367 9.4.2.1 Background 367 9.4.2.2 Tribal Capacity and Inclusion 369 9.4.2.3 Lessons Learned 369 9.4.3 The Florida Department of Health Perspective 369 9.4.3.1 Harmful Algal Blooms 370 9.5 HAB-Related Stressors and Human Resilience 370 9.6 Conclusion 371 References and Further Reading 371 10 Marine Biotoxin and Harmful Algae Monitoring and Management 377Gregg W. Langlois and Steve L. Morton 10.1 Introduction 377 10.2 Identifying Sampling Program Needs 383 10.3 Developing a Sampling Program for Shellfish Monitoring 384 10.3.1 Shellfish Sampling Stations 384 10.3.2 Monitoring Shellfish Toxicity 386 10.4 Developing a Sampling Program for Phytoplankton Monitoring 388 10.4.1 Phytoplankton Sampling Stations 388 10.4.2 Monitoring Phytoplankton 389 10.5 Monitoring Other Fisheries 394 10.6 Novel Approaches and Advanced Tools to Enhance Monitoring Programs 396 10.6.1 Diversifying Program Participation: Volunteer Monitors 396 10.6.2 Field Testing for Toxins: PSP and ASP 399 10.6.3 Screening Tests for Toxins: DSP and PSP 401 10.6.4 SPATT 401 10.6.5 Oceanographic Data 402 10.7 Management Considerations 408 10.7.1 Commercial Shellfish 408 10.7.2 Recreational Shellfishing 411 10.8 Phytoplankton Sampling Protocol Examples 413 10.9 HAB Forecasting Links 413 Acknowledgments 413 References and Further Reading 413 11 Harmful Algal Bloom Education and Outreach 419Mare Timmons, Mary Sweeney-Reeves, and Steve L. Morton 11.1 Introduction 419 11.2 K–12 Education 426 11.3 Web-Based and Distance Learning Education 427 11.4 Citizen Science 428 11.4.1 Contributions of Citizen Science 429 11.4.2 Connecting Citizen Science to Ocean Learning 431 11.4.2.1 Safety 431 11.4.2.2 Training Sessions 431 11.5 Conclusion 432 References and Further Reading 432 12 Prevention, Control, and Mitigation of Harmful Algal Bloom Impacts on Fish, Shellfish, and Human Consumers 435Kevin G. Sellner and J.E. (Jack) Rensel 12.1 Introduction 435 12.2 HAB Prevention 435 12.2.1 Aquaculture Site Selection or Relocation 435 12.2.2 Nutrient Load Reductions 436 12.2.3 Phytoplankton Mixing, Increasing Turbulence, and Decreasing Residence Times (Mostly Freshwater Systems) 440 12.2.4 Reducing HA Introductions 441 12.3 Preventing and Reducing HAB Impacts on Shellfish and Fish 442 12.3.1 Preventing Human and Animal Exposures 442 12.3.1.1 Shellfish and Finfish Monitoring 442 12.3.1.2 Depuration and Detoxification 444 12.3.1.3 Food Processing 444 12.3.1.4 Cooking 445 12.3.1.5 Aerosols 445 12.3.1.6 Medical Treatments 445 12.4 HAB Controls 445 12.4.1 Protections 445 12.4.2 Biomass Removal 446 12.4.3 Capping 446 12.4.4 Nutrient Trapping in Sediments 446 12.4.5 Reductions of Algal Resting Stages (Cysts) 446 12.5 Mitigation of HAB 447 12.5.1 Detection 447 12.5.2 Chemical Additions 448 12.5.3 Flocculation 451 12.5.4 Barely Straw (Hordeum vulgare) 454 12.5.5 Other Treatments 455 12.5.5.1 UV Exposure 455 12.5.5.2 Cavitation 455 12.5.5.3 Ultrasound 455 12.5.5.4 Electrolysis 456 12.5.5.5 Hydraulics and Mixing 456 12.5.5.6 Biological Controls 456 12.6 Shellfish 458 12.7 Fish Mariculture 459 12.7.1 HAB Mitigation for Fish Mariculture 459 12.7.2 Best Management Practices for Fish Mariculture Siting, Including HAB and Eutrophication Issues 460 12.7.2.1 Local Land Use 460 12.7.2.2 Plankton Monitoring and Water Quality Assessments 460 12.7.2.3 Physical Hydrographic Considerations 461 12.7.2.4 Vertical Mixing Considerations 461 12.7.3 Mitigation of HAB at Fish Mariculture Facilities 461 12.7.4 HAB Mitigation Methods for Fish Mariculture 462 12.7.4.1 Feeding and Handling Practices 462 12.8 Conclusions 470 Acknowledgments 474 References 474 Further Reading 492 13 Harmful Algae Introductions: Vectors of Transfer, Mitigation, and Management 493Shauna Murray and Gustaaf Hallegraeff 13.1 Summary 493 13.2 The Biogeographic Ranges of Harmful Algal Bloom Species 493 13.3 Vectors of Transfer 494 13.3.1 Natural Factors 494 13.3.2 Ballast Water 494 13.3.3 Translocation of Aquaculture Products 494 13.4 Molecular Evidence for Introductions of New Species to a Region 494 13.4.1 The Stalk-Forming Freshwater Fouling Diatom Didymosphenia geminata 495 13.4.2 Alexandrium pacificum and A. minutum in European and Japanese Waters 496 13.4.3 Gymnodinium catenatum in Australia and Europe 497 13.5 Prevention and Risk Reduction 498 13.5.1 Code of Practice on Translocation with Aquaculture Products 498 13.5.2 Warning for HAB in Ballast Water-Uptake Zones and When Translocating Aquaculture Products 498 13.5.3 Ballast Water Management 498 13.5.4 Other Precautionary Measures 500 13.6 Emergency Treatment Options 501 References 502 14 Culture and Culture Collections 507Gary H. Wikfors and Steve L. Morton 14.1 Introduction 507 14.2 Step 1: Sampling the Environment 507 14.3 Step 2: Processing a Field Sample in the Laboratory to Confirm Presence of the Target Organism 509 14.4 Step 3: From Spark to Flame 511 14.5 Step 4: Long-Term Perpetuation of HAB Cultures 511 14.6 Epilogue 512 Further Reading 513 15 Harmful Macroalgal Blooms in a Changing World: Causes, Impacts, and Management 515Brian E. Lapointe, JoAnn M. Burkholder, and Kathryn L. Van Alstyne 15.1 Introduction 515 15.2 Freshwater and Other Inland Macroalgae 516 15.3 Estuarine and Coastal Marine Macroalgae 519 15.4 Influences on Bloom Development 525 15.5 Nutrient Pollution 525 15.5.1 Sources 525 15.5.2 Indicators of Nutrient Pollution and Nutrient Sources 526 15.6 Uptake/Adsorption of Other Contaminants 526 15.7 Impacts on Human Health: Macroalgae as Substrata for Pathogens 527 15.8 Non-native Invasions 528 15.9 Ecological and Ecosystem-Level Impacts 529 15.9.1 Regime Shifts 530 15.9.2 Freshwater Macroalgal HAB 532 15.9.2.1 Filamentous Cyanobacteria 532 15.9.2.2 Filamentous Green Algae 533 15.9.3 Estuarine and Coastal Marine HAB 534 15.10 Effects of Blooms on the Chemistry of the Oceans and the Atmosphere 535 15.10.1 Changes to Carbonate Chemistry and pH 535 15.10.2 Release of Materials and Chemicals into Seawater 536 15.10.3 Release of Volatile Compounds 537 15.11 Management Strategies 537 15.12 Economic Impacts 539 15.13 Recycling Macroalgae Biomass 541 15.14 Forecast 542 References and Further Reading 542 16 Harmful Algal Species Fact Sheets 561 Alexandrium 563Allan D. Cembella Amphidomataceae 575Urban Tillmann Aureococcus anophagefferens Hargraves et Sieburth & Aureoumbra lagunensis DeYoe et Stockwell – Brown Tides 583Christopher J. Gobler Ceratium furca (Ehrenberg) Claparede & Lachmann 585Steve L. Morton Chattonella marina 587Carmelo R. Tomas Cochlodinium – Rust Tide 589Christopher J. Gobler Cyanobacteria 591JoAnn M. Burkholder, Christopher J. Gobler, and Judith M. O’Neil Dinophysis 597Steve L. Morton Fibrocapsa japonica 599Carmelo R. Tomas Gambierdiscus 601Michael L. Parsons, Mindy L. Richlen, and Alison Robertson Gymnodinium catenatum 605Allan D. Cembella and Christine J. Band-Schmidt Heterosigma akashiwo 613Carmelo R. Tomas Karenia brevis (Davis) Hansen et Moestrup – Florida Red Tide 615Larry E. Brand Ostreopsis 617Michael L. Parsons, Mindy L. Richlen, and Alison Robertson Pfiesteria piscicida Steidinger & Burkholder and Pfiesteria shumwayae Glasgow & Burkholder 621JoAnn M. Burkholder and Harold G. Marshall Prorocentrum 625Patricia M. Glibert and JoAnn M. Burkholder Prymnesium parvum (Carter) – “Golden Algae” 629Daniel L. Roelke and Schonna R. Manning Pseudo-nitzschia – seriata group; delicatissima group 633Raphael Kudela Takayama 637Larry E. Brand Appendix 1 Websites That Routinely Distribute Bulletins on the Presence of Harmful Algal Blooms (HAB) for Public Health 639 Appendix 2 State Agencies Providing Information and Updates on Toxic and Harmful Algal Blooms and Water Quality 641 Appendix 3 List of General Web Resources 645 Index 647

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Book SynopsisBacteria in various habitats are subject to continuously changing environmental conditions, such as nutrient deprivation, heat and cold stress, UV radiation, oxidative stress, dessication, acid stress, nitrosative stress, cell envelope stress, heavy metal exposure, osmotic stress, and others. In order to survive, they have to respond to these conditions by adapting their physiology through sometimes drastic changes in gene expression. In addition they may adapt by changing their morphology, forming biofilms, fruiting bodies or spores, filaments, Viable But Not Culturable (VBNC) cells or moving away from stress compounds via chemotaxis. Changes in gene expression constitute the main component of the bacterial response to stress and environmental changes, and involve a myriad of different mechanisms, including (alternative) sigma factors, bi- or tri-component regulatory systems, small non-coding RNA's, chaperones, CHRIS-Cas systems, DNA repair, toxin-antitoxin systems, the stringent rTable of ContentsVOLUME 1 Preface, xiii Acknowledgements, xiv List of contributors, xv 1 Introduction, 1Frans J. de Bruijn Section 2: Key overview chapters, 3 2.1 Stress-induced changes in transcript stability, 5Dvora Biran and Eliora Z. Ron 2.2 StressChip for monitoring microbial stress response in the environment, 9Joy D. Van Nostrand, Aifen Zhou and Jizhong Zhou 2.3 A revolutionary paradigm of bacterial genome regulation, 23Akira Ishihama 2.4 Role of changes in σ70-driven transcription in adaptation of E. coli to conditions of stress or starvation, 37Umender K. Sharma 2.5 The distribution and spatial organization of RNA polymerase in Escherichia coli: growth rate regulation and stress responses, 48Ding Jun Jin, Cedric Cagliero, Jerome Izard, Carmen Mata Martin, and Yan Ning Zhou 2.6 The ECF classification: a phylogenetic reflection of the regulatory diversity in the extracytoplasmic function σ factor protein family, 64Daniela Pinto andThorsten Mascher 2.7 Toxin–antitoxin systems in bacteria and archaea, 97Yoshihiro Yamaguchi and Masayori Inouye 2.8 Bacterial sRNAs: regulation in stress, 108Marimuthu Citartan, Carsten A. Raabe, Chee-Hock Hoe, Timofey S. Rozhdestvensky, andThean-Hock Tang 2.9 Bacterial stress responses as determinants of antimicrobial resistance, 115Michael Fruci and Keith Poole 2.10 Transposable elements: a toolkit for stress and environmental adaptation in bacteria, 137Anna Ullastres, Miriam Merenciano, Lain Guio, and Josefa González 2.11 CRISPR–Cas system: a new paradigm for bacterial stress response through genome rearrangement, 146Joseph A. Hakim, Hyunmin Koo, Jan D. van Elsas, Jack T. Trevors, and Asim K. Bej 2.12 The copper metallome in prokaryotic cells, 161Christopher Rensing, Hend A. Alwathnani, and Sylvia F. McDevitt 2.13 Ribonucleases as modulators of bacterial stress response, 174Cátia Bárria, Vánia Pobre, Afonso M. Bravo, and Cecília M. Arraiano 2.14 Double-strand-break repair, mutagenesis, and stress, 185Elizabeth Rogers, Raul Correa, Brittany Barreto, María Angélica Bravo Núñez, P.J. Minnick, Diana Vera Cruz, Jun Xia, P.J. Hastings, and Susan M. Rosenberg 2.15 Sigma factor competition in Escherichia coli: kinetic and thermodynamic perspectives, 196Kuldeepkumar Ramnaresh Gupta and Dipankar Chatterji 2.16 Iron homeostasis and iron–sulfur cluster assembly in Escherichia coli, 203Huangen Ding 2.17 Mechanisms underlying the antimicrobial capacity of metals, 215Joe A. Lemire and Raymond J. Turner 2.18 Acyl-homoserine lactone-based quorum sensing in members of the marine bacterial Roseobacter clade: complex cell-to-cell communication controls multiple physiologies, 225Alison Buchan, April Mitchell,W. Nathan Cude, and Shawn Campagna 2.19 Native and synthetic gene regulation to nitrogen limitation stress, 234J örg Schumacher Section 3: One-, two-, and three-component regulatory systems and stress responses, 247 3.1 Two-component systems that control the expression of aromatic hydrocarbon degradation pathways, 249\Tino Krell 3.2 Cross-talk of global regulators in Streptomyces, 257Juan F. Martín, Fernando Santos-Beneit, Alberto Sola-Landa, and Paloma Liras 3.3 NO–H-NOX-regulated two-component signaling, 268Dhruv P. Arora, Sandhya Muralidharan, and Elizabeth M. Boon 3.4 The two-component CheY system in the chemotaxis of Sinorhizobium meliloti, 277Martin Haslbeck 3.5 Stimulus perception by histidine kinases, 282Hannah Schramke, Yang Wang, Ralf Heermann, and Kirsten Jung Section 4: Sigma factors and stress responses, 301 4.1 The extracytoplasmic function sigma factor EcfO protects Bacteroides fragilis against oxidative stress, 303Ivan C. Ndamukong, Samantha Palethorpe, Michael Betteken, and C. Jeffrey Smith 4.2 Regulation of energy metabolism by the extracytoplasmic function (ECF) σ factors of Arcobacter butzleri, 311Irati Martinez-Malaxetxebarria, Rudy Muts, Linda van Dijk, Craig T. Parker, William G. Miller, Steven Huynh,Wim Gaastra, Jos P.M. van Putten, Aurora Fernandez-Astorga, and Marc M.S.M Wösten 4.3 Extracytoplasmic function sigma factors and stress responses in Corynebacterium pseudotuberculosis, 321Thiago L.P. Castro, Nubia Seyffert, Anne C. Pinto, Artur Silva, Vasco Azevedo, and Luis G.C. Pacheco 4.4 The complex roles and regulation of stress response σ factors in Streptomyces coelicolor, 328Jan Kormanec, Beatrica Sevcikova, Renata Novakova, Dagmar Homerova, Bronislava Rezuchova, and Erik Mingyar 4.5 Proteolytic activation of extra cytoplasmic function (ECF) σ factors, 344JessicaL. Hastie and Craig D. Ellermeier 4.6 The ECF family sigma factor σH in Corynebacterium glutamicum controls the thiol-oxidative stress response, 352Tobias Busche and Jörn Kalinowski 4.7 Posttranslational regulation of antisigma factors of RpoE: a comparison between the Escherichia coli and Pseudomonas aeruginosa systems, 361Sundar Pandey, Kyle L. Martins, and Kalai Mathee Section 5: Small noncoding RNAs and stress responses, 369 5.1 Bacterial small RNAs in mixed regulatory circuits, 371Jonathan Jagodnik, DenisThieffry, and Maude Guillier 5.2 Role of small RNAs in Pseudomonas aeruginosa virulence and adaptation, 383Hansi Kumari, Deepak Balasubramanian, and Kalai Mathee 5.3 Physiological effects of posttranscriptional regulation by the small RNA SgrS during metabolic stress inEscherichia coli, 393Gregory R. Richards 5.4 Three rpoS-activating small RNAs in pathways contributing to acid resistance of Escherichia coli, 402Geunu Bak, Kook Han, Daun Kim, Kwang-sun Kim, and Younghoon Lee 5.5 Thermal stress noncoding RNAs in prokaryotes and eukaryotes: a comparative approach, 412Mercedes de la Fuente and José Luis Martínez-Guitarte Section 6: Toxin-antitoxin systems and stress responses, 423 6.1 Epigenetics mediated by restriction modification systems, 425Iwona Mruk and Ichizo Kobayashi 6.2 Toxin–antitoxin systems as regulators of bacterial fitness and virulence, 437Brittany A. Fleming and Matthew A. Mulvey 6.3 Mechanisms of stress-activated persister formation in Escherichia coli, 446Stephanie M. Amato and Mark P. Brynildsen 6.4 Identification and characterization of type II toxin–antitoxin systems in the opportunistic pathogenAcinetobacter baumannii, 454Edita Sûziedéliené, Milda Jurénaité, and Julija Armalyté 6.5 Transcriptional control of toxin–antitoxin expression: keeping toxins under wraps until the time is right, 463Barbara Kℷedzierska and Finbarr Hayes 6.6 Opposite effects of GraT toxin on stress tolerance of Pseudomonas putida, 473Rita Hõrak and Hedvig Tamman Section 7: Stringent response to stress, 479 7.1 Preferential cellular accumulation of ppGpp or pppGpp in Escherichia coli, 481K. Potrykus and M. Cashel 7.2 Global Rsh-dependent transcription profile of Brucella suis during stringent response unravels adaptation to nutrient starvation and cross-talk with other stress responses, 489Stephan Köhler, Nabil Hanna, Safia Ouahrani-Bettache, Kenneth L. Drake, L. Garry Adams, and Alessandra Occhialini 7.3 The stringent response and antioxidant defences in Pseudomonas aeruginosa, 500Gowthami Sampathkumar, Malika Khakimova, Tevy Chan, and Dao Nguyen 7.4 Molecular basis of the stringent response in Vibrio cholerae, 507Shreya Dasgupta, Bhabatosh Das, Pallabi Basu, and Rupak K. Bhadra Section 8: Responses to UV irradiation, 517 8.1 UV stress-responsive genes associated with ICE SXT/R391 group, 519Patricia Armshaw and J. Tony Pembroke 8.2 Altered outer membrane proteins in response to UVC radiation in Vibrio parahaemolyticus and Vibrio alginolyticus, 528Fethi Ben Abdallah 8.3 Ultraviolet-B radiation effects on the community, physiology, and mineralization of magnetotactic bacteria, 532Yingzhao Wang and Yongxin Pan 8.4 Nucleotide excision repair system and gene expression in Mycobacterium smegmatis, 545Angelina Cordone Section 9: SOS and double stranded repair systems and stress, 551 9.1 The SOS response modulates bacterial pathogenesis, 553Darja ¢§Zgur Bertok 9.2 RNAP secondary-channel interactors in Escherichia coli: makers and breakers of genome stability, 561Priya Sivaramakrishnan and Christophe Herman 9.3 How a large gene network couples mutagenic DNA break repair to stress in Escherichia coli, 570Elizabeth Rogers, P.J. Hastings, María Angélica Bravo Núñez, and Susan M. Rosenberg 9.4 Double-strand DNA break repair in mycobacteria, 577Richa Gupta and Michael S. Glickman Section 10: Adaptation to oxidative stress, 587 10.1 Peroxide-sensing transcriptional regulators in bacteria, 58James M. Dubbs and Skorn Mongkolsuk 10.2 Regulation of oxidative stress–related genes implicated in the establishment of opportunistic infections by Bacteroides fragilis, 603Felipe Lopes Teixeira, Regina Maria Cavalcanti Pilotto Domingues, and Leandro Araujo Lobo 10.3 Investigation into oxidative stress response of Shewanella oneidensis reveals a distinct mechanism, 609Jie Yuan, Fen Wan, and Haichun Gao 10.4 An omics view on the response to singlet oxygen, 619Bork A. Berghoff and Gabriele Klug 10.5 Regulators of oxidative stress response genes in Escherichia coli and their conservation in bacteria, 632Herb E. Schellhorn, Mohammad Mohiuddin, Sarah M. Hammond, and Steven Botts 10.6 Hydrogen peroxide resistance in Bifidobacterium animalis subsp. lactis and Bifidobacterium longum, 638Taylor S. Oberg and Jeff R. Broadbent Section 11: Adaptation to osmotic stress, 647 11.1 Interstrain variation in the physiological and transcriptional responses of Pseudomonas syringae to osmotic stress, 649Gwyn A. Beattie, Chiliang Chen, Lindsey Nielsen, and Brian C. Freeman 11.2 Management of osmotic stress by Bacillus subtilis: genetics and physiology, 657Tamara Hoffmann and Erhard Bremer 11.3 Hyperosmotic response of Streptococcus mutans: from microscopic physiology to transcriptomic profile, 677Lu Wang and Xin Xu 11.4 Defective ribosome maturation or function makes Escherichia coli cells salt-resistant, 687Hyouta Himeno, Takefusa Tarusawa, Shion Ito, and Simon Goto Section 12: Dessication tolerance and drought stress, 693 12.1 Consequences of elevated salt concentrations on expression profiles in the rhizobium S. meliloti 1021 likely involved in heat and desiccation stress, 695Jan A.C. Vriezen, Caroline M. Finn, and Klaus Nüsslein 12.2 Genes involved in the formation of desiccationresistant cysts in Azotobacter vinelandii, 709Guadalupe Espín 12.3 Osmotic and desiccation tolerance in Escherichia coli O157:H7 and Salmonella enterica requires rpoS (σ38), 716Zach Pratt, Megan Shiroda, Andrew J. Stasic, Josh Lensmire, and C.W. Kaspar 12.4 Desiccation of Salmonella enterica induces cross-tolerance to other stresses, 725Shlomo Sela (Saldinger) and Chellaiah Edward Raja Index, i1 VOLUME 2 Preface, xiii Acknowledgements, xiv List of contributors, xv Section 13: Heat shock responses, 737 13.1 Heat shock response in bacteria with large genomes: lessons from rhizobia, 739Ana Alexandre and Solange Oliveira 13.2 Small heat shock proteins in bacteria, 747Martin Haslbeck 13.3 Transcriptome analysis of bacterial response to heat shock using next-generation sequencing, 754Kok-Gan Chan 13.4 Comparative analyses of bacterial transcriptome reorganisation in response to temperature increase, 757Bei-Wen Ying and Tetsuya Yomo 13.5 Participation of Ser–Thr protein kinases in regulation of heat stress responses in Synechocystis, 766Anna A. Zorina, Galina V. Novikova, and Dmitry A. Los Section 14: Chaperonins and stress, 781 14.1 GroEL/ES chaperonin: unfolding and refolding reactions, 783Victor V. Marchenkov, Nataliya A. Ryabova, Olga M. Selivanova, and Gennady V. Semisotnov 14.2 Functional comparison between the DnaK chaperone systems of Streptococcus intermedius and Escherichia coli, 791Toshifumi Tomoyasu and Hideaki Nagamune 14.3 Coevolution analysis illuminates the evolutionary plasticity of the chaperonin system GroES/L, 796Mario A. Fares 14.4 ClpL ATPase: a novel chaperone in bacterial stress responses, 812Pratick Khara and Indranil Biswas 14.5 Duplicated groEL genes inMyxococcus xanthus DK1622, 820Yan Wang, Xiao-jing Chen, and Yue-zhong Li Section 15: Cold shock responses, 827 15.1 Gene regulation by cold shock proteins via transcription antitermination, 829Sangita Phadtare and Konstantin Severinov 15.2 Metagenomic analysis of microbial cold stress proteins in polar lacustrine ecosystems, 837Hyunmin Koo, Joseph A. Hakim, and Asim K. Bej 15.3 Role of two-component systems in cold tolerance of Clostridium botulinum, 845Yâgmur Derman, Elias Dahlsten, and Hannu Korkeala 15.4 Cold shock CspA protein production during periodic temperature cycling in Escherichia coli, 854David Stopar and Tina Ivancic 15.5 Cold shock response in Escherichia coli: a model system to study posttranscriptional regulation, 859Anna Maria Giuliodori 15.6 New insight into cold shock proteins: RNA-binding proteins involved in stress response and virulence, 873Charlotte Michaux and Jean-Christophe Giard 15.7 Light regulation of cold stress responses in Synechocystis, 881Kirill S. Mironov and Dmitry A. Los 15.8 Escherichia coli cold shock gene profiles in response to overexpression or deletion of CsdA, RNase R, andPNPase and relevance to low-temperature RNA metabolism, 890Sangita Phadtare Section 16: Adaptation to acid stress, 897 16.1 Acid-adaptive responses of Streptococcus mutans, and mechanisms of integration with oxidative stress, 899Robert G. Quivey Jr., Roberta C. Faustoferri, Brendaliz Santiago, Jonathon Baker, Benjamin Cross, and Jin Xiao 16.2 Acid survival mechanisms in neutralophilic bacteria, 911Eugenia Pennacchietti, Fabio Giovannercole, and Daniela De Biase 16.3 Two-component systems in sensing and adapting to acid stress in Escherichia coli, 927Yoko Eguchi and Ryutaro Utsumi 16.4 Slr1909, a novel two-component response regulator involved in acid tolerance in Synechocystis sp. PCC 6803, 935Lei Chen, Qiang Ren, Jiangxin Wang, and Weiwen Zhang 16.5 Comparative mass spectrometry–based proteomics to elucidate the acid stress response in Lactobacillusplantarum, 944Tiaan Heunis, Shelly Deane, and Leon M.T. Dicks Section 17: Adaptation to nitrosative stress, 95317.1 Transcriptional regulation by thiol-based sensors of oxidative and nitrosative stress, 955Timothy Tapscott, Matthew A. Crawford, and Andr´es Vázquez-Torres 17.2 Haemoglobins of Mycobacterium tuberculosis and their involvement in management of environmental stress, 967Kanak L. Dikshit 17.3 What is it about NO that you don’t understand? The role of heme and HcpR in Porphyromonas gingivalis’s response to nitrate (NO3), nitrite (NO2), and nitric oxide (NO), 976Janina P. Lewis and Benjamin R. Belvin 17.4 Di-iron RICs: players in nitrosative-oxidative stress defences, 989Lígia S. Nobre and Lí©¥gia M. Saraiva 17.5 The Vibrio cholerae stress response: an elaborate system geared toward overcoming host defenses during infection, 997Karl-Gustav Rueggeberg and Jun Zhu 17.6 Ensemble modeling enables quantitative exploration of bacterial nitric oxide stress networks, 1009Jonathan L. Robinson and Mark P. Brynildsen Section 18: Adaptation to cell envelope stress, 1015 18.1 The Cpx inner membrane stress response, 1017Randi L. Guest and Tracy L. Raivio 18.2 New insights into stimulus detection and signal propagation by the Cpx-envelope stress system, 1025Patrick Hoernschemeyer and Sabine Hunke 18.3 Promiscuous functions of cell envelope stress-sensing systems in Klebsiella pneumoniae and Acinetobacterbaumannii, 1031Vijaya Bharathi Srinivasan and Govindan Rajamohan 18.4 Influence of BrpA and Psr on cell envelope homeostasis and virulence of Streptococcus mutans, 1043Zezhang T.Wen, Jacob P. Bitoun, Sumei Liao, and Jacqueline Abranches 18.5 Modulators of the bacterial two-component systems involved in envelope stress, transport, and virulence, 1055Rajeev Misra Section 19: Iron homeostasis, 1065 19.1 Iron homeostasis and environmental responses in cyanobacteria: regulatory networks involving Fur, 1067María Luisa Peleato, María Teresa Bes, and María F. Fillat 19.2 Interplay between O2 and iron in gene expression: environmental sensing by FNR, ArcA, and Fur in bacteria, 1079Bryan Troxell and Hosni M. Hassan 19.3 The iron–sulfur cluster biosynthesis regulator IscR contributes to iron homeostasis and resistance tooxidants in Pseudomonas aeruginosa, 1090Adisak Romsang, James M. Dubbs, and Skorn Mongkolsuk 19.4 Transcriptional analysis of iron-responsive regulatory networks in Caulobacter crescentus, 1103José F. da Silva Neto 19.5 Protein–protein interactions regulate the release of iron stored in bacterioferritin, 1109Huili Yao, YanWang, and Mario Rivera 19.6 Protein dynamics and ion traffic in bacterioferritin function: a molecular dynamics simulation study onwild-type and mutant Pseudomonas aeruginosa BfrB, 1118Huan Rui, Mario Rivera, and Wonpil Im Section 20: Metal resistance, 1131 20.1 Nickel toxicity, regulation, and resistance in bacteria, 1133Lee Macomber and Robert P. Hausinger 20.2 Metabolic networks to counter Al toxicity in Pseudomonas fluorescens: a holistic view, 1145Christopher Auger, Nishma D. Appanna, and Vasu D. Appanna 20.3 Genomics of the resistance to metal and oxidative stresses in cyanobacteria, 1154Corinne Cassier-Chauvat and Franck Chauvat 20.4 Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria, 1165Jiangxin Wang, Gang Wu, Lei Chen, and Weiwen Zhang 20.5 The extracytoplasmic function sigma factor–mediated response to heavy metal stress in Caulobacter crescentus, 1171Rogério F. Lourenco and Suely L. Gomes 20.6 Metal ion toxicity and oxidative stress in Streptococcus pneumoniae, 1184Christopher A. McDevitt, Stephanie L. Begg, and James C. Paton Section 21: Quorum sensing, 1195 21.1 Quorum sensing and bacterial social interactions in biofilms: bacterial cooperation and competition, 1197Yung-Hua Li and Xiao-Lin Tian 21.2 Recent advances in bacterial quorum quenching, 1206Kok-Gan Chan, Wai-Fong Yin, and Kar-Wai Hong 21.3 LuxR-type quorum-sensing regulators that are antagonized by cognate pheromones, 1221Stephen C. Winans, Ching-Sung Tsai, Gina T. Ryan, Ana Lidia Flores-Mireles, Esther Costa, Kevin Y. Shih, Thomas C.Winans, Youngchang Kim, Robert Jedrzejczak, and Gekleng Chhor 21.4 Adaptation to environmental stresses in Streptococcus mutans through the production of its quorum-sensing peptide pheromone, 1232Delphine Dufour, Vincent Leung, and Céline M. Lévesque 21.5 Quorum sensing in Bacillus cereus in relation to cysteine metabolism and the oxidative stress response, 1242Eugénie Huillet and Michel Gohar Section 22: Chemotaxis and biofilm formation, 1253 22.1 The flagellum as a sensor, 1255Rasika M. Harshey 22.2 Flagellar motility and fitness in xanthomonads, 1265Marie-Agnès Jacques, Jean-Françis Guimbaud, Martial Briand, Arnaud Indiana, and Armelle Darrasse 22.3 Understanding Listeriamonocytogenes biofilms: perspectives into mechanisms of adaptation and regulation under stress conditions, 1274Lizziane Kretli Winkelströter, Fernanda Barbosa dos Reis-Teixeira, Gabriela Satti Lameu, and Elaine Cristina Pereira De Martinis 22.4 Biofilm formation and environmental signals in Bordetella, 1279Tomoko Hanawa 22.5 Biofilm formation by rhizobacteria in response to water-limiting conditions, 1287Pablo Bogino, Fiorela Nievas, and Walter Giordano 22.6 Stress conditions triggering mucoid-to-nonmucoid morphotype variation in Burkholderia, and effects onvirulence and biofilm formation, 1295Leonilde M. Moreira, Inês N. Silva, Ana S. Ferreira, and Mário R. Santos 22.7 Effect of environmental conditions present in the fishery industry on the biofilm-forming ability of Staphylococcus aureus, 1304Daniel Vázquez-Sánchez 22.8 Biofilm development and stress response in the cholera bacterium, 1310Anisia J. Silva and Jorge A. Benitez 22.9 Outer membrane vesicle secretion: from envelope stress to biofilm formation, 1322Thomas Baumgarten and Hermann J. Heipieper Section 23: Viable but nonculturable (VBNC) cells, 1329 23.1 Resuscitation of Vibrios fromthe viable but nonculturable state is induced by quorum-sensing molecules, 1331Mesrop Ayrapetyan, Tiffany C. Williams, and James D. Oliver 23.2 Differential resuscitative effects of pyruvate and its analogs on VBNC (viable but nonculturable)Salmonella, 1338Fumio Amano 23.3 Environmental persistence of Shiga toxin–producing E. coli, 1346Philipp Aurass and Antje Flieger 23.4 Of a tenacious and versatile relic: the role of inorganic polyphosphate (poly-P) metabolism in the survival, adaptation, and virulence of Campylobacter jejuni, 1354Issmat I. Kassem and Gireesh Rajashekara Index, i1

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Book SynopsisKnowledge of the evolutionary history of birds has much improved in recent decades. Fossils from critical time periods are being described at unprecedented rates and modern phylogenetic analyses have provided a framework for the interrelationships of the extant groups. This book gives an overview of the avian fossil record and its paleobiological significance, and it is the only up-to-date textbook that covers both Mesozoic and more modern-type Cenozoic birds in some detail. The reader is introduced to key features of basal avians and the morphological transformations that have occurred in the evolution towards modern birds. An account of the Cenozoic fossil record sheds light on the biogeographic history of the extant avian groups and discusses fossils in the context of current phylogenetic hypotheses. This review of the evolutionary history of birds not only addresses students and established researchers, but it may also be a useful source of information for anyone else with an inTrade Review"Of all the works on the evolution of birds, it is the most modern, complete summary, with just enough fossil figures (no reconstructions), including 16 central color pencils, morphological descriptions and of genealogical trees. A mine of reflections that illuminate our current settlements" Ornithos, 24:5 (2017)Table of ContentsForeword ix Preface xi Acknowledgments xiii Chapter 1 An Introduction to Birds, the Geological Settings of Their Evolution, and the Avian Skeleton 1 Birds Are Evolutionarily Nested within Theropod Dinosaurs 2 The Geological Settings of Avian Evolution in a Nutshell 4 Characteristics of the Avian Skeleton 6 Chapter 2 The Origin of Birds 18 Archaeopteryx: The German “Urvogel” and Its Bearing on Avian Evolution 19 The Closest Maniraptoran Relatives of Birds 22 Feather Evolution 32 The Origin of Avian Flight 37 Chapter 3 The Mesozoic Flight Way towards Modern Birds 43 Jeholornithids: Early Cretaceous Long-Tailed Birds 44 Confuciusornis, Sapeornis, and Kin: Basal Birds with a Pygostyle 45 Ornithothoraces and the Origin of Sustained Flapping Flight Capabilities 50 The Ornithuromorpha: Refinement of Modern Characteristics 55 Ornithurae and the Origin of Modern Birds 59 Chapter 4 Mesozoic Birds: Interrelationships and Character Evolution 64 The Interrelationships of Mesozoic Birds: Controversial Phylogenetic Placements and Well-Supported Clades 65 Character Evolution in Mesozoic Birds 68 Ontogenetic Development of Mesozoic Birds 81 Chapter 5 The Interrelationships and Origin of Crown Group Birds (Neornithes) 84 Phylogenetic Interrelationships of Neornithine Birds 85 The Mesozoic Fossil Record of Neornithine-Like and Neornithine Birds 88 Chapter 6 Palaeognathous Birds (Ostriches, Tinamous, and Allies) 94 The Interrelationships of Extant Palaeognathae 95 Early Cenozoic Palaeognathous Birds of the Northern Hemisphere 95 Long-Winged Ostriches, Rheas, and Tinamous 97 Short-Winged Palaeognathous Birds 101 Biogeography: A Textbook Example of Gondwanan Vicariance Has Been Dismantled 105 Chapter 7 Galloanseres: “Fowl” and Kin 107 Galliformes: From Herbivorous Forest Dwellers to Seed Eaters of Open Landscapes 108 The Waterfowl 113 Gastornithids: Giant Herbivorous Birds in the Early Paleogene of the Northern Hemisphere 118 Dromornithids (Mihirungs or Thunderbirds): Gastornis-Like Birds from Australia 120 Pelagornithids: Bony-Toothed Birds 121 Chapter 8 The “Difficult-to-Place Groups”: Biogeographic Surprises and Aerial Specialists 125 The Columbiform Birds: Doves, Sandgrouse, … and Mesites? 126 The Hoatzin: A South American Relict Species 127 Turacos and Cuckoos 129 Bustards 131 The “Wonderful” Mirandornithes, or How Different Can Sister Taxa Be? 132 Strisores: The Early Diversification of Nocturnal Avian Insectivores 136 Chapter 9 Shorebirds, Cranes, and Relatives 147 Charadriiformes: One of the Most Diverse Groups of Extant Birds 148 From Rail to Crane 156 Chapter 10 Aequornithes: Aquatic and Semi-Aquatic Carnivores 161 Loons: Foot-Propelled Divers of the Northern Hemisphere 162 Pelagic Tubenoses and Albatrosses 164 Penguins: More Than 60 Million Years of Flightlessness 168 The Polyphyletic “Pelecaniformes” and “Ciconiiformes” 174 Late Cenozoic Turnovers in Marine Avifaunas 187 Chapter 11 Cariamiforms and Diurnal Birds of Prey 189 Seriemas and Allies: Two Species Now, Many More in the Past 190 Diurnal Birds of Prey: Multiple Cases of Convergence among Raptorial Birds 197 Chapter 12 The Cenozoic Radiation of Small Arboreal Birds 204 The Courol and Mousebirds: Two African Relict Groups 205 The Long Evolutionary History of Owls 210 Parrots and Passerines: An Unexpected Sister Group Relationship and Its Potential Evolutionary Implications 212 Trogons, Rollers, and Woodpeckers: Cavity-Nesters with Diverse Foot Morphologies 223 Chapter 13 Insular Avifaunas Now and Then, on Various Scales 233 Islands and Isolated Continents as Refugia 234 The Evolution of Flightlessness in Predator-Free Environments 235 Insular Gigantism and Islands as Cradles of Unusual Morphologies 241 Glossary 245 References 248 Index 289

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Book SynopsisComprehensive resource on probiotics as applied to ice cream and frozen desserts, covering fundamentals, development, technology, and quality control Probiotic Ice Cream is the first book to look at probiotics as applied to ice cream and frozen desserts, covering the whole product development process, from essential fundamentals to formulation and characterization of the final product. Written by a highly qualified specialist with significant research experience in this unique field, Probiotic Ice Cream includes information on: Science of probiotic ice cream, covering principles of probiotics and how to select appropriate probiotic strains for use in ice cream Physical protection of probiotics in ice cream conditions, as well as nutritional value of functional ice cream for humans Technology of probiotic ice cream, covering the definition, formulation, and characterization of prebiotic, probiotic, synbiotic and postbiotic ice cre

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Book SynopsisSeascape Ecology provides a comprehensive look at the state-of-the-science in the application of landscape ecology to the seas and provides guidance for future research priorities.Table of ContentsContributors xiii Foreword xix Preface xxiii Part I Spatial Patterning in the Sea 1 1 Introducing Seascape Ecology 3Simon J. Pittman 1.1 Introduction 3 1.2 Landscape Ecology and the Emergence of Seascape Ecology 4 1.3 What is a Seascape? 6 1.3.1 The Patch-Matrix and Patch-Mosaic Models of Seascape Structure 8 1.3.2 The Spatial Gradient Model of Seascape Structure 11 1.3.3 Combining Spatial Gradients and Patch Mosaics 12 1.3.4 Chemical Seascapes and Ocean Soundscapes 13 1.4 Why Scale Matters in Seascape Ecology 14 1.5 Seascape Ecology can Inform Marine Stewardship 16 1.6 Conclusions and Future Directions 18 References 19 2 Mapping and Quantifying Seascape Patterns 27Bryan Costa, BrianWalker and Jennifer A. Dijkstra 2.1 Introduction 27 2.2 Defining Seascape Applications 30 2.3 Identifying Scales for Seascape Mapping 31 2.4 Sensor Selection for Seascape Mapping 33 2.4.1 Passive and Active Sensors 34 2.4.2 Environmental Conditions Limiting Passive and Active Sensors 36 2.5 Representing Patterns in Seascape Maps 37 2.5.1 The Continuous Gradient Concept 37 2.5.2 The Patch-Mosaic Model 39 2.5.3 Spatial Surrogates (Proxies) 42 2.6 Quantifying Seascape Structure 43 2.6.1 Sensitivity to Scale 45 2.7 Applications of Seascape Maps and Spatial Pattern Metrics 45 2.7.1 Understanding Uncertainty in Seascape Maps 47 2.8 Conclusions and Future Research Priorities 48 References 49 3 Pelagic Seascapes 57Kylie L. Scales, Diego Alvarez-Berastegui, Clare Embling and Simon Ingram 3.1 Introduction 57 3.2 Pattern and Process in the Pelagic Realm 58 3.2.1 Broad-scale Biogeographic Provinces 60 3.2.2 Finer Scale Patchiness and Patch Dynamics 61 3.2.3 Ecoclines and Ecotones in Pelagic Seascapes 62 3.2.4 Beneath the Surface: the Vertical Dimension of Pelagic Seascapes 64 3.3 Spatial Pattern Metrics for Pelagic Seascapes 66 3.3.1 Patch Mosaic Metrics 67 3.3.2 Surface Model Metrics – Identifying Ecoclines and Ecotones 67 3.3.3 Lagrangian Approaches 69 3.4 Spatial Ecoinformatics in the Pelagic Realm: from Physics to Predators 71 3.4.1 Broad-scale Migrations across Pelagic Seascapes 71 3.4.2 Linking AnimalMovements to the Spatial Patterning of Pelagic Seascapes 72 3.4.3 Incorporating the Vertical Dimension in Spatial Ecoinformatics 73 3.5 Conclusions and Future Research Priorities 74 3.6 Glossary 75 References 76 4 Scale and Scaling in Seascape Ecology 89David C. Schneider 4.1 Introduction 89 4.1.1 The Development of the Concept of Scale in the Twentieth Century 90 4.1.2 Prevalence and Usage of ‘Scale‘ in the Scientific Literature 91 4.1.3 Definition of Scale 94 4.2 Expressions of Scale 95 4.2.1 Graphical Expression of Scale 95 4.2.2 Graphical Expression of Scale in Research Planning 98 4.2.3 Formal Expression of Scale: Scope, Similarity and Power Laws 98 4.2.4 Scaling Manoeuvres 101 4.2.5 Ratio of Rates in Research Planning 104 4.3 Spatial and Temporal Scaling in Estimating Uncertainty 107 4.4 Spatial and Temporal Scaling in the Pelagic and Benthic Realms 107 4.5 Looking to the Future: Scaling Concepts and Practice in Seascape Ecology 108 4.5.1 From Useful Fictions to Calculation 108 4.5.2 From Comparative to Confirmatory Modes of Investigation 109 4.5.3 From Hypothesis Testing to Likelihood 110 4.5.4 From Scaling on a Mosaic to Scaling on the Continuum 111 4.6 From Ceteris Paribus to DimensionalThinking 112 4.7 Acknowledgements 112 References 113 Part II Linking Seascape Patterns and Ecological Processes 119 5 Ecological Consequences of Seagrass and Salt-Marsh Seascape Patterning on Marine Fauna 121Christoffer Bostrom, Simon J. Pittman and Charles Simenstad 5.1 Introduction 121 5.1.1 Seagrasses and Salt Marshes: Global Distributions and Ecosystem Functions 122 5.2 Structural Processes and Change in Coastal Seascapes 122 5.2.1 Processes Creating and Maintaining Seagrass Seascapes 125 5.2.2 Processes Creating and Maintaining Salt-Marsh Seascapes 125 5.2.2.1 Tidal Channel Networks in Salt Marshes 128 5.3 Ecological Consequences of Seascape Structure 128 5.3.1 Seagrass Patch-size Effects on Epifauna and Fish 128 5.3.2 Patch Edges: Conceptual Framework and Application 130 5.3.2.1 Seagrass Edge Effects on Faunal Recruitment and Distribution 132 5.3.3 Effects of Salt-Marsh Patch Size, Edges and Connectivity on Faunal Patterns and Processes 133 5.3.4 Faunal Linkages between Salt Marshes and Seagrass Meadows 135 5.4 Challenges and Opportunities in Seascape Ecology 138 References 140 6 Seascape Patch Dynamics 153Emma L. Jackson, Rolando O. Santos-Corujo and Simon J. Pittman 6.1 Introduction 153 6.2 From Patch Dynamics to Seascape Ecology 155 6.3 Scale 158 6.4 Factors Influencing Seascape Patchiness 160 6.5 Mapping and Quantifying Seascape Change 163 6.5.1 Habitat Mapping for Change Analysis 164 6.5.2 Characterization of Spatial Patterns 166 6.5.2.1 Continuous metrics and surface analysis 167 6.5.2.2 Metrics, Scale and Sensitivity Analysis 168 6.5.2.3 Quantifying Seascape Change 168 6.5.3 Seascape Habitat Loss versus Fragmentation 170 6.5.4 Seascape Modelling 173 6.6 The Future of Seascape Dynamics Research 175 References 177 7 AnimalMovements through the Seascape: Integrating Movement Ecology with Seascape Ecology 189Simon J. Pittman, Benjamin Davis and Rolando O. Santos-Corujo 7.1 Introduction 189 7.1.1 Why AnimalMovement is Central to Seascape Ecology 191 7.1.2 Advances in Movement Ecology and its Application in Marine Systems 193 7.1.3 Tracking and Mapping Capabilities 194 7.2 Using Animal Movements to Scale Ecological Studies 196 7.2.1 Building Movement Scales into Conceptual and Operational Frameworks 199 7.2.1.1 Component 1: Build a ConceptualModel 199 7.2.1.2 Component 2: Selecting Scale 199 7.2.1.3 Component 3: Tools Identification 201 7.3 Advances in the Visualization and Quantification of Space-use Patterns 201 7.3.1 Estimating and Mapping Utilization Distributions 201 7.3.2 Analysing Spatiotemporal Utilization Patterns 204 7.3.3 VisualizingMovement Patterns across Three Spatial Dimensions 206 7.4 Linking AnimalMovement Patterns to Seascape Patterns 208 7.4.1 Linking IndividualMovement Trajectories to Seascape Structure 209 7.4.2 IndividualMovement and Seascape Connectivity 211 7.4.3 Linking Species Interactions and Physiology with Movements across Seascapes 212 7.4.4 Experimental Seascapes to Investigate Animal Response to Seascape Patterns 214 7.4.5 Mechanistic Models 215 7.5 Implications of Animal-Seascape Understanding for Marine Stewardship 215 References 217 8 Using Individual-based Models to Explore Seascape Ecology 229Kevin A. Hovel and Helen M. Regan 8.1 Introduction 229 8.1.1 What are IBMs? 229 8.2 Why use IBMs to Study Seascape Ecology? 231 8.2.1 The Effects of Habitat Structure on Populations are Consequences of Organismal Behaviour 231 8.2.2 IBMs Allow for Extensive Manipulation of Seascapes 235 8.2.3 IBMs can be Used to Test for Ecological Effects of Habitat Configuration versus Habitat Amount 239 8.2.4 IBMs Allow Tests of How Seascape Change Influences Ecological Processes 241 8.2.5 IBMs Allow the Coupling of Processes Operating over Different Scales 245 8.3 Data for Parameterizing Seascape Ecology IBMs 246 8.3.1 Parameterization 246 8.3.2 Movement and Habitat Selection 247 8.3.3 Seascape and Habitat Structure 248 8.3.4 Other Factors 249 8.4 Challenges and Future Directions in Using IBMs to Explore Seascapes 249 References 251 Part III Seascape Connectivity 259 9 Connectivity in Coastal Seascapes 261Andrew D. Olds, Ivan Nagelkerken, Chantal M. Huijbers, Ben L. Gilby, Simon J. Pittman and Thomas A. Schlacher 9.1 Introduction 261 9.2 Global Synthesis of Connectivity Research 261 9.2.1 ResearchTheme 263 9.2.2 Geographical Distribution 264 9.2.3 Biological and Functional Consequences 266 9.2.4 Connectivity is Scale Dependent 267 9.3 Quantifying Connectivity: Advances in Key Tools and Techniques 268 9.3.1 Tags and Telemetry 268 9.3.2 Ecogeochemical Markers 269 9.3.3 Genetics 269 9.4 Application of Seascape Connectivity to Coastal Seascapes: Focal Topics 270 9.4.1 Focal Topic 1: Fish Movements Connecting Tropical Coastal Seascapes 270 9.4.2 Focal Topic 2: Connectivity across the Land-Sea Interface 273 9.5 Integrating Connectivity into Marine Spatial Planning 275 9.6 Conclusions and Future Research Priorities 279 References 280 10 Networks for Quantifying and Analysing Seascape Connectivity 293Eric A. Treml and Johnathan Kool 10.1 Introduction 293 10.1.1 Structural Connectivity 295 10.1.2 Functional Connectivity 296 10.1.3 Realized Connectivity 296 10.2 Network Models of Connectivity: Representing Pattern and Process 297 10.2.1 Defining Nodes and Links 297 10.3 Modelling Marine Population Connectivity 300 10.3.1 Empirical Estimates of Marine Population Connectivity 301 10.4 Network Analysis of Marine Population Connectivity 303 10.4.1 Node and Neighbourhood-level Metrics 305 10.4.2 Components, Subgraphs and Clusters 306 10.4.3 Graph-level Metrics 306 10.4.4 Insights from Classic Networks 307 10.4.5 Planar Networks 308 10.4.6 Random Networks 308 10.4.7 Scale-free Networks 308 10.4.8 Small-world Networks 309 10.5 Case Study in Marine Connectivity: Hawaiian Islands 309 10.6 Conclusions and Future Research Priorities 312 10.7 Acknowledgements 313 References 313 11 Linking Landscape and Seascape Conditions: Science, Tools andManagement 319Kirsten L. L. Oleson, Kim A. Falinski, Donna-marie Audas, Samantha Coccia-Schillo,Paul Groves, Lida Teneva and Simon J. Pittman 11.1 Introduction 319 11.2 Landscape Ecology as a Guiding Framework for Integrated Land-sea Management 322 11.3 Modelling and Evaluating the Connections between Land and Sea 324 11.3.1 Measuring Threat Exposure from Land-based Sources 324 11.3.2 SpatialModelling of Land-Sea Processes 325 11.3.2.1 Spatial Proxies 325 11.3.2.2 Hydrological Models 325 11.3.2.3 Nearshore Dynamics 326 11.3.2.4 Ecological Response and Social-ecological Systems Models 327 11.3.3 Decision Analysis and Support 329 11.4 Case Studies 330 11.4.1 Hawai’i 330 11.4.1.1 Estimating Spatial Patterns of Erosion from Land Cover Change and Exposure of Reefs in Maui 331 11.4.2 Caribbean 334 11.4.2.1 Summit to Sea Runoff Modelling for St John, US Virgin Islands 334 11.4.2.2 Land-sea Decision Support Modelling for the Northeast Marine Corridor, Puerto Rico 336 11.4.3 Australia 339 11.4.3.1 Edgecumbe Bay ReceivingWaters (Gregory and Eden Lassie Creek Sub-basins) 342 11.5 Towards Applying Landscape Ecology to Land-Sea Modelling and Management 347 References 350 Part IV People and Seascapes 365 12 Advancing a Holistic Systems Approach in Applied Seascape Ecology 367Simon J. Pittman, Chris A. Lepczyk, Lisa M.Wedding and Camille Parrain 12.1 Introduction 367 12.1.1 What can Landscape Ecology Offer? 369 12.1.2 A Shift towards a more Holistic Systems Approach for Marine Stewardship 370 12.2 People as Part of the Seascape 373 12.3 How Holistic Systems Science can Help Seascape Ecology 375 12.3.1 Properties of an Ecological Systems Approach 376 12.3.2 The Rise ofWhole-of-System Modelling 377 12.4 Connecting Seascape Patterns to Human Health, Livelihoods and Wellbeing 379 12.5 Conclusions and Future Research Priorities 381 References 384 13 Human Ecology at Sea:Modelling andMapping Human-Seascape Interactions 391Steven Saul and Simon J. Pittman 13.1 Introduction 391 13.2 Seascape Ecology, Spatial Patterns and Scale 393 13.2.1 Scale and Scaling 395 13.3 Human Use Data Types and Geographical Information Systems 396 13.3.1 Mapping Human Behaviour across the Seascape 397 13.3.1.1 Remote Sensing 398 13.3.1.2 Participatory Mapping and Spatial Analysis 401 13.3.1.3 Social Sensing 402 13.3.1.4 Mapping Ecosystem Services 402 13.4 Modelling Human-Seascape Interactions with a Systems Approach 403 13.4.1 Custom-built StatisticalModels 405 13.4.2 Predefined Statistical Routines 406 13.4.3 Discrete Choice Models 407 13.4.4 Simulation Modelling 408 13.4.5 Agent-based Models 411 13.4.6 Pattern-orientedModelling 412 13.5 Conclusions and Future Research Priorities 415 References 418 14 Applying Landscape Ecology for the Design and Evaluation of Marine Protected Area Networks 429Mary A. Young, Lisa M.Wedding and Mark H. Carr 14.1 Introduction 429 14.2 Applying Landscape Ecology Principles in the Marine Environment 430 14.3 Case Study: Applying Landscape Ecology to Evaluate a Network of MPAs in California 438 14.3.1 California Seafloor Data Sets 439 14.3.2 MPA Goal: Habitat Replication and Representativeness 441 14.3.3 MPA Goal: Protect Diversity and Abundance of Marine Life 442 14.3.4 MPA Goal: Reduce Movement across Boundaries 444 14.4 Synthesis 448 14.4.1 Mapping Technologies 448 14.4.2 MPA Effects on Biodiversity and Populations 449 14.4.3 Scale of Interaction between Species and Environment 449 14.4.4 Across-system Interactions 450 14.4.5 Population Connectivity 450 14.5 Conclusions and Future Research Priorities 451 References 452 15 Seascape Economics: Valuing EcosystemServices across the Seascape 465Edward B. Barbier 15.1 Introduction 465 15.2 Habitat Connectivity and Seascape Goods and Services 467 15.3 Valuing Seascape Goods and Services 468 15.4 Example of a Mangrove-Coral Reef Seascape 472 15.5 Conclusions and Future Research Priorities 476 References 478 Part V Epilogue 483 16 Landscape Ecologists’ Perspectives on Seascape Ecology 485Simon J. Pittman, JohnA. Wiens, Jianguo Wu and Dean L. Urban 16.1 Introduction 485 16.2 From Landscapes to Seascapes (and Back Again) 485 16.3 Seascape Ecology and Landscape Ecology: Distinct, Related and Synergistic 487 16.3.1 Landscape Ecology 488 16.3.2 Seascape Ecology 488 16.3.3 How can Landscape and Seascape Ecology Interact with Each Other? 489 16.4 Seascape Ecology 491 References 493 Index 495

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Book SynopsisAn inspiring introduction to a vital scientific field. The reader is taken through ten mathematical derivations that lead to important results, explaining in a hands-on manner the key concepts and methods of theoretical population genetics. The derivations are carefully worked out and easy to follow.Table of ContentsIntroduction: On the constancy of allele frequencies 1 Derivation 1 Balance between forward and backward mutation 7 Derivation 2 Heterozygote advantage 23 Derivation 3 Breakdown of linkage disequilibrium 45 Derivation 4 Time to coalescence 63 Derivation 5 The evolution of genetic diversity 85 Derivation 6 Fixation of mutations with and without selection 105 Derivation 7 Nonhomogeneous populations 131 Derivation 8 Cost and benefit of sib-interactions 151 Derivation 9 Selection on a quantitative trait 167 Derivation 10 Evolutionary genetic analysis of the sex ratio 187 What’s next? 205 Epilogue 215 Thanks 217 Glossary 219 Answers 233 References 257 Index 263

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Book SynopsisAwarded Bookauthority''s Best Aquaculture Books of all TimeA comprehensive resource that covers all the aspects of sex control in aquaculture written by internationally-acclaimed scientists Comprehensive in scope, Sex Control in Aquaculture first explains the concepts and rationale for sex control in aquaculture, which serves different purposes. The most important are: to produce monosex stocks to rear only the fastest-growing sex in some species, to prevent precocious or uncontrolled reproduction in other species and to aid in broodstock management. The application of sex ratio manipulation for population control and invasive species management is also included. Next, this book provides detailed and updated information on the underlying genetic, epigenetic, endocrine and environmental mechanisms responsible for the establishment of the sexes, and explains chromosome set manipulation techniques, hybridization and the latest gene knockout approaches. Table of ContentsList of Contributors xv Preface xvii Acknowledgments xix Part I Theoretical and Practical Bases of Sex Control in Aquaculture 1 1 Sex Control in Aquaculture: Concept to Practice 3Han-Ping Wang and Zhi-Gang Shen 2 Sex Determination and Differentiation in Fish: Genetic, Genomic, and Endocrine Aspects 35Yann Guiguen, Alexis Fostier, and Amaury Herpin 3 Epigenetics of Sex Determination and Differentiation in Fish 65Francesc Piferrer 4 Environmental Sex Determination and Sex Differentiation in Teleosts -- How Sex Is Established 85Zhi-Gang Shen and Han-Ping Wang 5 Gene Knockout and Its Principle and Application in Sex Control of Fish Species 117Ze-Xia Gao and Bruce W. Draper 6 Chromosome Manipulation Techniques and Applications to Aquaculture 137Katsutoshi Arai and Takafumi Fujimoto 7 Hybridization and Its Application in Aquaculture 163M. Aminur Rahman, Sang-Go Lee, Fatimah Md. Yusoff, and S.M. Rafiquzzaman 8 Population Consequences of Releasing Sex-Reversed Fish: Applications and Concerns 179Claus Wedekind Part II Sex Determination and Control in Cichlidae 189 9 Sex Control in Tilapias 191Jean-Francois Baroiller and Helena D'Cotta 10 Quantitative Genetics of Sexual Dimorphism in Tilapia and Its Application to Aquaculture 235Nguyen Hong Nguyen Part III Sex Determination and Control in Salmonidae 249 11 Sex Determination and Sex Control in Salmonidae 251Yann Guiguen, Sylvain Bertho, Amaury Herpin, and Alexis Fostier 12 Development and Application of Sex-Linked Markers in Salmonidae 281Cristian Araneda, Natalia Lam, and Patricia Iturra 13 Polyploidy Production in Salmonidae 297James J. Nagler Part IV Sex Determination and Control in Moronidae 305 14 Genetic and Environmental Components of Sex Determination in the European Sea Bass 307Marc Vandeputte and Francesc Piferrer 15 Morphological and Endocrine Aspects of Sex Differentiation in the European Sea Bass and Implications for Sex Control in Aquaculture 327Mercedes Blazquez and Eric Saillant 16 The Induction of Polyploidy, Gynogenesis, and Androgenesis in the European Sea Bass 347Alicia Felip and Francesc Piferrer Part V Sex Determination and Control in Centrarchidae 359 17 Sex Determination, Differentiation, and Control in Bluegill 361Han-Ping Wang, Zhi-Gang Shen, Ze-Xia Gao, Hong Yao, Dean Rapp, and Paul O'Bryant 18 Sex-Determining Mechanisms and Control of Sex Differentiation in Largemouth Bass and Crappies 385Tulin Arslan 19 Hybridization and its Application in Centrarchids 405Zhi-Gang Shen and Han-Ping Wang Part VI Sex Determination and Sex Control in Percidae 429 20 Sex Determination and Monosex Female Production in Yellow Perch 431Han-Ping Wang, Zhi-Gang Shen, Hong Yao, Paul O'Bryant, and Dean Rapp 21 Sex Determination and Control in Eurasian Perch 445Carole Rougeot 22 Sexual Dimorphism in Body Size and Form in Yellow Perch 461Hong-Wei Liang, Han-Ping Wang, Yan Meng, Hong Yao, Zhi-Gang Shen, and Gui-Wei Zou Part VII Sex Determination and Sex Control in Catfish 477 23 Sex Determination, Gonadal Sex Differentiation, and Sex Control in Channel Catfish 479Reynaldo Patino 24 Sexual Size Dimorphism, Sex Determination, and Sex Control in Yellow Catfish 495Jie Mei and Jian-Fang Gui 25 Mechanisms of Feminization and Sex Differentiation in Southern Catfish 509Si-Ping Deng, Zhi-Hao Liu, and De-Shou Wang Part VIII Sex Determination and Sex Control in Flatfishes 525 26 Genomic and Epigenetic Aspects of Sex Determination in Half-Smooth Tongue Sole 527Song-Lin Chen, Qian Zhou, and Chang-Wei Shao 27 Sex Identification and Control in Half-Smooth Tongue Sole 547Song-Lin Chen and Wen-Teng Xu 28 Reproduction and Sex Control in Turbot 565Xoana Taboada, Diego Robledo, Carmen Bouza, Francesc Piferrer, Ana María Vinas, and Paulino Martínez 29 Sex Control in Southern and Summer Flounder 583Xiang-Shan Ji, Song-Lin Chen, Yan Zhao, Jamie Mankiewicz Honeycutt, Russell J. Borski, and J. Adam Luckenbach 30 Gynogenesis and Sex Control in Japanese Flounder 603Ji-Lun Hou and Hai-Jin Liu 31 Sex Determination, Differentiation, and Control in Atlantic Halibut and Pacific Halibut 621Tillmann J. Benfey 32 Sex-Specific Markers, Gynogenesis, and Sex Control in Spotted Halibut 631Hong-Yu Ma, Song-Lin Chen, and Xiang-Shan Ji Part IX Sex Determination and Sex Control in Sturgeons 645 33 Sex Determination in Sturgeon 647Sven Wuertz, Hilal Güralp, Martin Psenicka, and Mikhail Chebanov 34 Hybridization and Polyploidization in Sturgeon 669Milos Havelka and Katsutoshi Arai Part X Sex Determination and Sex Control in Crustaceans 689 35 Sex Control in Cultured Decapod Crustaceans 691Tom Levy, Eliahu D. Aflalo, and Amir Sagi 36 Sex Reversal and Determination and Sex Control in Shrimp and Prawn 705Danitzia A. Guerrero-Tortolero and Rafael Campos-Ramos Part XI Sex Determination and Sex Control in Other Fish Species 723 37 Sex Determination, Differentiation, and Control in Atlantic Cod 725Tillmann J. Benfey 38 Sex Differentiation, Sex Change, and Sex Control in Groupers 735Masaru Nakamura and Yasuhisa Kobayashi 39 Artificial Gynogenesis and Sex Control in Large Yellow Croaker 751Zhi-Yong Wang and Ming-Yi Cai 40 Sex Determination and Control in Eels 775Xian-Cheng Qu 41 Sex Control and Chromosome Manipulation in Cyprinidae: Common Carp and Grass Carp 793Boris Gomelsky and William L. Shelton Index - Species 825 Index - Subjects 832

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