Biology, life sciences Books

Book SynopsisThe Black real estate entrepreneur Philip Payton played a central role in Harlem’s transformation into a Black community in the early twentieth century. In this biography, Kevin McGruder explores Payton’s career and its implications for the history of residential segregation.Trade ReviewKevin McGruder renders a poignant and revealing portrait of one of Black America’s pioneering entrepreneurs, the Harlem real estate impresario Philip Payton. This timely and important biography brings to life the limits of trying to achieve racial justice by playing by the capitalist rules of a segregated economy. -- Khalil Gibran Muhammad, author of The Condemnation of Blackness: Race, Crime, and the Making of Modern Urban AmericaThis meticulously researched must-read biography of Harlem’s pioneering Black businessman Philip Payton masterfully shows the promises and pitfalls of Black capitalism on the eve of the New Negro Renaissance. -- Shannon King, author of Whose Harlem Is This, Anyway? Community Politics and Grassroots Activism during the New Negro EraHow do you promote racial equity but still maximize profits? That was the balance that Philip Payton had to strike as a Black real estate broker in Harlem in the early 1900s. His Afro-American Realty Company said “Race prejudice is a luxury.” But this fascinating biography shows what a formidable obstacle it was. -- Laurence Pearl, former attorney at the Department of Housing and Urban DevelopmentDespite his extraordinarily significant role in American urban history, Philip Payton’s story has remained obscure and elusive. McGruder weaves together an engaging biography of a complex figure whose ups and downs in Harlem reveal the halting progress and profound tradeoffs that attended efforts to find decent housing for Black Americans. -- Brian Goldstein, author of The Roots of Urban Renaissance: Gentrification and the Struggle over HarlemKevin McGruder reveals the central role Philip Payton played in increasing the Black population in housing by maximizing profits and promoting racial equality. This is an expert addition to the growing list of biographies on major lesser-known African Americans. -- David Canton, author of Raymond Pace Alexander: A New Negro Lawyer Fights for Civil Rights in PhiladelphiaMcGruder's meticulous concern for the facts and the community's history are compelling. * New York Amsterdam News *Table of ContentsAcknowledgmentsIntroduction1. The Paytons Before and in Westfield2. The Provincial in New York City3. Entering the Field of Battle4. Battles in the Streets and the Courtroom5. To Liberia and Back6. Fifty Years of Freedom National7. The Last Big DealEpilogueChronologyNotesBibliographyIndex

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Book SynopsisIn 1952, John T. “Jack” Downey, a twenty-three-year-old CIA officer, was shot down over Manchuria. He was captured by the Chinese and held for the next twenty years. Lost in the Cold War is the never-before-told story of Downey’s decades as a prisoner of war and the efforts to bring him home.Trade ReviewAn engrossing read, Lost in the Cold War is a testament to one man’s incomparable strength of character and endurance-both physical and mental. Inspiring and enlightening all at once. -- Ret. Lt. Gen. James Clapper, former U.S. director of national intelligenceMost Cold War historians knew that Jack Downey had spent twenty years in Chinese captivity, but because of the low profile he kept following his release, they didn't know him. Now, posthumously, he's introduced himself with an extraordinary account of endurance, perseverance, and ultimately quiet triumph. Highly recommended indeed. -- John Lewis Gaddis, author of The Cold War: A New HistoryIn this extraordinary book, Jack Downey vividly describes how he, an American POW and an American hero, lived through the horror of twenty years of solitary confinement in Mao’s China. Thomas J. Christensen insightfully narrates the larger background—why and how confrontation was replaced by rapprochement between Beijing and Washington. -- Chen Jian, author of Mao’s China and the Cold WarThis inviting, smartly observed account of one man’s experience is all the more emotionally palpable because of its unsentimental presentation. The impressive interspersed chapters add perspective that will be invaluable to readers. -- Charles Hayford, former editor of the Journal of American-East Asian RelationsUnique and worthy of reading. * International Journal of Intelligence and Counterintelligence *Lost in the Cold War tells what happens to an American who bears the brunt of foolish policymaking. * Foreign Affairs *Table of ContentsNote to the Reader1. A Perfect Ambush2. An American Hero on a Fool’s Mission3. Who I Am, Where I Came From4. The Korean Watershed: The Cold War Begins for Downey and America5. The Making of a Mission6. The Flight Over China7. Interrogation Days in Shenyang8. Of Soldiers and Spies9. A Man in a Box10. The Long Confession11. The Trial12. B-29 Crew Were Released from China13. The China I Saw, with America in My Mind14. “Your Government Does Not Want You Back”: The Failure of U.S.-PRC Negotiations at Geneva15. Prison Life16. Cellmates17. Keepers and Comrades18. A Pinhole View on a Massive Tragedy: 1958–197019. Family Visits20. U.S.-PRC Rapprochement and Jack Downey’s Release: 1968–197321. Coming HomeAfterwordAcknowledgmentsNotesIndex

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Book SynopsisRuth DeFries argues that a surprising set of time-tested strategies from the natural world can help humanity weather contemporary crises. Exploring the lessons that life on Earth can teach us about coping with complexity, What Would Nature Do? offers timely options for civilization to reorganize for a safe and prosperous future.Trade ReviewDeFries is an excellent writer, using elegant storytelling to offer a hopeful delineation of pathways to a sustainable future. She builds on evolutionary history, the theory of complex adaptive systems, and examples of the emergence of cooperation in biological systems, including human societies—distilling a complex topic for a broad audience. -- Simon A. Levin, James S. McDonnell Distinguished University Professor in Ecology and Evolutionary Biology, Princeton UniversityDeFries has an unparalleled ability to think deeply about major societal trends and to distill the dynamics that explain these patterns. Each chapter is exquisitely written and illustrated by many interrelated examples, ranging from historical events from ancient times to current unsolved dilemmas faced by society. -- F. Stuart Chapin III, Professor Emeritus, University of Alaska–FairbanksOur world has become more interconnected yet less diverse, increasing our vulnerability to the unforeseen. To defend against catastrophe, Ruth DeFries says we must capture the lessons of evolution: how nature and humans have coped with the messy challenges they have faced over millennia. In What Would Nature Do?, she connects the dots with beautiful writing and rigorous research that will make you smile and say, “aha.” -- Len Baker, Partner, Sutter Hill VenturesSturdy science applied to society’s biggest problems and good food for thought. * Kirkus *A highly readable guide. An important book that identifies some of the limits of contemporary thinking. * Journal of Geography *Positively packed with fascinating history, science and analysis. 'What Would Nature Do?’ is a fascinating and mind-expanding book that helps the reader see the world in a different way, with more interconnectivity and similarities across fields of inquiry and scales of existence than before. Read it-you won’t regret it! * The Weekly Anthropocene *This thought-provoking book packs at least 20 different disciplines into a satisfying exploration of the myriad ways the natural world contends with existential challenges that threaten equilibrium. . . . Extensive footnotes plus at least 375 references and a detailed index make this text equally useful for a first-year liberal arts seminar, an upper-level course in ecological modeling, or a community read for concerned citizens. * Choice *Table of ContentsPrologue1. The Dragons Are Back2. Recovery from a Crash: Install Circuit Breakers3. Hedges for Bets: Invest in Diversity4. Mind the Net: Defend Against Cascading Failure5. One Size Fits No One: Make Decisions from the Bottom Up6. Cycles of RenewalAcknowledgmentsNotesReferencesIndex

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Book SynopsisRuth DeFries argues that a surprising set of time-tested strategies from the natural world can help humanity weather contemporary crises. Exploring the lessons that life on Earth can teach us about coping with complexity, What Would Nature Do? offers timely options for civilization to reorganize for a safe and prosperous future.Trade ReviewDeFries is an excellent writer, using elegant storytelling to offer a hopeful delineation of pathways to a sustainable future. She builds on evolutionary history, the theory of complex adaptive systems, and examples of the emergence of cooperation in biological systems, including human societies—distilling a complex topic for a broad audience. -- Simon A. Levin, James S. McDonnell Distinguished University Professor in Ecology and Evolutionary Biology, Princeton UniversityDeFries has an unparalleled ability to think deeply about major societal trends and to distill the dynamics that explain these patterns. Each chapter is exquisitely written and illustrated by many interrelated examples, ranging from historical events from ancient times to current unsolved dilemmas faced by society. -- F. Stuart Chapin III, Professor Emeritus, University of Alaska–FairbanksOur world has become more interconnected yet less diverse, increasing our vulnerability to the unforeseen. To defend against catastrophe, Ruth DeFries says we must capture the lessons of evolution: how nature and humans have coped with the messy challenges they have faced over millennia. In What Would Nature Do?, she connects the dots with beautiful writing and rigorous research that will make you smile and say, “aha.” -- Len Baker, Partner, Sutter Hill VenturesSturdy science applied to society’s biggest problems and good food for thought. * Kirkus *A highly readable guide. An important book that identifies some of the limits of contemporary thinking. * Journal of Geography *Positively packed with fascinating history, science and analysis. 'What Would Nature Do?’ is a fascinating and mind-expanding book that helps the reader see the world in a different way, with more interconnectivity and similarities across fields of inquiry and scales of existence than before. Read it-you won’t regret it! * The Weekly Anthropocene *This thought-provoking book packs at least 20 different disciplines into a satisfying exploration of the myriad ways the natural world contends with existential challenges that threaten equilibrium. . . . Extensive footnotes plus at least 375 references and a detailed index make this text equally useful for a first-year liberal arts seminar, an upper-level course in ecological modeling, or a community read for concerned citizens. * Choice *Table of ContentsPrologue1. The Dragons Are Back2. Recovery from a Crash: Install Circuit Breakers3. Hedges for Bets: Invest in Diversity4. Mind the Net: Defend Against Cascading Failure5. One Size Fits No One: Make Decisions from the Bottom Up6. Cycles of RenewalAcknowledgmentsNotesReferencesIndex

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Book SynopsisThis book explores the natural history of sex in urban bacteria, fungi, plants, and nonhuman animals. Kenneth D. Frank illuminates the reproductive behavior of scores of species.Trade ReviewCities are renowned as hot spots of human diversity. This book demonstrates that although less well known, this is equally true of biodiversity. Here this is viewed through the unusual lens of reproductive diversity—the variety of means by which organisms perpetuate their lineages. It is a volume filled with insight and lots of natural history nuggets, and it is beautifully illustrated. I imagine that most readers will find ‘I didn’t know that’ moments throughout. -- Kevin J. Gaston, University of ExeterAlthough there are many theories about how nonhuman life survives in cities, new insight comes from a firsthand look at the diverse range of organisms that live alongside us. Flowering plants, birds, reptiles... Kenneth D. Frank takes readers on a walk through the city, illuminating a universal biological principle: finding a mate. Lavishly illustrated, full of naturalist erudition and evolutionary curiosities, this book reveals that courses in ecology can be found within walking distance. -- P.-O. Cheptou, evolutionary ecologist, CNRS, FranceTable of ContentsForewordPrefaceAcknowledgmentsIntroduction1. Nonflowering Plants2. Herbaceous Annual Plants3. Herbaceous Perennial Plants4. Trees and Woody Vines5. Butterflies and Moths6. Bees, Wasps, and Ants7. Dragonflies and Praying Mantises8. Other Insects9. Invertebrates Exclusive of Insects10. Reptiles, Amphibians, and Fish11. Mammals12. Birds13. Fungi, Bacteria, and LichensConclusionGlossaryNotesPhoto CreditsIndex

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Book SynopsisThis book explores the natural history of sex in urban bacteria, fungi, plants, and nonhuman animals. Kenneth D. Frank illuminates the reproductive behavior of scores of species.Trade ReviewCities are renowned as hot spots of human diversity. This book demonstrates that although less well known, this is equally true of biodiversity. Here this is viewed through the unusual lens of reproductive diversity—the variety of means by which organisms perpetuate their lineages. It is a volume filled with insight and lots of natural history nuggets, and it is beautifully illustrated. I imagine that most readers will find ‘I didn’t know that’ moments throughout. -- Kevin J. Gaston, University of ExeterAlthough there are many theories about how nonhuman life survives in cities, new insight comes from a firsthand look at the diverse range of organisms that live alongside us. Flowering plants, birds, reptiles... Kenneth D. Frank takes readers on a walk through the city, illuminating a universal biological principle: finding a mate. Lavishly illustrated, full of naturalist erudition and evolutionary curiosities, this book reveals that courses in ecology can be found within walking distance. -- P.-O. Cheptou, evolutionary ecologist, CNRS, FranceTable of ContentsForewordPrefaceAcknowledgmentsIntroduction1. Nonflowering Plants2. Herbaceous Annual Plants3. Herbaceous Perennial Plants4. Trees and Woody Vines5. Butterflies and Moths6. Bees, Wasps, and Ants7. Dragonflies and Praying Mantises8. Other Insects9. Invertebrates Exclusive of Insects10. Reptiles, Amphibians, and Fish11. Mammals12. Birds13. Fungi, Bacteria, and LichensConclusionGlossaryNotesPhoto CreditsIndex

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Book SynopsisIn this unconventional book, Kay Harel uses biophilia as a lens to explore Charles Darwin’s life and thought in deeply original ways. In a set of interrelated essays, she considers how the love of life enabled him to see otherwise unseen evolutionary truths.Trade ReviewA playful, erudite, and fresh take on the emotional and imaginative dimensions of Darwin’s work, probing the many connections between his family relationships and the spirit of wonder with which he observed relationships in the living world. -- Ruth Padel, author of Darwin: A Life in PoemsThis is a joyful book. Instead of dwelling on the role of competition and extinction in Darwin's theory, as is so often done, Kay Harel emphasizes that love of life in all its varieties is crucial to Darwin's thinking and practice. The result is a deeply sympathetic study. -- Gillian Beer, author of Darwin’s Plots: Evolutionary Narrative in Darwin, George Eliot, and Nineteenth-Century Fiction[A] mighty debut. Harel’s lyrical musings delight, and they make for an original approach to a familiar topic. The science- and literary-minded alike will relish this thoughtful collection. * Publishers Weekly *A wonderful holistic understanding of Charles Darwin’s life and his own evolution. Recommended for fans of biologist/writer E. O. Wilson. * Library Journal *Gentle but stirring essays. [Kay] Harel's focus on the confluences of Darwin's life rather than its conflicts offers a refreshing take on his legacy. * Scientific American *A "must read." * The Next Big Idea Club *Table of ContentsPreface1. A Study in Biophilia2. It’s Dogged as Does It3. The Glories and Limits of Facts4. The Dance of Plants, the Roots of Mind5. The Varieties of Passionate Experience6. Beauty Is Life, Life Beauty7. The One Great Love of Two True MindsSelected BibliographyIndex

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Book SynopsisTrade ReviewBonnan combines wit and passion with the sensibilities of a talented instructor in this encyclopedic tour of the vertebrate skeleton . . . accessible even for those without a background in anatomy. * Publishers Weekly *No bones about it, a text like The Bare Bones was sorely needed in the popular literature of vertebrate paleontology. Matthew Bonnan's tome on the evolution, form, and function of the vertebrate skeleton may seem daunting in size, but it is written in an enjoyable and readable fashion that will absolutely delight all sorts of readers from expert to soon-to-be-expert. * Palaeontologia Electronica *The Bare Bones covers a lot of ground, much of it familiar, but it is a remarkably fun book to read. Bonnan avoids the most intimidating jargon of anatomy and phylogenetics, elucidating the necessary concepts through clear writing and clever application of nonbiological analogies. He is forthcoming about the simplifications and omissions that make the volume so readable, and his conversational style and wit make this an unintimidating yet highly informative book that would work wonderfully in college courses. * The Quarterly Review of Biology *Table of ContentsPrefaceAcknowledgmentsPart One: Setting the StageChapter 1. Introduction: How Vertebrates and Cars Are (and Are Not) SimilarChapter 2. Evolution to Deep Time, Pedigree to AnatomyPart Two: The Origin and Early Evolution of the Vertebrate ChassisChapter 3. Inferring the Basic Vertebrate ChassisChapter 4. Evolution of a Bony ChassisPart Three: The Evolution of the Jawed Vertebrate Chassis and Something FishyChapter 5. The Jawed Vertebrate Chassis: A PrimerChapter 6. Placoderms and Cartilaginous FishesChapter 7. The Fish-like Osteichthyes, Part 1Chapter 8. The Fish-like Osteichthyes, Part 2Part Four: The Vertebrate Chassis Moves to LandChapter 9. The Tetrapod Chassis: A PrimerChapter 10. The Tetrapod Chassis in TransitionChapter 11. The Amphibian ChassisChapter 12. The Amniote Chassis: A Primer and the Lead Up to True AmniotesPart Five: Deep Scaly I: Reptilian Chasses from Early Reptiles to Sea MonstersChapter 13. Lizards and the Tuatara as an IntroductionChapter 14. Early Reptiles and TurtlesChapter 15. Snakes and Sea DragonsPart Six: Deep Scaly II: The Archosaur Chassis, Those Ruling ReptilesChapter 16. The Archosaur Chassis, Part 1: Modern ArchosaursChapter 17. The Archosaur Chassis, Part 2: A Primer on Archosaur Posture and DiversityChapter 18. The Archosaur Chassis, Part 3: Pterosaurs, Dinosaurs, and the Origins of BirdsPart Seven: Overcome By Fur: The Mammalian ChassisChapter 19. The Mammalian Chassis: A PrimerChapter 20. The Evolution of the Mammal ChassisChapter 21. Brains, Milk, and the Modern Radiations of MammalsAppendix: The Cards of TimeReferences CitedIndex

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Book SynopsisTrade ReviewThis indispensable volume unequivocally demonstrates that ichnology has an important contribution to make toward a better understanding of dinosaur paleobiology. * BirdBooker Report *[This] book is very well produced and is in color throughout with numerous figures and artwork, and the reproduction of the images is generally excellent. In a field so dominated by interpretation of complex and subtle forms this is an important aspect of the volume and adds significantly to its appeal. This book is an excellent compendium and a timely piece on a rapidly expanding and changing area of research. * Quarterly Review of Biology *Dinosaur Tracks is a benchmark and a must-have for all researchers working on dinosaur tracks and on dinosaurs in general. * Swiss Journal of Palaeontology *Any scientist that considers the study of dinosaur (or other tetrapod) tracks should buy Dinosaur Tracks. For any person, scientifically informed illustrations presented in the book, will give a long-standing positive impression and thus show a value of dinosaur ichnology. -- Andrej Spiridonov * Priscum, The Newsletter of the Palentological Society *Table of ContentsIntroduction / Peter L. Falkingham, Daniel Marty, and Annette RichterPart I. Approaches and Techniques for Studying Dinosaur Tracks1. Experimental and Comparative Ichnology / Jesper Milàn and Peter L. Falkingham2. Close-Range Photogrammetry for 3D Ichnology: The Basics of Photogrammetric Ichnology / Neffra Matthews, Tommy Noble, and Brent Breithaupt3. The Early Cretaceous Dinosaur Trackways in Münchehagen (Lower Saxony, Germany): 3D Photogrammetry as Basis for Geometric Morphometric Analysis of Shape Variation and Evaluation of Material Loss during Excavation / Oliver Wings, Jens N. Lallensack, and Heinrich Mallison4. Applying Objective Methods to Subjective Track Outlines / Peter L. Falkingham5. Beyond Surfaces: A Particle-Based Perspective on Track Formation / Stephen M. Gatesy and Richard G. Ellis6. A Numerical Scale for Quantifying the Quality of Preservation of Vertebrate Tracks / Matteo Belvedere and James O. Farlow7. Evaluating the Dinosaur Track Record: An Integrative Approach to Understanding the Regional and Global Distribution, Scientific Importance, Preservation and Management of Tracksites / Luis Alcalá, Martin G. Lockley, Alberto Cobos, Luis Mampel, and Rafael Royo-TorresPart II. Palaeobiology and Evolution from Tracks8. Iberian Sauropod Tracks through Time: Variations in Sauropod Manus and Pes Morphologies / Diego Castanera, Vanda F. Santos, Laura Piñuela, Carlos Pascual, Bernat Vila, José I. Canudo, and José Joaquin Moratalla9. The Flexion of Sauropod Pedal Unguals and Testing the Substrate Grip Hypothesis Using the Trackway Fossil Record / Lee E. Hall, Ashley E. Fragomeni, and Denver W. Fowler10. Dinosaur Swim Track Assemblages: Characteristics, Contexts, and Ichnofacies Implications / Andrew R. C. Milner, and Martin G. Lockley11. Two-Toed Tracks through Time: On the Trail of "Raptors" and their Allies / Martin G. Lockley, Jerry D. Harris, Rihui Li, Lida Xing, and Torsten van der Lubbe12. Diversity, Ontogeny, or Both? A Morphometric Approach to Iguanodontian Ornithopod (Dinosauria: Ornithischia) Track Assemblages from the Berriasian (Lower Cretaceous) of North Western Germany / Jahn J. Hornung, Annina Böhme, Nils Schlüter, and Mike Reich13. Uncertainty and Ambiguity in the Interpretation of Sauropod Trackways / Kent A. Stevens, Scott Ernst, and Daniel Marty14. Dinosaur Tracks as "Four-Dimensional Phenomena" Reveal How Different Species Moved / Alberto Cobos, Francisco Gascó, Rafael Royo-Torres, Martin G. Lockley, and Luis AlcaláPart III. Ichnotaxonomy and Trackmaker Identification15. Analysing and Resolving Cretaceous Avian Ichnotaxonomy Using Multivariate Statistical Analyses: Approaches and Results / Lisa G. Buckley, Richard T. McCrea, and Martin G. Lockley16. Elusive Ornithischian Tracks in the Famous Berriasian (Lower Cretaceous) "Chicken Yard" Tracksite of Northern Germany: Quantitative Differentiation between Small Tridactyl Trackmakers / Tom HübnerPart IV. Depositional Environments and their Influence on the Track Record17. Too Many Tracks: Preliminary Description and Interpretation of the Diverse and Heavily Dinoturbated Early Cretaceous "Chicken Yard" Ichnoassemblage (Obernkirchen Tracksite, Northern Germany) / Annette Richter and Annina Böhme18. Dinosaur Tracks in Eolian Strata: New Insights into Track Formation, Walking Kinetics, and Trackmaker Behaviour / David B. Loope, and Jesper Milàn19. Analysis of Desiccation Crack Patterns for Quantitative Interpretation of Fossil Tracks / Tom Schanz, Maria Datcheva, Hanna Haase, and Daniel Marty20. A Review of the Dinosaur Track Record from Jurassic and Cretaceous Shallow Marine Carbonate Depositional Environments / Simone D'Orazi Porchetti, Massimo Bernardi, Andrea Cinquegranelli, Vanda Faria dos Santos, Daniel Marty, Fabio Massimo Petti, Paulo Sá Caetano, and Alexander WagensommerDinosaur Track Terminology: A Glossary of TermsList of ContributorsIndex

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Book SynopsisTrade ReviewProfusely illustrated and meticulously researched, Noah's Ravens quantitatively explores a variety of approaches to interpreting the tracks, carefully examining within-species and across-species variability in foot and footprint shape in nonavian dinosaurs and their close living relatives. * The Birdbooker Report *[A] stunning achievement: a life's worth; a life's work. * Quarterly Review of Biology *Table of ContentsAcknowledgments1. Introduction: Noah's Ravens2. Intraspecific and Interspecific Variability in Pedal Phalangeal and Digital Dimensions and Proportions in Non-Avian Dinosaurs, Birds, and Crocodylians 3. Pedal Shape and Phylogenetic Relationships 4. Toe Tapering Profiles in Non-Avian Dinosaurs and Ground Birds 5. Ontogenetic and Across-Species Trends in Hindfoot and Hindlimb Proportions 6. Intraspecific Variability in Pedal Size and Shape in Alligator mississippiensis 7. Footprints of the Emu (Dromaius novaehollandiae) and Other Ground Birds 8. Summing Up the Comparative Analyses 9. Noah's Ravens: Interpreting the Makers of Tridactyl Dinosaur Footprints of the Newark Supergroup, Early Jurassic, Eastern North America 10. Final Thoughts References Appendix Tables

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Book SynopsisBioart, art that uses either living materials (such as bacteria or transgenic organisms) or more traditional materials to comment on, or even transform, biotechnological practice. This book offers a theoretical account of the art form, situating it in the contexts of art history, laboratory practice, and media theory.Trade Review"In this concise, clearly written work, Mitchell explores bioengineered life as an artistic medium creating flows between the sciences and the humanities. Recommended." * Choice *Table of ContentsAcknowledgments Introduction: Living Art 1. Defining Bioart: Representation and Vitality 2. The Three Eras of Vitalist Bioart 3. Bioart and the Folding of Social Space 4. Affect, Framing, and Mediacy 5. The Strange Vitality of Media 6. Bioart and the "Newness" of Media Notes Works Cited Index

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Book SynopsisBioart, art that uses either living materials (such as bacteria or transgenic organisms) or more traditional materials to comment on, or even transform, biotechnological practice. This book offers a theoretical account of the art form, situating it in the contexts of art history, laboratory practice, and media theory.Trade Review"In this concise, clearly written work, Mitchell explores bioengineered life as an artistic medium creating flows between the sciences and the humanities. Recommended." * Choice *Table of ContentsAcknowledgments Introduction: Living Art 1. Defining Bioart: Representation and Vitality 2. The Three Eras of Vitalist Bioart 3. Bioart and the Folding of Social Space 4. Affect, Framing, and Mediacy 5. The Strange Vitality of Media 6. Bioart and the "Newness" of Media Notes Works Cited Index

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Book SynopsisTrade Review“Dümpelmann tracks the history of the modern street tree . . . A deep, scholarly dive into urban society’s need for—and relationship with—trees that sought to return the natural world to the concrete jungle.”—Adrian Higgins, Washington Post"The book makes a convincing alternative case from the more traditional approach of "nature versus culture" dichotomy. Instead, Dümpelmann portrays street trees as an integral part of the urban fabric. Professionals in forestry, urban development, and landscape architecture, as well as readers with a strong interest in the history of the urban landscape, will find this book enlightening as we move towards resilient cities of tomorrow."—Lumi Kirk, Garten + LandschaftSeeing Trees has won the 2019 John Brinckerhoff Jackson prize, sponsored by the Foundation for Landscape Studies Winner of the 2022 Elisabeth Blair MacDougall Book Award sponsored by the Society of Architectural HistoriansFinalist for the 2019 Julia Ward Howe award for non-fiction, sponsored by The Boston Authors Club“In this imaginative and deeply researched work, Sonja Dümpelmann truly helps us to ‘see trees’ in the careful chronologies she develops and the political messages that these trees represented within their times and places.”—Keith Morgan, Boston University"In Seeing Trees the distinguished scholar Sonja Dümpelmann employs her linguistic ability, knowledge, and imaginative use of the archival resources in both Berlin and New York to extend the boundaries of landscape history.”—Kenneth Helphand, University of Oregon, author of Defiant Gardens: Making Gardens in Wartime“Sonja Dümpelmann distills a rich and textured history of street trees—the people involved, technical approaches employed, and the way street trees served as both a polemic and as a point of unification for people.”—Susan Herrington, author of Landscape Theory in Design“This meticulously researched and beautifully illustrated book chronicles the multifaceted identities of trees—as food, fuel, shelter, and defense—and offers us new ways of reading social history into the natural world.”—Jennifer S. Light, Massachusetts Institute of Technology“A signal contribution to the history of landscape design and city planning. Writing with narrative verve, Sonja Dümpelmann turns rigorous scholarship into a fascinating story of time and place for both the academic and general reader.”—Elizabeth Barlow Rogers, President, Foundation for Landscape Studies

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Book SynopsisTrade Review“[Heard’s] focus, bringing to life minutiae of both the living world and the practice of science, is welcome.”—Simon Ings, Spectator“[E]nchanting…Written in an easy-going, chatty style and accompanied by some lovely drawings by Emily Damstra, Heard’s book covers a wide range of organisms.”—Matthew Cobb, Current Biology Magazine“Informative, highly entertaining, and at times even intellectually confrontational...Writing in an enjoyable style that interweaves a scholarly seriousness with amiable playfulness well attuned to his broad audience, Heard presents his readers with a parade of creatures named for a host of personages spanning the famous, the fictional and the personal.”—Johannes E. Riutta, Archives of Natural History “No matter the platform, science communicators need skills in how to transfer niche, technical knowledge to a broad audience with curious minds. It looks like Yale University Press knew this when publishing Stephen B. Heard’s most recent book.”—Joanna Cobley, Museum Worlds: Advances in Research“In Charles Darwin’s Barnacle and David Bowie’s Spider, Stephen Heard tells some of the remarkable stories behind the names of species—and teaches us about how scientists make sense of the natural world along the way. A true pleasure to read.”—Carl Zimmer, author of She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity“More fun than you’ve ever had with taxonomy in your whole entire life! Delightfully written, thoroughly researched, makes you want to learn Latin, and will give good dinner party stories forever.”—Diana Gabaldon, author of the Outlander series, and PhD in Quantitative Behavioral Ecology“Charles Darwin's Barnacle and David Bowie's Spider is carefully researched, well-written, and contains a wealth of insightful comments. Stephen Heard is a talented writer with a good sense of humor, and he knows how to tell a story.”—Paul Faber, Oregon State University“Stephen Heard’s prose fairly sings with enthusiasm, and he presents truly fascinating stories about the names of living things – stories I guarantee you’ve never heard before.”—Daniel Lewis, author of Belonging on an Island“In a poignant, precise, and friendly style, Stephen Heard introduces the foibles of Western science—or, perhaps more accurately, Western scientists. The result is beautiful, welcoming, and illuminating.”—Nicole Palffy-Muhoray, Yale Peabody Museum

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Book SynopsisTrade Review“Not only a very engaging book, but one that provokes thought. . . . Fuentes . . . offers what is, to my knowledge, the first comprehensive etiological view of the origins and evolution of belief as an essential component of the human niche.”—Luis Oviedo, ESSSAT News & ReviewsAwarded the Popular Book Award sponsored by the International Society for Science and Religion“A wholly impressive look at how our capacity for belief evolved, with fresh insights, especially about early Homo sapiens. I found Fuentes’ case studies on religion, economics, and love fascinating.”—Barbara J. King, author of Evolving God“We are the believing species. Much of what we are and what we do is driven by belief of one kind or another. Agustin Fuentes, a gifted writer and teacher, helps us understand both the power and role of belief in this brilliant book. Why We Believe is an exciting intellectual tour through culture, neurobiology, prehistory, religion, economies, love, war, and more. Read it to better know yourself and your species.”—Guy P. Harrison, author of At Least Know This: Essential Science to Enhance Your Life and Think: Why You Should Question Everything

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Book SynopsisPrepare to discover life unlike any we’ve seen before.Trade Review"An ingenious overview of anything that might be alive. The author remains true to science while coming to delightfully bizarre conclusions." -- Kirkus Reviews"Weird life, Toomey teaches us in his mind-bending book, is not just weirder than anything we can imagine, it is the weirdest thing we have ever imagined." -- Justin Nobel, author of Orion

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Book SynopsisWeird indeed, and not a little wonderful.NatureTrade Review"A breakneck tour through natural history, encounters of an impossible kind, researchers as weird as the organisms they pursue that leads the reader to wonder where science ends and fantasy begins." -- Richard Fortey - New York Times Book Review"Conveys these far-out theories with precision and humor." -- Jascha Hoffman - New York Times"Toomey is calm and clear-eyed. . . . A good man to have watching the skies, and the ocean floor." -- AV Club"Starred review. An ingenious overview of anything that might be alive." -- Kirkus Reviews

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Book SynopsisBiology's great discoveries and the people who make them.

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Book SynopsisCoaching Science and Coaching Studies courses are appearing in increasing numbers in many universities. The textbooks used in most of these courses are either theoretically based sports science texts or practically based coaching books. The former are generally lacking in application while the latter rarely have any scientific input. The reader is, therefore, left to make the links themselves. Coaching Science will bridge that gap covering both theory and practice and, most important, showing how theory informs practice. The book will be multi- and, to some extent, inter-disciplinary, as it is not possible to examine the interaction between coach, performer and task from a single discipline perspective. Each chapter will include overviews of the main theories, but the bulk of the material will be concerned with how such theories can be applied in practice. Good and frequent use of examples will be provided. Throughout, the student will be given problems to solve. At the end Table of ContentsSeries Preface. Preface. I SOCIO-PSYCHOLOGICAL FACTORS. 1 Motivation. 2 Leadership and Cohesion. 3 Anxiety, Arousal and Performance. 4 Coaching and Learning Styles. II SKILL ACQUISITION. 5 Learning. 6 Practice. 7 Observation and Feedback. III PHYSIOLOGICAL FACTORS. 8 Physiological Demands of Track Athletics. 9 Factors that Limit Performance. 10 Principles of Physical Training. IV DEVELOPMENTAL FACTORS. 11 Cognitive and Social Development. 12 Physiological and Motor Development. V INTEGRATED FACTORS. 13 Developing Annual Programmes. 14 Integrated Warm-Up. 15 Integrating Practice and Training. References. Index.

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Book SynopsisThis comprehensive, up-to-date book presents the latest research and applied practice to address all of the key issues relating to sport and eating disorders. The book begins by looking at the underlying factors behind the development of disordered eating.Table of ContentsForeword by Mark Andersen ix List of Contributors xiii Introduction xv 1 Good eating habits in sport 1 1.1 Introduction 1 1.2 Balanced diet in sport 2 1.2.1 What is a balanced diet? 2 1.2.2 Energy requirements 3 1.2.3 Elaborating a nutritional plan 4 1.3 Nutrients required by humans and athletes 5 1.3.1 Macronutrients 6 1.3.2 Micronutrients 12 1.3.3 Water 15 1.4 The need for ergogenic aids 17 1.5 Nutritional information for athletes 19 1.6 Conclusions 21 2 The importance of weight in some sports 23 2.1 Introduction 24 2.2 High-risk sports 24 2.3 Weight-loss methods in sport 28 2.4 The difference between 'real weight', 'ideal weight' and 'sports weight' 33 2.4.1 Ideal weight vs. real weight 34 2.4.2 Real weight vs. sports weight 37 2.4.3 Ideal weight vs. sports weight 39 2.5 Conclusions 40 3 Eating disorders and the athlete's environment 41 3.1 Introduction 42 3.2 Pressures in the athlete's environment 43 3.2.1 The role of the family 47 3.2.2 The role of the coach 50 3.2.3 The role of the team-mates 53 3.3 The prevention of eating disorders in sport 55 3.4 Eating disorders prevention programmes for athletes 57 3.5 Conclusions 62 4 Diagnosis and assessment of eating disorders in sport 65 4.1 Introduction 65 4.2 Diagnostic criteria for eating disorders in sport 67 4.2.1 Anorexia in sport 68 4.2.2 Bulimia in sport 72 4.2.3 Bigorexia and orthorexia 74 4.2.4 Eating disorders not otherwise specifi ed (EDNOS) 78 4.3 Methods for diagnosing eating disorders in sport 79 4.3.1 Interviews 79 4.3.2 The assessment of body weight: anthropometrical indices 82 4.3.3 Body image perception: dissatisfaction and disturbance 83 4.3.4 The female athlete triad 84 4.3.5 Observation 87 4.3.6 Questionnaires 90 4.4 Conclusions 96 5 Eating disorders in different sports 99 5.1 Introduction 99 5.2 The aetiology of eating disorders in sport 100 5.3 Research into eating disorders in 'high-risk' sports 102 5.3.1 Aesthetic sports: gymnastics, figure/ice skating and ballet dancing 102 5.3.2 Weight division sports: judo, wrestling and rowing 106 5.3.3 Gym sports: aerobics and bodybuilding 111 5.3.4 Endurance sports and disciplines requiring low weight for high performance: athletics, swimming, and horser acing 113 5.4 Eating disorders symptoms: the sporting discipline and gender 116 5.4.1 The influence of the sporting discipline 117 5.4.2 The influence of gender 119 5.5 Conclusions 121 6 Treating eating disorders in sport 123 6.1 Introduction 123 6.2 The treatment regime 124 6.3 The treatment steps 125 6.3.1 Developing the motivation to change 125 6.3.2 Treatment objectives 127 6.3.3 Techniques and methods used in the treatment of eating disorders 132 6.3.4 Sequencing treatment 134 6.4 Types of treatment 140 6.4.1 Individual treatment 140 6.4.2 Family and/or couple therapy 142 6.4.3 Group therapy 142 6.4.4 Pharmaceutical therapy 142 6.5 Conclusions 143 7 Cyberpsychology and eating disorders in sport 145 7.1 Introduction 145 7.2 Psychology and new technologies: cyberpsychology 146 7.3 Cyber-sport-psychology and eating disorders 148 7.4 The Internet: information about eating disorders in sport 149 7.5 On-line diagnosis and treatment of eating disorders in sport 153 7.5.1 Commencing on-line treatment of an eating disorder in sport 155 7.5.2 Contact with professionals 157 7.5.3 The initial assessment 159 7.5.4 The objectives of on-line therapy 160 7.5.5 On-line sessions 161 7.5.6 The sports psychologist and on-line treatment 162 7.5.7 Paying for on-line sessions 164 7.5.8 The advantages and disadvantages of using on-line therapy to treat eating disorders in sport 164 7.6 Conclusions 167 8 Case studies in high-risk sports 169 8.1 Introduction 169 8.2 A case study of eating disorders in athletics 170 8.2.1 Case description 170 8.2.2 Analysis of the situation 171 8.2.3 Treatment and follow-up 172 8.3 A case of eating disorders in taekwondo 176 8.3.1 Case description 177 8.3.2 Analysis of the situation 177 8.3.3 'Urgent' treatment 178 8.4 A case of eating disorders in gymnastics 179 8.4.1 Case description 179 8.4.2 Analysis of the situation 180 8.4.3 Treatment 180 8.5 A case of eating disorders in aerobics 181 8.5.1 Case description 181 8.5.2 Analysis of the situation 182 8.5.3 Treatment 182 8.6 Sport: a solution to combat anorexia 183 8.6.1 Case description 184 8.6.2 Treatment 184 8.7 Conclusions 185 References 187 Index 205

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Book SynopsisPharmaceutical Biotechnology offers students taking Pharmacy and related Medical and Pharmaceutical courses a comprehensive introduction to the fast-moving area of biopharmaceuticals.Table of ContentsPreface. Acronyms. 1 Pharmaceuticals, biologics and biopharmaceuticals. 1.1 Introduction to pharmaceutical products. 1.2 Biopharmaceuticals and pharmaceutical biotechnology. 1.3 History of the pharmaceutical industry. 1.4 The age of biopharmaceuticals. 1.5 Biopharmaceuticals: current status and future prospects. 2 Protein structure. 2.1 Introduction. 2.2 Overview of protein structure. 2.3 Higher level structure. 2.4 Protein stability and folding. 2.5 Protein post-translational modifi cation. 3 Gene manipulation and recombinant DNA technology. 3.1 Introduction. 3.2 Nucleic acids: function and structure. 3.3 Recombinant production of therapeutic proteins. 3.4 Classical gene cloning and identifi cation. 4 The drug development process. 4.1 Introduction. 4.2 Discovery of biopharmaceuticals. 4.3 The impact of genomics and related technologies upon drug discovery. 4.4 Gene chips. 4.5 Proteomics. 4.6 Structural genomics. 4.7 Pharmacogenetics. 4.8 Initial product characterization. 4.9 Patenting. 4.10 Delivery of biopharmaceuticals. 4.10.3 Nasal, transmucosal and transdermal delivery systems. 4.11 Preclinical studies. 4.12 Pharmacokinetics and pharmacodynamics. 4.13 Toxicity studies. 4.14 The role and remit of regulatory authorities. 4.15 Conclusion. 5 Sources and upstream processing. 5.1 Introduction. 5.2 Sources of biopharmaceuticals. 5.3 Upstream processing. 6 Downstream processing. 6.1 Introduction. 6.2 Initial product recovery. 6.3 Cell disruption. 6.4 Removal of nucleic acid. 6.5 Initial product concentration. 6.6 Chromatographic purifi cation. 6.7 High-performance liquid chromatography of proteins. 6.8 Purifi cation of recombinant proteins. 6.9 Final product formulation. 7 Product analysis. 7.1 Introduction. 7.2 Protein-based contaminants. 7.3 Removal of altered forms of the protein of interest from the product stream. 7.4 Detection of protein-based product impurities. 7.5 Immunological approaches to detection of contaminants. 7.6 Endotoxin and other pyrogenic contaminants. 8 The cytokines: The interferon family. 8.1 Cytokines. 8.1.1 Cytokine receptors. 8.1.2 Cytokines as biopharmaceuticals. 8.2 The interferons. 8.3 Interferon biotechnology. 8.4 Conclusion. 9 Cytokines: Interleukins and tumour necrosis factor. 9.1 Introduction. 9.2 Interleukin-2. 9.3 Interleukin-1. 9.4 Interleukin-11. 9.5 Tumour necrosis factors. 10 Growth factors. 10.1 Introduction. 10.2 Haematopoietic growth factors. 10.3 Growth factors and wound healing. 11 Therapeutic hormones. 11.1 Introduction. 11.2 Insulin. 11.3 Glucagon. 11.4 Human growth hormone. 11.5 The gonadotrophins. 11.6 Medical and veterinary applications of gonadotrophins. 11.7 Additional recombinant hormones now approved. 11.8 Conclusion. 12 Recombinant blood products and therapeutic enzymes. 12.1 Introduction. 12.2 Haemostasis. 12.3 Anticoagulants. 12.4 Thrombolytic agents. 12.5 Enzymes of therapeutic value. 13 Antibodies, vaccines and adjuvants. 13.1 Introduction. 13.2 Traditional polyclonal antibody preparations. 13.3 Monoclonal antibodies. 13.4 Vaccine technology. 13.5 Adjuvant technology. 14 Nucleic-acid- and cell-based therapeutics. 14.1 Introduction. 14.2 Gene therapy. 14.3 Vectors used in gene therapy. 14.4 Gene therapy and genetic disease. 14.5 Gene therapy and cancer. 14.6 Gene therapy and AIDS. 14.7 Antisense technology. 14.8 Oligonucleotide pharmacokinetics and delivery. 14.9 Aptamers. 14.10 Cell- and tissue-based therapies. 14.11 Conclusion. Index.

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Book SynopsisThis volume is a very valuable and much needed contribution.Quarterly Review of Biology AT LAST - A comprehensive, accessible textbook on glial neurobiology! Glial cells are the most numerous cells in the human brain but for many years have attracted little scientific attention. Neurophysiologists concentrated their research efforts instead, on neurones and neuronal networks because it was thought that they were the key elements responsible for higher brain function. Recent advances, however, indicate this isn't exactly the case. Not only are astroglial cells the stem elements from which neurones are born, but they also control the development, functional activity and death of neuronal circuits. These ground-breaking developments have revolutionized our understanding of the human brain and the complex interrelationship of glial and neuronal networks in health and disease. Features of this book: an accessible introduTrade Review"This volume is a very valuable and much needed contribution." (Quarterly Review of Biology, December 2008)Table of ContentsPreface. List of abbreviations. PART I Physiology of Glia. 1 Introduction to Glia. 1.1 Founders of glial research: from Gabriel Valentin to Karl-Ludwig Schleich. 1.2 Beginning of the modern era. 1.3 Changing concepts: Glia express molecules of excitation. 1.4 Glia and neurones in dialogue. 2 General Overview of Signalling in the Nervous System. 2.1 Intercellular signalling: Wiring and volume modes of transmission. 2.2 Intracellular signalling. 3 Morphology of Glial Cells. 3.1 Astrocytes. 3.2 Oligodendrocytes. 3.3 NG2 expressing glia. 3.4 Schwann cells. 3.5 Microglia. 4 Glial Development. 4.1 Phylogeny of glia and evolutionary specificity of glial cells in human brain. 4.2 Macroglial cells. 4.3 Astroglial cells are brain stem cells. 4.4 Schwann cell lineage. 4.5 Microglial cell lineage. 5 General Physiology of Glial Cells. 5.1 Membrane potential and ion distribution. 5.2 Ion channels. 5.3 Receptors to neurotransmitters and neuromodulators. 5.4 Glial syncytium – gap junctions. 5.5 Glial calcium signalling. 5.6 Neurotransmitter release from astroglial cells. 5.7 Glial neurotransmitter transporters. 5.8 Glial cells produce and release neuropeptides. 5.9 Glial cell derived growth factors. 6 Neuronal–Glial Interactions. 6.1 Close apposition of neurones and astroglia: the tripartite synapse. 6.2 Neuronal–glial synapses. 6.3 Signalling from neurones to astrocytes. 6.4 Signalling from astrocytes to neurones. 6.5 Signalling between oligodendrocytes and neurones. 6.6 Signalling between Schwann cells and peripheral nerves and nerve endings. PART II Glial Cells and Nervous System Function. 7 Astrocytes. 7.1 Developmental function – producing new neural cells. 7.2 Developmental function – neuronal guidance. 7.3 Regulation of synaptogenesis and control of synaptic maintenance and elimination. 7.4 Structural function – creation of the functional microarchitecture of the brain. 7.5 Vascular function – creation of glial–vascular interface (blood–brain barrier) and glia–neurone–vascular units. 7.6 Regulation of brain microcirculation. 7.7 Ion homeostasis in the extracellular space. 7.8 Regulation of extracellular glutamate concentration. 7.9 Water homeostasis and regulation of the extracellular space volume. 7.10 Neuronal metabolic support. 7.11 Astroglia regulate synaptic transmission. 7.12 Integration in neuronal–glial networks. 7.13 Astrocytes as cellular substrate of memory and consciousness? 8 Oligodendrocytes, Schwann Cells and Myelination. 8.1 The myelin sheath. 8.2 Myelination. 8.3 Myelin and propagation of the action potential. PART III Glia and Nervous System Pathology. 9 General Pathophysiology of Glia. 9.1 Reactive astrogliosis. 9.2 Wallerian degeneration. 9.3 Activation of microglia. 10 Glia and Diseases of the Nervous System. 10.1 Alexander’s disease. 10.2 Spreading depression. 10.3 Stroke and ischaemia. 10.4 Cytotoxic brain oedema. 10.5 Neurodegenerative diseases. 10.6 Neuropathic pain. 10.7 Demyelinating diseases. 10.8 Infectious diseases. 10.9 Peripheral neuropathies. 10.10 Psychiatric diseases. 10.11 Gliomas. Conclusions. Recommended literature. Author Index. Subject Index.

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Book SynopsisMedical Mycology: Cellular and Molecular techniques is a clear and concise overview of the subject that details the techniques essential for ongoing research in the area. Drawing together contributions from both scientists and clinicians working in the field, the text will provide a valuable perspective on the applicability of specific techniques to patient care. A wide range of molecular, immunological and cytological techniques are discussed throughout, with the inclusion of protocol section in each chapter designed to provide both a background a up-to-date account of the applications of each procedure. Every technique is fully referenced and illustrations are provided where required to enhance student understanding. comprehensive introduction to the key techniques critical to the study of medical mycology clear explanation of how each technique is applied in the lab contributions from internationally recogniseTrade Review"There is no other current book that gives the details on experimental procedures that this one does…a very worthwhile acquisition for investigators working with fungi." (Doody's Health Services) "Will be very useful to many students and bench scientists wishing to expand their repertoire of practical skills in medical mycology." (Microbiology Today, March 2008) Medical Mycology is a useful guide for molecular, immunological, and cytological techniques that will provide useful to researchers and students alike. (The Yale Journal of Biology and Medicine, June 2007) "Das Buch fasst kompakt und im Sinne einer detaillierten und kommentierten Arbeitsanleitung ein breites Spektrum essentieller und aktueller Methoden fur die Wissenschaft zusammen?. Ein weiterer Bonus ist das sehr umfangreiche Literaturverzeichnis nach jedem Kapitel und die hohe Aktualitat aller Beitrage, die den Stand bei Drucklegung wiedergeben. Insgesamt ist das Buch zum Einstieg in die mykologische Forschung und als methodisches Nachschlagewerk im Labor sehr gut geeignet." J Lab Med, Marz 2008Table of ContentsPreface xiii List of Contributors xv 1 Diagnosis of Candida Infection in Tissue by Immunohistochemistry 1 Malcolm D. Richardson, Riina Rautemaa and Jarkko Hietanen 1.1 Introduction 1 1.2 Specificity of monoclonal antibody 3H8 for C. albicans 3 Protocol 1.1 Testing of specificity of monoclonal antibody 3H8 4 1.3 Evaluation of monoclonal antibody 3H8 for the detection of C. albicans morphological forms 6 Protocol 1.2 Evaluation of monoclonal antibody 3H8 for the detection of C. albicans morphological forms 6 1.4 Application of immunohistochemistry in the diagnosis of Candida periodontal disease 7 Protocol 1.3 Use of monoclonal antibody 3H8 in the detection of C. albicans in tissue 8 1.5 References 11 2 Transmission Electron Microscopy of Pathogenic Fungi 13 Guy Tronchin and Jean-Philippe Bouchara 2.1 Introduction 13 2.2 Glutaraldehyde-potassium-permanganate or glutaraldehyde-osmiumtetroxide fixation for ultrastructural analysis 16 Protocol 2.1 Glutaraldehyde-osmium tetroxide (#) or glutaraldehyde-potassium permanganate (*) fixation for ultrastructural analysis 17 2.3 Identification of the different compartments of the secretory pathway in yeasts 18 Protocol 2.2 Identification of the different compartments of the secretory pathway in yeasts 19 2.4 Cytochemical localization of acid phosphatase in yeasts 20 Protocol 2.3 Cytochemical localization of acid phosphatase in yeasts 21 2.5 Detection of anionic sites 23 Protocol 2.4 Detection of anionic sites 23 2.6 Detection of glycoconjugates by the periodic acid-thiocarbohydrazide-silver proteinate technique (PATAg) 25 Protocol 2.5 Detection of glycoconjugates by the periodic acid-thiocarbohydrazide-silver proteinate technique (PATAg) 26 2.7 Enzyme-gold approach for the detection of polysaccharides in the cell wall 28 Protocol 2.6 Enzyme-gold approach for the detection of polysaccharides in the cell wall 29 2.8 Detection of glycoconjugates by the lectin-gold technique 30 Protocol 2.7 Detection of glycoconjugates by the lectin-gold technique 31 2.9 Immunogold detection of antigens on ultrathin sections of acrylic resin 33 Protocol 2.8 Immunogold detection of antigens on ultrathin sections of acrylic resin 34 2.10 Cryofixation and freeze substitution for ultrastructural analysis and immunodetection 36 Protocol 2.9 Cryofixation and freeze substitution for ultrastructural analysis and immunodetection 37 2.11 Overview 38 2.12 References 39 3 Evaluation of Molecular Responses and Antifungal Activity of Phagocytes to Opportunistic Fungi 43 Maria Simitsopoulou and Emmanuel Roilides 3.1 Introduction 43 3.2 Preparation of conidia and hyphae of opportunistic fungi 45 Protocol 3.1 Preparation of conidia and hyphae of opportunistic fungi 45 Protocol 3.2 Preparation of hyphal fragments 47 3.3 Isolation of human monocytes from whole blood 48 Protocol 3.3 Isolation of human MNCs from whole blood 48 3.4 Analysis of human MNC function in response to fungal infection 51 Protocol 3.4 XTT microassay 52 Protocol 3.5 Superoxide anion assay in 96-well plate 53 Protocol 3.6 Hydrogen peroxide-rhodamine assay 55 Protocol 3.7 Phagocytosis assay 55 3.5 Evaluation of immunomodulators in response to fungal infection 57 Protocol 3.8 Analysis of gene expression by RT-PCR 58 Protocol 3.9 Analysis of pathway-specific gene expression by microarray technology 63 Protocol 3.10 Assessment of cytokines and chemokines by ELISA 66 3.6 Overview 67 3.7 References 68 4 Determination of the Virulence Factors of Candida Albicans and Related Yeast Species 69 Khaled H. Abu-Elteen and Mawieh Hamad 4.1 Introduction 69 4.2 Measurement of Candida species adhesion in vitro 70 Protocol 4.1 The visual assessment of candidal adhesion to BECs 70 Protocol 4.2 The radiometric measurement of candidal adhesion 73 4.3 Adhesion to inanimate surfaces 75 Protocol 4.3 Assessment of candidal adhesion to denture acrylic material 75 Protocol 4.4 Adherence of Candida to plastic catheter surfaces 76 4.4 C. albicans strain differentiation 77 Protocol 4.5 Resistogram typing 77 Protocol 4.6 The slide agglutination technique 79 Protocol 4.7 Serotyping of C. albicans by flow cytomerty 80 4.5 Phenotypic switching in C. albicans 81 Protocol 4.8 Evaluation of phenotype switching in C. albicans 82 4.6 Extracellular enzymes secreted by C. albicans 83 Protocol 4.9 Measurement of extracellular proteinase production by C. albicans 85 Protocol 4.10 Measurement of extracellular proteinase produced by C. albicans (staib method) 86 Protocol 4.11 Measurement of extracellular phospholipases of C. albicans 87 4.7 Germ-tube formation in C. albicans 88 Protocol 4.12 Germ-tube formation assay 88 4.8 References 89 5 Analysis of Drug Resistance in Pathogenic Fungi 93 Gary P. Moran, Emmanuelle Pinjon, David C. Coleman and Derek J. Sullivan 5.1 Introduction 93 5.2 Method for the determination of minimum inhibitory concentrations (MICs) of antifungal agents for yeasts 96 Protocol 5.1 Method for the determination of minimum inhibitory concentrations (MICs) of antifungal agents for yeasts 97 5.3 Measurement of Rhodamine 6G uptake and glucose-induced efflux by ABC transporters 102 Protocol 5.2 Measurement of rhodamine 6G uptake and glucose-induced efflux 102 5.4 Analysis of expression of multidrug transporters in pathogenic fungi 105 5.5 Analysis of point mutations in genes encoding cytochrome P- 450 lanosterol demethylase 106 5.6 Qualitative detection of alterations in membrane sterol contents 108 Protocol 5.3 Qualitative detection of alterations in membrane sterol contents 109 5.7 Overview 110 5.8 References 110 6 Animal Models for Evaluation of Antifungal Efficacy Against Filamentous Fungi 115 Eric Dannaoui 6.1 Introduction 115 6.2 Disseminated zygomycosis in non-immunosuppressed mice 118 Protocol 6.1 Disseminated zygomycosis in non-immunosuppressed mice 118 6.3 Animal model of disseminated aspergillosis 125 Protocol 6.2 Disseminated aspergillosis in neutropoenic mice 126 6.4 Study design for evaluation of antifungal combinations therapy in animal models 130 Protocol 6.3 Study design for the evaluation of combination therapy in animal models 131 6.5 References 133 7 Proteomic Analysis of Pathogenic Fungi 137 Alan Murphy 7.1 Introduction 137 Protocol 7.1 2D SDS-PAGE of protein samples 139 7.2 Protein digestion in preparation for mass spectrometry by MALDI-TOF 140 Protocol 7.2 Peptide mass fingerprinting (PMF) by MALDI-TOF mass spectrometry 141 Protocol 7.2a In-gel digestion 142 Protocol 7.2b In-solution digestion 143 7.3 MALDI-TOF mass spectrometry 145 Protocol 7.3 Preparation of matrix for MALDI-TOF 147 7.4 Peptide mass fingerprinting (PMF) 149 Protocol 7.4 Post-source decay (PSD) and chemically assisted fragmentation (CAF) 150 7.5 Interpreting MALDI-TOF result spectra 152 7.6 Overview 156 7.7 References 157 8 Extraction and Detection of DNA and RNA from Yeast 159 Patrick Geraghty and Kevin Kavanagh 8.1 Introduction 159 8.2 The extraction of yeast DNA with the aid of phenol: chloroform 161 Protocol 8.1 Whole-cell DNA extraction from C. albicans using phenol: chloroform 161 Protocol 8.2 Rapid extraction of DNA from C. albicans colonies for PCR 164 8.3 Detection of yeast DNA using radio-labelled probes 165 Protocol 8.3 DNA detection by Southern blotting 165 8.4 Extraction of whole-cell RNA using two different protocols 169 Protocol 8.4 The extraction of whole-cell RNA from yeast using phenol: chloroform 170 Protocol 8.5 Rapid extraction of whole-yeast-cell RNA 172 8.5 Detection and expression levels of specific genes by the examination of mRNA in yeast 174 Protocol 8.6 Examining mRNA content as a means of investigating gene-expression profile by northern blot analysis 175 Protocol 8.7 Examining mRNA content as a means of investigating gene-expression profile by RT-PCR analysis 176 8.6 References 179 9 Microarrays for Studying Pathogenicity in Candida Albicans 181 André Nantel, Tracey Rigby, Hervé Hogues and Malcolm Whiteway 9.1 Introduction 181 9.2 DNA microarrays 182 9.3 Building a second-generation 2-colour long oligonucleotide microarray for C. albicans 183 Protocol 9.1 Isolation of C. albicans RNA 185 Protocol 9.2 Isolation of total RNA using the hot phenol method 186 Protocol 9.3 Isolation of Poly-A+ mRNA 187 Protocol 9.4 Determination of the efficiency of incorporation of the probe 192 Protocol 9.5 Hybridization to DNA microarrays 194 9.4 Experiment design 196 9.5 Microarray-based studies in C. albicans 200 9.6 Conclusion 205 9.7 References 205 10 Molecular Techniques for Application with Aspergillus Fumigatus 211 Nir Osherov and Jacob Romano 10.1 Introduction 211 10.2 Preparation of knockout vectors for gene disruption and deletion in A. fumigatus 212 Protocol 10.1 Preparation of knockout vectors for gene disruption and deletion in A. fumigatus 213 10.3 Transformation of A. fumigatus 217 Protocol 10.2 Chemical transformation of A. fumigatus 218 10.4 Molecular verification of correct single integration (PCR-based) 220 Protocol 10.3 Molecular verification of correct integration by PCR 221 10.5 General strategies for the phenotypic characterization of A. fumigatus mutant strains 223 Protocol 10.4 General strategies for the phenotypic characterization of mutants 223 10.6 References 229 11 Promoter Analysis and Generation of Knock-out Mutants in Aspergillus Fumigatus 231 Matthias Brock, Alexander Gehrke, Venelina Sugareva and Axel A. Brakhage 11.1 Introduction 231 11.2 Site-directed mutagenesis of promoter elements 233 Protocol 11.1 Site-directed mutation of promoter elements 233 11.3 lacZ as a reporter gene 236 Protocol 11.2 lacZ as a reporter gene: discontinuous determination of b-galactosidase activity 237 Protocol 11.3 lacZ as a reporter gene: continuous determination of b-galactosidase activity 239 11.4 Transformation of A. fumigatus 241 Protocol 11.4 Transformation of A. fumigatus 242 11.5 Hygromycin B as a selection marker for transformation 246 Protocol 11.5 Hygromycin B as a selection marker for transformation 247 11.6 pyrG as a selection marker for transformation 249 Protocol 11.6 pyrG as a selection marker for transformation 249 11.7 URA-blaster (A. niger pyrG) as a reusable selection marker system for gene deletions/disruptions 251 Protocol 11.7 URA-blaster (A. niger pyrG) as a reusable selection marker system for gene deletions/disruptions 253 11.8 References 255 12 Microarray Technology for Studying the Virulence of Aspergillus Fumigatus 257 Darius Armstrong-James and Thomas Rogers 12.1 Introduction 257 12.2 Isolation of RNA from A. fumigatus 259 Protocol 12.1 Isolation of total RNA from A. fumigatus 260 12.3 Reverse transcription of RNA and fluorescent labelling of cDNA 263 Protocol 12.2 Indirect labelling of cDNA with fluorescent dyes 264 12.4 Hybridization of fluorescent probes to DNA microarrays and post-hybridization washing 266 Protocol 12.3 Hybridization of fluorescent probes to DNA microarrays and post-hybridization washing 267 12.5 Image acquisition from hybridized microarrays 269 Protocol 12.4 Image acquisition from hybridized microarrays 269 12.6 Microarray image analysis 270 Protocol 12.5 Microarray image analysis 271 12.7 References 272 13 Techniques and Strategies for Studying Virulence Factors in Cryptococcus Neoformans 275 Nancy Lee and Guilhem Janbon 13.1 Introduction 275 13.2 Construction of C. neoformans gene-disruption cassettes 278 Protocol 13.1 Construction of C. neoformans gene-disruption cassettes 278 13.3 Genetic transformation of C. neoformans 283 Protocol 13.2 Biolistic transformation of C. neoformans 283 Protocol 13.3 Transformation via electroporation 286 13.4 Extraction of genomic DNA from C. neoformans 287 Protocol 13.4 DNA for use in library construction and hybridization analysis 288 Protocol 13.5 DNA for use in PCR 291 13.5 Screening and identification of deletion strains 292 Protocol 13.6 Screening and identification of deletion strains 292 13.6 Measuring capsule size in C. neoformans 297 Protocol 13.7 Measuring capsule size in C. neoformans 298 13.7 Purification of glucuronoxylomannan (GXM) 298 Protocol 13.8 Purification of glucuronoxylomannan (GXM) 299 13.8 References 301 14 Genetic Manipulation of Zygomycetes 305 Ashraf S. Ibrahim and Christopher D. Skory 14.1 Introduction 305 14.2 Genetic tools to manipulate mucorales 306 14.3 Selectable markers used with mucorales fungi 307 14.4 Introduction of DNA used for transformation 308 Protocol 14.1 Protoplasting of R. oryzae 309 Protocol 14.2 Biolistic delivery system transformation of R. oryzae 313 Protocol 14.3 A. tumefaciens-mediated transformation 316 14.5 Molecular analysis of transformants 319 14.6 Overview 322 14.7 References 323 Index 327

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Book SynopsisBioinformatics is an extremely popular and rapidly growing new discipline that has evolved around the use of algorithmic and computer techniques to analyze large datasets being generated in genomics and related fields. Bioinformatics: Genomics and Post-Genomics provides a clear and concise introduction to the popular new science of bioinformatics.Trade Review"...provides a clear and concise introduction to the popular new science of bioinformatics." (Bioautomation, volume 7)Table of ContentsChapter 1. Genome sequencing. 1.1 Automatic sequencing. 1.2 Sequencing strategies. 1.3 Fragmentation strategies. 1.4 Sequence assembly. 1.5 Filling gaps. 1.6 Obstacles to reconstruction. 1.7 Utilizing a complementary ‘large’ clone library. 1.8 The first large-scale sequencing project: The Haemophilus influenzae genome. 1.9 cDNA and EST. Chapter 2. Sequence comparisons. 2.1 Introduction: Comparison as a sequence prediction method. 2.2 A sample molecule: the human and rosterone receptor. 2.3 Sequence homologies - functional homologies. 2.4 Comparison matrices. 2.5 The problem of insertions and deletions. 2.6 Optimal alignment: the dynamic programming method. 2.7 Fast heuristic methods. 2.8 Sensitivity, specificity, and confidence level. 2.9 Multiple alignments. Chapter 3. Comparative genomics. 3.1 General properties of genomes. 3.2 Genome comparisons. 3.3 Gene evolution and phylogeny: applications to annotation. Chapter 4. Genetic information and biological sequences. 4.1 Introduction: Coding levels. 4.2 Genes and the genetic code. 4.3 Expression signals. 4.4 Specific sites. 4.5 Sites located on DNA. 4.6 Sites present on RNA. 4.7 Pattern detection methods. Chapter 5. Statistics and sequences. 5.1 Introduction. 5.2 Nucleotide base and amino acid distribution. 5.3 The biological basis of codon bias. 5.4 Using statistical bias for prediction. 5.5 Modeling DNA sequences. 5.6 Complex models. 5.7 Sequencing errors and hidden Markov models. 5.8 Hidden Markov processes: a general sequence analysis tool. 5.9 The search for genes - a difficult art. Chapter 6. Structure prediction. 6.1 The structure of RNA. 6.2 Properties of the RNA molecule. 6.3 Secondary RNA structures. 6.4 Thermodynamic stability of RNA structures. 6.5 Finding the most stable structure. 6.6 Validation of predicted secondary structures. 6.7 Using chemical and enzymatic probing to analyze folding. 6.8 Long-distance interactions and three-dimensional structure prediction. 6.9 Protein structure. 6.10 Secondary structure prediction. 6.11 Three-dimensional modeling based on homologous protein structure. 6.12 Predicting folding. Chapter 7. Transcriptome and proteome: macromolecular networks. 7.1 Introduction. 7.2 Post-genomic methods. 7.3 Macromolecular networks. 7.4 Topology of macromolecular networks. 7.5 Modularity and dynamics of macromolecular networks. 7.6 Inference of regulatory networks. Chapter 8. Simulation of Biological Processes in the Genome Context. 8.1 Types of simulations. 8.2 Prediction and explanation. 8.3 Simulation of molecular networks. 8.4 Generic post-genomic simulators. Index.

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Book SynopsisSustainability is a key driving force for industries in the chemical, food, packaging, agricultural and pharmaceutical sectors, and quantitative sustainability indicators are being incorporated into company reports. This is driving the uptake of renewable resources and the adoption of renewables.Table of ContentsContributors. Foreword. Series Preface. Preface. List of Abbreviations. Part I: Renewables as a Resource and Sustainability Performance Indicators. 1 The Contribution of Renewables to Society (Göran Berndes). 2 The Potential of Renewables as a Feedstock for Chemistry and Energy (Wilfried G. J. H. M. van Sark, Martin K. Patel, André P. C. Faaij and Monique M. Hoogwijk). 3 Sustainability Performance Indicators (Alexei Lapkin). Part II: Relevant Assessment Tools. 4 Life Cycle Inventory Analysis Applied to Renewable Resources (Niels Jungbluth and Rolf Frischknecht). 5 Net Energy Balancing and Fuel-Cycle Analysis (Hosein Shapouri, Michael Wang and James A. Duffield). 6 Life Cycle Assessment as an Environmental Sustainability Tool (Adisa Azapagic). 7 Exergy (Jo Dewulf and Herman Van Langenhove). 8 Material Flow Analysis and the Use of Renewables from a Systems Perspective (Stefan Bringezu). 9 Ecological Footprints and Biocapacity: Essential Elements in Sustainability Assessment (William E. Rees). 10 The Sustainable Process Index (SPI) (Michael Narodoslawsky and Anneliese Niederl). Part III:Case Studies. 11 Assessment of Sustainable Land Use in Producing Biomass (Helmut Haberl and Karl-Heinz Erb). 12 Assessment of the Forest Products Industries (Klaus Richter, Frank Werner and Hans-Jörg Althaus). 13 Assessment of the Energy Production Industry: Modern Options for Producing Secondary Energy Carriers from Biomass (André Faaij). 14 Assessment of Biofuels (James A. Duffield, Hosein Shapouri and Michael Wang). 15 Assessment of Organic Waste Treatment (Jan-Olov Sundqvist). 16 Oleochemical and Petrochemical Surfactants: An Overall Assessment (Erwan Saouter, Gert Van Hoof, Mark Stalmans and Alan Brunskill). 17 Assessment of Bio-Based Packaging Materials (Andreas Detzel, Martina Krüger and Axel Ostermayer). 18 Assessment of Biotechnology-Based Chemicals (Peter Saling and Andreas Kicherer). 19 Assessment of Bio-Based Pharmaceuticals: The Cephalexin Case (Alle Bruggink and Peter Nossin). Part IV:Conclusions. 20 Conclusions (Jo Dewulf and Herman Van Langenhove). Index.

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Book SynopsisThe prebiotic concept works on the basis that many potentially health-promoting microorganisms are already present in humans. Prebiotics are non-digestible food ingredients that stimulate activity in targeted microorganisms, to improve the health of the individual.Trade Review"…a valuable addition to the literature and recommended for libraries supporting food and pharmaceutical microbiology." (Journal of the Agricultural & Food Information, January 2008) "…they have assembled a surprisingly uniform book that progresses through the topic of prebiotics in an orderly and organized fashion." (Doody's Health Services)Table of ContentsList of Contributors. 1. Human Colonic Microbiology and the Role of Dietary Intervention: Introduction to Prebiotics (C.L. Vernazza, B.A. Rabiu and G.R. Gibson). 2. Manufacture of Prebiotic Oligosaccharides (T. Casci and R.A. Rastall). 3. Inulin-type Fructans as Prebiotics (J. Van Loo). 4. Galacto-oligosaccharides as Prebiotics (R.A. Rastall). 5. Emerging Prebiotic Carbohydrates (R. Crittenden). 6. Molecular Microbial Ecology of the Human Gut (K.M. Tuohy and A.L. McCartney). 7. Dietary Intervention for Improving Human Health: Acute Disorders (W. Brück). 8. Dietary Intervention for Improving Human Health: Chronic Disorders (N.R. Bullock and M.R. Jones). 9. Extra Intestinal Effects of Prebiotics and Probiotics (G. Reid). 10. Prebiotic Impacts on Companion Animals (K.S. Swanson and G.C. Fahey Jr.). 11. Prebiotics: Past, Present and Future (J. Leach, R.A. Rastall and G.R. Gibson). Index.

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Book SynopsisAssuming only a basic knowledge of bioinformatics, Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data illustrates the value of bioinformatics as a constantly evolving avenue into novel approaches to study genetics.Trade Review" …an excellent resource…this book should ensure that any researcher’s skill base is maintained" (Genetical Research, 2007) "…this book contains some essential reading for almost any person working in the field of molecular genetics." (European Journal Of Human Genetics, 2007) “Over 19 chapters, the authors cover an impressive terrain. The focus is mainly on human genetics and genomics, with research in other species also presented, particularly where it supports and advances our understanding of human genetics. Although a thoughtful discussion of the relevant literature and techniques is found in each chapter, the book is not overly technical and does not present advanced mathematical, statistical, or genetic concepts in great depth. Instead, focus is on practical applications, available tools, software, and databases, and the presentation supporting real world research examples. The end result is one of the best available and most accessible texts on bioinformatics and genetics in the postgenome age…this book in its current edition still serves as one of the best resources available, particularly in chapters on noncoding RNAs, pharmacogenetics, and drug discovery, microarrays/gene expression, regulatory polymorphisms, and the potential impacts of amino acid changes. The writing is clear, with succinct subsections within each chapter….Without reservation, I endorse this text as the best resource I’ve encountered that neatly introduces and summarizes many points I’ve learned through years of experience. The gems of truth found in this book will serve well those who wish to apply bioinformatics in their daily work, as well as help them advise others in this capacity.” (Circulation: Cardiovascular Genetics, 2008)Table of ContentsForeword. Preface. Contributors. Glossary. SECTION I AN INTRODUCTION TO BIOINFORMATICS FOR THE GENETICIST. 1 Bioinformatics challenges for the geneticist (Michael R. Barnes). 1.1 Introduction. 1.2 The role of bioinformatics in genetics research. 1.3 Genetics in the post-genome era. 1.4 Conclusions. References. 2 Managing and manipulating genetic data (Karl W. Broman and Simon C. Heath). 2.1 Introduction. 2.2 Basic principles. 2.3 Data entry and storage. 2.4 Data manipulation. 2.5 Examples of code. 2.6 Resources. 2.7 Summary. References. SECTION II MASTERING GENES, GENOMES AND GENETIC VARIATION DATA. 3 The HapMap – A haplotype map of the human genome (Ellen M. Brown and Bryan J. Barratt). 3.1 Introduction. 3.2 Accessing the data. 3.3 Application of HapMap data in association studies. 3.4 Future Perspectives. References. 4 Assembling a view of the human genome (Colin A. M. Semple). 4.1 Introduction. 4.2 Genomic sequence assembly. 4.3 Annotation from a distance: the generalities. 4.4 Annotation up close and personal: the specifics. 4.5 Annotation: the next generation. References. 5 Finding, delineating and analysing genes (Christopher Southan and Michael R. Barnes). 5.1 Introduction. 5.2 Why learn to predict and analyse genes in the complete genome era? 5.3 The evidence cascade for gene products. 5.4 Dealing with the complexities of gene models. 5.5 Locating known genes in the human genome. 5.6 Genome portal inspection. 5.7 Analysing novel genes. 5.8 Conclusions and prospects. References. 6 Comparative genomics (Martin S. Taylor and Richard R. Copley). 6.1 Introduction. 6.2 The Genomic landscape. 6.3 Concepts. 6.4 Practicalities. 6.5 Technology. 6.6 Applications. 6.7 Challenges and future directions. 6.8 Conclusion. References. SECTION III BIOINFORMATICS FOR GENETIC STUDY DESIGN AND ANALYSIS. 7 Identifying mutations in single gene disorders (David P. Kelsell, Diana Blaydon and Charles A. Mein). 7.1 Introduction. 7.2 Clinical Ascertainment. 7.3 Genome-wide mapping of monogenic diseases. 7.4 The nature of mutation in monogenic diseases. 7.5 Considering epigenetic effects in mendelian traits. 7.6 Summary. References. 8 From Genome Scan Culprit Gene (Ian C. Gray). 8.1 Introduction. 8.2 Theoretical and practical considerations. 8.3 A stepwise approach to locus refinement and candidate gene identification. 8.4 Conclusion. 8.5 A list of the software tools and Web links mentioned in this chapter. References. 9 Integrating Genetics, Genomics and Epigenomics to Identify. Disease Genes (Michael R. Barnes). 9.1 Introduction. 9.2 Dealing with the (draft) human genome sequence. 9.3 Progressing loci of interest with genomic information. 9.4 In silico characterization of the IBD5 locus – a case study. 9.5 Drawing together biological rationale – hypothesis building. 9.6 Identification of potentially functional polymorphisms. 9.7 Conclusions. References. 10 Tools for statistical genetics (Aruna Bansal, Charlotte Vignal and Ralph McGinnis). 10.1 Introduction. 10.2 Linkage analysis. 10.3 Association analysis. 10.4 Linkage disequilibrium. 10.5 Quantitative trait locus (QTL) mapping in experimental crosses. 10.6 Closing remarks. References. SECTION IV MOVING FROM ASSOCIATED GENES TO DISEASE ALLELES. 11 Predictive functional analysis of polymorphisms: An overview (Mary Plumpton and Michael R. Barnes). 11.1 Introduction. 11.2 Principles of predictive functional analysis of polymorphisms. 11.3 The anatomy of promoter regions and regulatory elements. 11.4 The anatomy of genes. 11.5 Pseudogenes and regulatory mRNA. 11.6 Analysis of novel regulatory elements and motifs in. nucleotide sequences. 11.7 Functional analysis of non-synonymous coding polymorphisms. 11.8 Integrated tools for functional analysis of genetic variation. 11.9 A note of caution on the prioritization of in silico predictions for. further laboratory investigation. 11.10 Conclusions. References. 12 Functional in silico analysis of gene regulatory polymorphism (Chaolin Zhang, Xiaoyue Zhao, Michael Q. Zhang). 12.1 Introduction. 12.2 Predicting regulatory regions. 12.3 Modelling and predicting transcription factor-binding sites. 12.4 Predicting regulatory elements for splicing regulation. 12.5 Evaluating the functional importance of. regulatory polymorphisms. References. 13 Amino-acid properties and consequences of substitutions (Matthew J. Betts and Robert B. Russell). 13.1 Introduction. 13.2 Protein features relevant to amino-acid behaviour. 13.3 Amino-acid classifications. 13.4 Properties of the amino acids. 13.5 Amino-acid quick reference. 13.6 Studies of how mutations affect function. 13.7 A summary of the thought process. References. 14 Non-coding RNA bioinformatics (James Brown, Steve Deharo, Barry Dancis, Michael R. Barnes and Philippe Sanseau). 14.1 Introduction. 14.2 The non-coding (nc) RNA universe. 14.3 Computational analysis of ncRNA. 14.4 ncRNA variation in disease. 14.5 Assessing the impact of variation in ncRNA. 14.6 Data resources to support small ncRNA analysis. 14.7 Conclusions. References. SECTION V ANALYSIS AT THE GENETIC AND GENOMIC DATA INTERFACE. 15 What are microarrays? (Catherine A. Ball and Gavin Sherlock). 15.1 Introduction. 15.2 Principles of the application of microarray technology. 15.3 Complementary approaches to microarray analysis. 15.4 Differences between data repository and research database. 15.5 Descriptions of freely available research database packages. References. 16 Combining quantitative trait and gene-expression data (Elissa J. Chesler). 16.1 Introduction: the genetic regulation of endophenotypes. 16.2 Transcript abundance as a complex phenotype. 16.3 Scaling up genetic analysis and mapping models for microarrays. 16.4 Genetic correlation analysis. 16.5 Systems genetic analysis. 16.6 Using expression QTLs to identify candidate genes for the regulation of complex phenotypes. 16.7 Conclusions. References. 17 Bioinformatics and cancer genetics (Joel Greshock). 17.1 Introduction. 17.2 Cancer genomes. 17.3 Approaches to studying cancer genetics. 17.4 General resources for cancer genetics. 17.5 Cancer genes and mutations. 17.6 Copy number alterations in cancer. 17.7 Loss of heterozygosity in cancer. 17.8 Gene-expression data in cancer. 17.9 Multiplatform gene target identification. 17.10 The epigenetics of cancer. 17.11 Tumour modelling. 17.12 Conclusions. References. 18 Needle in a haystack? dealing with 500 SNP genome scans (Michael R. Barnes and Paul S. Derwent). 18.1 Introduction. 18.2 Genome scan analysis issues. 18.3 Ultra-high-density genome-scanning technologies. 18.4 Bioinformatics for genome scan analysis. 18.5 Conclusions. References. 19 A bioinformatics perspective on genetics in drug discovery and development (Christopher D. Southan, Magnus Ulvsb¨ack and Michael R. Barnes). 19.1 Introduction. 19.2 Target genetics. 19.3 Pharmacogenetics (PGx). 19.4 Conclusions: toward ‘personalized medicine’. References. Appendix I. Appendix II. Index.

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Book SynopsisEpidemiology increasingly relies on laboratory-generated biomarker data, and an understanding of disease mechanisms is increasingly important in elucidating aetiology. Eagerly awaited, this book is the first in many years to bridge the gap between molecular biology and epidemiology.Trade Review"I think this is an excellent book—I recommend it to anyone involved in molecular epidemiology.... The 26 chapters are written by topic specialists, in an explanatory, easy to read style." (BTS Newsletter, Summer 2009) "This text provides an accessible and useful handbook for the epidemiologist who wants to survey the field, to become better informed, to look at recent developments and get some background on these or simply to appreciate further the relatively rapid changes in informatic and analytical technologies which increasingly will serve and underpin future epidemiological studies. One of the strengths in this book is the extensive array of practical illustrative examples, and it would also in my opinion have useful potential as a teaching text." (American Journal of Human Biology, March 2009)Table of ContentsContributors. Acknowledgements. 1. Introduction: why molecular epidemiology? (Chris Wild, Seymour Garte and Paolo Vineis). 2. Study design (Paolo Vineis). 3. Molecular epidemiological studies that can be nested within cohorts (Andrew Rundle and Habibul Ahsan). 4. Family studies, haplotypes and gene association studies (Jennifer H. Barrett, D. Timothy Bishop and Mark M. Iles). 5. Individual susceptibility and gene-environment interaction (Seymour Garte). 6. Biomarker validation (Paolo Vineis and Seymour Garte). 7. Exposure assessment (Mark J. Nieuwenhuijsen). 8. Carcinogen metabolites as biomarkers (Stephen S. Hecht). 9. Biomarkers of exposure: adducts (David H. Phillips). 10. Biomarkers of mutation and DNA repair capacity (Marianne Berwick and Richard J. Albertini). 11. High-throughput techniques -genotyping and genomics (Alison M. Dunning and Craig Luccarini). 12. Proteomics and molecular epidemiology (Jeff N. Keen and John B.C. Findlay). 13. Exploring the contribution of metabolic profiling to epidemiological studies (M. Bictash, Elaine Holmes, H. Keun, P. Elliott and J. K. Nicholson). 14. Univariate and multivariate data analysis (Yu-Kang Tu and Mark S. Gilthorpe). 15. Meta-analysis and pooled analysis - genetic and environmental data (Camille Ragin and Emanuela Taioli). 16. Analysis of Complex datasets (Jason H. Moore, Margaret R. Karagas and Angeline S. Andrew). 17. Some implications of random exposure measurement errors in occupational and environmental epidemiology (S. M. Rappaport and L . L. Kupper). 18. Bioinformatics (Jason H. Moore). 19. Biomarkers, disease mechanisms and their role in regulatory decisions (Pier Alberto Bertazzi and Antonio Mutti). 20. Biomarkers as endpoints in intervention studies (Lynnette R. Ferguson). 21. Biological resource centres in molecular epidemiology: collecting, storing and analysing biospecimens (Elodie Caboux, Pierre Hainaut and Emmanuelle Gormally). 22. Molecular epidemiogy and ethics: biomarkers for disease susceptibility (Kirsi Vähäkangas). 23. Biomarkers for dietary carcinogens: the example of heterocyclic amines in epidemiological studies (Rashmi Sinha, Amanda Cross and Robert J. Turesky). 24. Practical examples: hormones (Sabina Rinaldi and Rudolf Kaaks). 25. Aflatoxin, hepatitis B virus and liver cancer: a paradigm for molecular epidemiology (John D. Gropman,Thomas. W. Kensler and Chris Wild). 26. Complex exposures - air pollution (Steffen Loft, Elvira Vaclavik Brauner, Lykke Forchhammer, Marie Pedersen, Lisbeth E. Knudsen and Peter Moller). Index.

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Book SynopsisThe title captures the ethos and content precisely. It brings basic chemistry into real life with examples that illustrate how chemical principals are inherent to bioanalytical procedures, making them accessible to readers with a background in life sciences. Microbiology Today, July 2009 a good overview of the basic strategies to tackle the complexity of analysis in biological environments and provides some illustrative examples for a better understanding of the theoretical concepts provides a fundamental introduction to the tools adopted by life and health scientists in the evolving and exciting new age of omics specifically applied to the diagnosis, treatment, cure and prevention of disease Analytical and Bioanalytical Chemistry, October 2009 Although chemistry is core to the life and health sciences, it is often viewed as a challenging subject. Conventional textbooks tend to present chemistry in a way that is not always easily accessible to stTrade Review"The authors have attempted to create a text that is more palatable for undergraduate cohorts, and they have succeeded well in this aim. … [A] useful introductory text on the fundamentals of bioanalytical chemistry." (Australian Biochemist, December 2009) "This book provides a good introduction to the bioanalysis world … .The authors have succeeded in using real-life examples to illustrate chemical principles and applications." (Analytical and Bioanalytical Chemistry, October 2009) "The title captures the ethos and content precisely. It brings basic chemistry into real life with examples that illustrate how chemical principals are inherent to bioanalytical procedures, making them accessible to readers with a background in life sciences." (Microbiology Today, July 2009)Table of ContentsPreface ix 1 Introduction to biomolecules 1 1.1 Overview of chemical and physical attributes of biomolecules 2 1.2 Classification of biomolecules 5 1.3 Features and characteristics of major biomolecules 6 1.4 Structure–function relationships 21 1.5 Significance of biomolecules in nature and science 21 2 Analysis and quantification of biomolecules 29 2.1 Importance of accurate determination of biomolecules 30 2.2 Major methods to detect and quantify biomolecules 33 2.3 Understanding mass, weight, volume and density 34 2.4 Understanding moles and molarity 38 2.5 Understanding solubility and dilutions 46 3 Transition metals in health and disease 53 3.1 Structure and characteristics of key transition metals 54 3.2 Importance of transition metals in physiological processes 60 3.3 Transition metals as mediators of disease processes 64 3.4 Therapeutic implications of transition metals 71 3.5 Determination of transition metals in nature 73 4 Ions, electrodes and biosensors 77 4.1 Impact of ions and oxidation–reduction reactions on physical and life processes 78 4.2 pH, biochemical buffers and physiological regulation 83 4.3 Chemical and physical sensors and biosensors 88 4.4 Important measurements using specific electrodes 91 4.5 Specific applications of biosensors in life and health sciences 93 5 Applications of spectroscopy 99 5.1 An introduction to spectroscopic techniques 100 5.2 Major types of spectroscopy 104 5.3 Principles and applications of ultraviolet/visible spectrophotometry 105 5.4 Principles and applications of infrared spectroscopy 113 5.5 Principles and applications of fluorescence spectrofluorimetry 118 6 Centrifugation and separation 123 6.1 Importance of separation methods to isolate biomolecules 124 6.2 Basic principles underlying centrifugation 126 6.3 Features and components of major types of centrifuge 129 6.4 Major centrifugation methods for bioanalysis 133 6.5 Flow cytometry: principles and applications of this core method of separation 136 7 Chromatography of biomolecules 141 7.1 Chromatography: a key method for separation and identification of biomolecules 142 7.2 Principles, types and modes of chromatography 143 7.3 Applications of chromatography in life and health sciences 153 7.4 High-performance liquid chromatography and advanced separation technologies 154 7.5 Additional state-of-the-art chromatography techniques 160 8 Principles and applications of electrophoresis 163 8.1 Principles and theory of electrophoretic separation 164 8.2 Major types of electrophoresis 165 8.3 Electrophoresis in practice 169 8.4 Applications of electrophoresis in life and health sciences 177 8.5 Advanced electrophoretic separation methodologies for genomics and proteomics 178 9 Applications of mass spectrometry 183 9.1 Major types of mass spectrometry 184 9.2 Understanding the core principles of mass spectrometry 186 9.3 Major types of mass spectrometry in practice 191 9.4 Mass spectrometry: a key tool for bioanalysis in life and health sciences 194 9.5 Mass spectrometry: future perspectives 196 10 Immunochemical techniques and biological tracers 199 10.1 Antibodies: the keys to immunochemical measurements 200 10.2 Analytical applications of biological tracers 208 10.3 Principles and applications of radioimmunoassay (RIA) 212 10.4 Principles and applications of enzyme-linked immunosorbent assay (ELISA) 216 10.5 Immunohistochemistry: an important diagnostic tool 221 11 Bioanalysis by magnetic resonance technologies: NMR and MRI 225 11.1 Nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) technologies: key tools for the life and health sciences 226 11.2 Principles of NMR and the importance of this biomolecular analytical technique 229 11.3 Established and emerging applications of NMR 235 11.4 Principles and uses of MRI 236 11.5 MRI as a principal diagnostic and research tool 241 12 Bioanalytical approaches from diagnostic, research and pharmaceutical perspectives 247 12.1 Clinical genomics, proteomics and metabolomics 248 12.2 Clinical diagnosis and screening 251 12.3 Research and development 254 12.4 Emerging pharmaceutical products 258 12.5 Future perspectives 260 13 Self-Assessment 265 Appendix 1: International system of units (SI) and common prefixes 273 Appendix 2: The periodic table of the elements 275 Appendix 3: Common solvents and biological buffers 277 Appendix 4: Answers to self-assessment questions 279 Index 281

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Book SynopsisThis innovative book provides a completely fresh exploration of bioinformatics, investigating its complex interrelationship with biology and computer science. It approaches bioinformatics from a unique perspective, highlighting interdisciplinary gaps that often trap the unwary.Table of ContentsPreface x Acknowledgements xvii About the companion website xviii PART 1 1 Introduction 3 1.1 Overview 3 1.2 Bioinformatics 3 1.2.1 What is bioinformatics? 3 1.2.2 The provenance of bioinformatics 4 1.2.3 The seeds of bioinformatics 5 1.3 Computer Science 7 1.3.1 Origins of computer science 7 1.3.2 Computer science meets bioinformatics 9 1.4 What did we want to do with bioinformatics? 10 1.5 Summary 12 1.6 References 13 1.7 Quiz 14 1.8 Problems 16 2 The biological context 17 2.1 Overview 17 2.2 Biological data]types and concepts 17 2.2.1 Diversity of biological data]types 17 2.2.2 The central dogma 18 2.2.3 Fundamental building]blocks and alphabets 19 2.2.4 The protein structure hierarchy 29 2.2.5 RNA processing in prokaryotes and eukaryotes 30 2.2.6 The genetic code 33 2.2.7 Conceptual translation and gene finding 35 2.3 Access to whole genomes 42 2.4 Summary 43 2.5 References 43 2.6 Quiz 46 2.7 Problems 47 3 Biological databases 49 3.1 Overview 49 3.2 What kinds of database are there? 49 3.3 The Protein Data Bank (PDB) 50 3.4 The EMBL nucleotide sequence data library 56 3.5 GenBank 58 3.6 The PIR]PSD 61 3.7 Swiss]Prot 62 3.8 PROSITE 64 3.9 TrEMBL 69 3.10 InterPro 71 3.11 UniProt 73 3.12 The European Nucleotide Archive (ENA) 77 3.13 Summary 81 3.14 References 82 3.15 Quiz 85 3.16 Problems 87 4 Biological sequence analysis 89 4.1 Overview 89 4.2 Adding meaning to raw sequence data 89 4.2.1 Annotating raw sequence data 94 4.2.2 Database and sequence formats 96 4.2.3 Making tools and databases interoperate 101 4.3 Tools for deriving sequence annotations 103 4.3.1 Methods for comparing two sequences 103 4.3.2 The PAM and BLOSUM matrices 104 4.3.3 Tools for global and local alignment 110 4.3.4 Tools for comparing multiple sequences 114 4.3.5 Alignment]based analysis methods 115 4.4 Summary 131 4.5 References 132 4.6 Quiz 134 4.7 Problems 136 5 The gap 138 5.1 Overview 138 5.2 Bioinformatics in the 21st century 138 5.3 Problems with genes 139 5.4 Problems with names 142 5.5 Problems with sequences 143 5.6 Problems with database entries 146 5.6.1 Problems with database entry formats 147 5.7 Problems with structures 148 5.8 Problems with alignments 150 5.8.1 Different methods, different results 150 5.8.2 What properties do my sequences share? 154 5.8.3 How similar are my sequences? 157 5.8.4 How good is my alignment? 160 5.9 Problems with families 163 5.10 Problems with functions 168 5.11 Functions of domains, modules and their parent proteins 173 5.12 Defining and describing functions 176 5.13 Summary 179 5.14 References 180 5.15 Quiz 182 5.16 Problems 183 PART 2 6 Algorithms and complexity 187 6.1 Overview 187 6.2 Introduction to algorithms 187 6.2.1 Mathematical computability 189 6.3 Working with computers 191 6.3.1 Discretisation of solutions 191 6.3.2 When computers go bad 193 6.4 Evaluating algorithms 197 6.4.1 An example: a sorting algorithm 197 6.4.2 Resource scarcity: complexity of algorithms 199 6.4.3 Choices, choices 200 6.5 Data structures 201 6.5.1 Structural consequences 202 6.5.2 Marrying form and function 210 6.6 Implementing algorithms 211 6.6.1 Programming paradigm 212 6.6.2 Choice of language 214 6.6.3 Mechanical optimisation 216 6.6.4 Parallelisation 224 6.7 Summary 227 6.8 References 227 6.9 Quiz 227 6.10 Problems 229 7 Representation and meaning 230 7.1 Overview 230 7.2 Introduction 230 7.3 Identification 233 7.3.1 Namespaces 233 7.3.2 Meaningless identifiers are a good thing 233 7.3.3 Identifying things on the Web 236 7.3.4 Cool URIs don’t change 238 7.3.5 Versioning and provenance 238 7.3.6 Case studies 239 7.4 Representing data 243 7.4.1 Design for change 245 7.4.2 Contemporary data]representation paradigms 247 7.5 Giving meaning to data 255 7.5.1 Bio ontologies in practice 260 7.5.2 First invent the universe 263 7.6 Web services 264 7.6.1 The architecture of the Web 266 7.6.2 Statelessness 267 7.7 Action at a distance 268 7.7.1 SOAP and WSDL 270 7.7.2 HTTP as an API 270 7.7.3 Linked Data 272 7.8 Summary 275 7.9 References 275 7.10 Quiz 276 7.11 Problems 277 8 Linking data and scientific literature 279 8.1 Overview 279 8.2 Introduction 279 8.3 The lost steps of curators 281 8.4 A historical perspective on scientific literature 286 8.5 The gulf between human and machine comprehension 288 8.6 Research objects 295 8.7 Data publishing 297 8.8 Separating scientific wheat from chaff – towards semantic searches 298 8.9 Semantic publication 300 8.9.1 Making articles ‘semantic’ 301 8.10 Linking articles with their cognate data 305 8.10.1 What Utopia Documents does 305 8.10.2 A case study 306 8.11 Summary 314 8.12 References 315 8.13 Quiz 318 8.14 Problems 319 Afterword 321 Glossary 327 Quiz Answers 371 Problem Answers 378 Index 394

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Book SynopsisPlant Breeding Reviews presents state-of-the-art reviews on plant genetics and the breeding of all types of crops by both traditional means and molecular methods. Many of the crops widely grown today stem from a very narrow genetic base; understanding and preserving crop genetic resources is vital to the security of food systems worldwide. The emphasis of the series is on methodology, a fundamental understanding of crop genetics, and applications to major crops. It is a serial title that appears in the form of one or two volumes per year.Table of ContentsContributors. Chapter 1.Dedication: Theodore Hymowitz Scientist, Plant Explorer, Soybean Geneticist (Reid G. Palmer) Chapter 2. Blackberry Breeding and Genetics (John R. Clark, Eric T. Stafne, Harvey K. Hall, and Chad E. Finn) Chapter 3. Gooseberry and Currant is Sweden: History and Cultivar Development (Inger Hjalmarsson and Bjorn Wallace) Chapter 4. Hevea Rubber Breeding and Genetics (A. Clement-Demange, P.M. Priyadarshan, Tran Thi Thuy Hoa, and P. Venkatachalam) Chapter 5. Wild Plant Sampling Strategies: The Roles of Ecology and Evolution (Dale R. Lockwood, Christopher M. Richards, and Gayle M. Volk) Chapter 6. Development of Fire Blight Resistance by Recombinant DNA Technology (Mickael Malnoy and Herb S. Aldwinckle) Chapter 7. Molecular Mechanisms of Plant Adaptation to Phosphate Deficiency (Ajay Jain, Maria Jose Vasconcelos, K.G. Raghothama, and Shivendra V. Sahi) Subject Index. Cumulative Subject Index. Cumulative Contributor Index.

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Book SynopsisIn today's global marketplace, particular problems can arise when limited control is exercised over new and high-risk medicines. Providing a multidisciplinary approach, Quality Systems and Control for Pharmaceuticals provides a comprehensive overview of the highly regulated area of pharmaceutical manufacture.Table of ContentsPreface xi List of figures xv List of tables xix Glossary of terms and acronyms xxi Glossary of mathematical and statistical symbols xxiii SECTION A Most Suitable Environment 1 1. Introduction 31.1 The process of finding new lead medicines 41.2 A drug discovery framework 6 2. Technology transfer and the climate of change 112.1 Innovation and research 112.2 Method transfer 14 3. Quality systems structure and a maximum quality environment 153.1 The quality gurus and models for assurance 183.2 A cycle of continual improvement 223.3 Management structure and a functioning department 22 SECTION B Setting Process Bounderies 29 4. Validation 314.1 Process and manufacturing validation activities 354.2 Valid analytical methodologies (VAMs) 43 5. Good manufacturing practices 575.1 Manufacture of standard products 605.2 Manufacture of materials requiring specialised production facilities 755.3 Quality assurance aspects of medical gases, devices and miscellaneous product manufacture 88 6. Process control via numerical means 976.1 Charting and quality inspection 996.2 Sampling plans 1046.3 Measures of process compliance and variation 108 7. Product verification and the role of qualified personnel 1117.1 Batch documentation 1137.2 Standard operating procedures 1147.3 Guides, overviews and validation plans 1157.4 The duties of the qualified person 116 8. In-process and on-process QC testing and control 1198.1 Process analytical technologies 1208.2 Analytical validation and clinical test validation (CTV) 1218.3 LIMS and automation 126 SECTION C Starting from Scratch 131 9. Applications of QA to new medicinal products and new chemical entities formulation 1339.1 Start-up and initialisation 1349.2 Raw materials control 1349.3 The validation life cycle 1349.4 Top-down or bottom-up validations 135 10. New products manufacturing 13710.1 From inception to market place 13910.2 New product development: product design and specification 146 11. Questions and problems 15111.1 Specimen examples and exam questions 15111.2 Model answers to examples 162 References 169 Index 177

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Book SynopsisToday the Paralympic Movement is recognised as a global sporting phenomenon attracting thousands of athletes from an ever-increasing number of countries. Athlete First provides a thoroughly researched history and analysis of the Paralympic Movement, including the development and organisation of the International Paralympic Committee. As well as recounting factual achievements and events, the book examines the position of sport and international competition for people with a disability within their changing historical context and in relation to the Olympic Movement and able-bodied sport. The first history of the origins and development of the Paralympic movement Examines disabled sport and international competition within their changing historical context Includes details of key players in the movement on and off the field Written in an accessible style by a recognised historian Athlete First will prove invaluTrade Review“All in all this is an indispensable guide to the labyrinthine origins of disability and Paralympic sport and this book will be an absolutely vital source text for other scholars working in this area.” (Sport in History, 28 June 2012) “The book is the first cohesive history of the Paralympic Movement.” (Idrottsforum.org, June 2009) "This book successfully takes on the task of chronicling the story of the paralympic movement. Along the way, readers are introduced to some of the strong characters who have helped get the paralympians to their current position on the international sports stage." (Doody's, January 2009)Table of ContentsList of Figures and Boxes. Foreword: Sir Philip Craven. Foreword: Prof. Dr Gudrun Doll-Tepper. International Council of Sport Science and Physical Education. Preface. List of Abbreviations. Chapter 1. A Showcase of Ability. Chapter 2. An Air of Hopelessness. Chapter 3. The Era of Development: 1960 to 1980. Chapter 4. Fair, not Equal: 1980 to 1988. Chapter 5. Building Bridges not Walls: 1988 to 1992. Chapter 6. Spirit in Motion: 1992 to 1996. Chapter 7. Repair What Needs Repair? 1996 to 2000. Chapter 8. Sport is About Emotion: 2000 to 2004. Bibliography and Resources. Index.

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Book SynopsisAn accessible engaging biochemistry primer with short, 'bite sized' chapters that gently lead the reader through the essential chemistry and biochemistry they need to know without going into unnecessary and intimidating detail. Assumes only a basic understanding of chemistry and focuses on helping the reader to understand key concepts.Trade Review"For students embarking on careers in the health sciences, it is an essential academic companion and, retailing at approximately £28, it is excellent value for money". (The Biochemist, 1 June 2011) "It's not every day that one picks up a textbook that can claim to occupy a unique niche, given the multitude of scientific textbooks that are vying for a medical readership. However, with the recent publication of Pain-Free Biochemistry: An Essential Guide for the Health Sciences, which is specifically aimed at students of medicine and nursing, one could be left wondering just why nobody thought of this sooner." (Irish Medical News, September 08, 2010)Table of ContentsPreface x Section 1 Foundations 1 Topic 1 Why biochemistry? 3 Topic 2 Remarkableness of life 9 Chemistry I The basic structure of substances: atoms, molecules, elements and compounds 13 Chemistry II Atomic structure, valency and bonding 16 Chemistry III Protons, acids, bases, concentration and the pH scale 25 Topic 3 Shape, molecular recognition and proteins: an example 32 Topic 4 Proteins: molecular necklaces 38 Topic 5 Chemical transformations in the living organism: metabolism 43 Topic 6 Reactions, catalysts and enzymes 46 Topic 7 Specificity, saturation and active sites 49 Topic 8 Structure of metabolism: anabolism and catabolism 54 Chemistry IV Equilibrium 56 Topic 9 Catabolism: degradation vs energy metabolism 60 Chemistry V Oxidation and reduction 63 Topic 10 Oxidation and reduction in metabolism 67 Section 2 Catabolism 71 Chemistry VI Aldehydes, ketones and sugars 73 Topic 11 Carbohydrates: sugars and polysaccharides in metabolism 81 Topic 12 Glucose inside the body 85 Topic 13 Breakdown of sugar: glycolysis 88 Topic 14 Aerobic oxidation of pyruvate: Krebs cycle 94 Topic 15 Respiratory chain, oxidative phosphorylation and overall ATP yields 98 Topic 16 Mobilising the carbohydrate store: glycogenolysis 103 Chemistry VII Alcohols, esters, glycerol, fatty acids and triglycerides 106 Chemistry VIII Hydrophobic, hydrophilic and amphiphilic 109 Topic 17 Phospholipids and membranes 111 Chemistry IX Saturated and unsaturated 114 Topic 18 Fats as an energy source 119 Topic 19 Fats: digestion, transport, storage and mobilisation 122 Topic 20 Fats: oxidation of fatty acids 126 Topic 21 Ketone bodies in health and disease 133 Topic 22 Dietary fat: essential fatty acids 137 Topic 23 Protein and amino acid breakdown 140 Topic 24 Shedding excess amino groups: urea cycle 147 Section 3 Anabolism and Control 151 Topic 25 Is anabolism just catabolism backwards? 153 Topic 26 Making new glucose: gluconeogenesis 156 Topic 27 Fatty acid biosynthesis 161 Topic 28 Providing reducing power: NADPH and the pentose phosphate pathway 164 Chemistry X Isotopes 168 Topic 29 Red cells and white cells: defence against reactive oxygen and reactive oxygen as defence! 172 Topic 30 The need for metabolic control 176 Topic 31 Relationship of fats and carbohydrates: use by different tissues 179 Section 4 Genes and Protein Synthesis 181 Topic 32 The idea of genes 183 Topic 33 The chemistry of genes: DNA and the double helix 186 Topic 34 The genetic code and mRNA 190 Topic 35 Protein synthesis, ribosomes and tRNA 193 Topic 36 Genetic differences and disease 197 Topic 37 Genetic variability: drug metabolism and disease susceptibility 203 Topic 38 Mutation, radiation and ageing 205 Topic 39 Switching genes on and off: development, tissue specificity, adaptation and tolerance 207 Topic 40 DNA and protein synthesis as targets: chemotherapy, antibiotics, etc. 210 Section 5 Physiological Systems and Clinical Issues 217 Topic 41 Hormones and second messengers 219 Topic 42 Switching enzymes on and off: coarse and fine control 222 Topic 43 Insulin, glucagon and adrenaline 224 Topic 44 Diabetes 229 Topic 45 Steroid hormones and receptors: fertility control, pregnancy testing, etc. 233 Topic 46 Pituitary hormones and feedback loops 238 Topic 47 Thyroid hormones 240 Topic 48 Adrenal cortex 244 Topic 49 Prostaglandins and inflammation: aspirin 246 Topic 50 Membrane transport 250 Topic 51 Nerve and muscle 255 Topic 52 pH homeostasis 258 Topic 53 Diagnostic markers: biochemical tests 261 Topic 54 Blood, bleeding and clotting 265 Section 6 Appendices 271 Appendix 1 pH and neutrality 273 Appendix 2 Crystallography 274 Appendix 3 Protein forces, secondary structure and folding 277 Appendix 4 Equilibrium constant 281 Appendix 5 Phosphorus, phosphoric acid and phosphate esters 283 Appendix 6 Coenzymes, cofactors and prosthetic groups 285 Appendix 7 Coenzyme A 287 Appendix 8 Krebs cycle and evidence for a catalytic reaction sequence 289 Appendix 9 Knoop’s experiment pointing to β-oxidation of fatty acids 291 Appendix 10 Isoenzymes 293 Appendix 11 Genetic code 295 Appendix 12 Different kinds of mutation 297 Appendix 13 Restriction enzymes 299 Appendix 14 Enzyme inhibition 301 Appendix 15 Electrophoresis to separate proteins 304 Appendix 16 Chromatography and mass spectrometry to separate and identify metabolites 308 Glossary 313 MCQ answers 322 Index 323

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Book SynopsisConfidently face the challenges of proteomics research specific to plant science with the information in Plant Proteomics, which will introduce you to the techniques and methodologies required for the study of representative plant species. Read about proteomics studies in Arabidopsis, rice, and legumes and find information about common technologies like mass spectrometry and gel electrophoresis. Discover expression proteomics, functional proteomics, structural proteomics, bioinformatics, and systems biology, understand how to conduct proteomics studies in developing countries and underfunded laboratories, and gain access to guidelines for sample preparation.Table of ContentsPREFACE. CONTRIBUTORS. ACRONYMS AND ABBREVIATIONS. 1. AN INTRODUCTION TO PROTEOMICS: APPLICATIONS TO PLANT BIOLOGY (Ralph A. Bradshaw). PART I: TECHNOLOGIES. 2. GEL-BASED PROTEOMICS (Pier Giorgio Righetti, Paolo Antonioli, Carolina Simo, and Attilio Citterio). 3. MASS SPECTROMETRY-BASED PROTEOMICS: IDENTIFYING PLANT PROTEINS (Eveline Bergmuller, Sacha Baginsky, and Wilhelm Gruissem). 4. CHEMICAL PROTEOMICS (Miriam C. Hagenstein, Olaf Kruse, and Norbert Sewald). 5. THE ARABIDOPSIS LOCALIZOME: SUBCELLULAR PROTEIN LOCALIZATION AND INTERACTIONS IN ARABIDOPSIS (Georgios Kitsios, Nicolas Tsesmetzis, Max Bush, and John H. Doonan). 6. SECRETOME: TOWARD DECIPHERING THE SECRETORY PATHWAYS AND BEYOND (Young-Ho Jung, Ganesh Kumar Agrawal, Randeep Rakwal, and Nam-Soo Jwa). 7. PEPTIDOMICS (Peter Schulz-Knappe). PART II: COMPUTATIONAL PROTEOMICS. 8. BIOINFORMATICS IN GEL-BASED PROTEOMICS (Asa M. Wheelock and Craig E. Wheelock). 9. BIOINFORMATICS IN MS-BASED PROTEOMICS (Jacques Colinge). PART III: EXPRESSION PROTEOMICS. 10. AN OVERVIEW OF THE ARABIDOPSIS PROTEOME (Jacques Bourguignon and Michel Jaquinod). 11. RICE PROTEOME AT A GLANCE (Ganesh Kumar Agrawal and Randeep Rakwal). 12. PROTEOMICS OF LEGUME PLANTS (Satish Nagaraj, Zhentian Lei, Bonnie Watson, and Lloyd W. Sumner). 13. PROTEOME OF SEED DEVELOPMENT AND GERMINATION (Julie Catusse, Loıc Rajjou, Claudette Job, and Dominique Job). 14. ENDOSPERM AND AMYLOPLAST PROTEOMES OF WHEAT GRAIN (William J. Hurkman, William H. Vensel, Frances M. DuPont, Susan B. Altenbach, and Bob B. Buchanan). 15. ROOT PROTEOME (Kuo-Chen Yeh, Chyi-Chuann Chen, and Chuan-Ming Yeh). 16. LEAF PROTEOME (Bin Kang, Shuyang Tu, Jiyuan Zhang, and Siqi Liu). 17. ANTHER PROTEOME (Nijat Imin). 18. POLLEN PROTEOME (Sandra Noir). 19. MICROTUBULE-BINDING PROTEINS (Lori A. Vickerman and Douglas G. Muench). PART IV: ORGANELLE PROTEOMICS. 20. CELL WALL (Elisabeth Jamet, Herv´e Canut, Cecile Albenne, Georges Boudart, and Rafael Pont-Lezica). 21. PLASMA MEMBRANE: A PECULIAR STATUS AMONG THE CELL MEMBRANE SYSTEMS (Geneviève Ephritikhine, Anne Marmagne, Thierry Meinnel, and Myriam Ferro). 22. NUCLEUS (Subhra Chakraborty, Aarti Pandey, Asis Datta, and Niranjan Chakraborty). 23. CHLOROPLAST (Thomas Kieselbach and Wolfgang P. Schröder). 24. ETIOPLAST (Anne von Zychlinski, Sonja Reiland, Wilhelm Gruissem, and Sacha Baginsky). 25. THE PLANT MITOCHONDRIAL PROTEOME AND THE CHALLENGE OF HYDROPHOBIC PROTEIN ANALYSIS (Yew-Foon Tan and A. Harvey Millar). 26. PEROXISOME (Yuko Arai, Youichiro Fukao, Makoto Hayashi, and Mikio Nishimura). 27. UNRAVELING PLANT VACUOLES BY PROTEOMICS (Songqin Pan and Natasha Raikhel). 28. OIL BODIES (Pascale Jolivet, Luc Negroni, Sabine d’Andrea, and Thierry Chardot). PART V: MODIFICATION PROTEOMICS. 29. PHOSPHOPROTEINS: WHERE ARE WE TODAY? (Florian Wolschin and Wolfram Weckwerth). 30. PROTEOME ANALYSIS OF THE UBIQUITIN PATHWAY (Junmin Peng). 31. ANALYSIS OF THE N-GLYCOSYLATION OF PROTEINS IN PLANTS (Willy Morelle). 32. FUNCTIONAL ANALYSIS AND PHOSPHORYLATION SITE MAPPING OF LEUCINE-RICH REPEAT RECEPTOR-LIKE KINASES (Steven D. Clouse, Michael B. Goshe, Steven C. Huber, and Jia Li). 33. TIME TO SEARCH FOR PROTEIN KINASE SUBSTRATES (Birgit Kersten). 34. TYROSINE PHOSPHORYLATION IN PLANTS: EMERGING EVIDENCE (Andrea Carpi, Valeria Rossi, and Francesco Filippini). 35. 14–3–3 PROTEINS: REGULATORS OF KEY CELLULAR FUNCTIONS (Peter C. Morris). PART VI: MULTIPROTEIN COMPLEX. 36. TAP-TAGGING SYSTEM IN RICE FOR PROTEIN COMPLEX ISOLATION (Jai S. Rohila and Michael E. Fromm). 37. TAP STRATEGY IN ARABIDOPSIS PROTEIN COMPLEX ISOLATION (Vicente Rubio and Xing Wang Deng). 38. BLUE-NATIVE PAGE IN STUDYING PROTEIN COMPLEXES (Holger Eubel and A. Harvey Millar). 39. PROTEIN–PROTEIN INTERACTION MAPPING IN PLANTS (Joachim F. Uhrig). PART VII: PLANT DEFENSE AND STRESS. 40. PROTEOMICS IN PLANT DEFENSE RESPONSE (Sun Tae Kim and Kyu Young Kang). 41. PROTEOME ANALYSIS OF CELLULAR RESPONSES TO ABIOTIC STRESSES IN PLANTS (Hans-Peter Mock and Andrea Matros). 42. PROTEOMICS OF BIOTROPHIC PLANT–MICROBE INTERACTIONS: SYMBIOSES LEAD THE MARCH (Ghislaine Recorbet and Eliane Dumas-Gaudot). 43. PROTEOMICS APPROACHES TO CONSTRUCT CALCIUM SIGNALING NETWORKS IN PLANTS (Irene S. Day and A.S.N. Reddy). PART VIII: STRUCTURAL PROTEOMICS. 44. CELL-FREE EXPRESSION SYSTEM FOR EUKARYOTIC PROTEINS (Yaeta Endo and Tatsuya Sawasaki). 45. PROTEIN STRUCTURE DETERMINATION (Jian-Hua Zhao and Hsuan-Liang Liu). PART IX: OTHER TOPICS IN PLANT PROTEOMICS. 46. PROTEOMICS IN CONTEXT OF SYSTEMS BIOLOGY (Serhiy Souchelnytskyi). 47. PROTEOMICS IN DEVELOPING COUNTRIES (Nat N. V. Kav, Sanjeeva Srivastava, William Yajima, and Shakir Ali). INDEX.

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Book SynopsisThe first book to present a unified account of symbolic data analysis methods in a consistent statistical framework, Symbolic Data Analysis features a substantial number of examples from a range of application areas, including health, the social sciences, economics, and computer science.Trade Review“Primarily aimed at statisticians and Data analysts, SDA is also ideal for scientists…” (Zentralblatt MATH, 2007)Table of Contents1. Introduction. References. 2. Symbolic Data. 2.1 Symbolic and Classical Data. 2.2 Categories, Concepts and Symbolic Objects. 2.3 Comparison of Symbolic and Classical Analysis. 3. Basic Descriptive Statistics: One Variate. 3.1 Some Preliminaries. 3.2 Multi-valued Variables. 3.3 Interval-valued Variables. 3.4 Multi-valued Modal variables. 3.5 Interval-valued Modal Variables. 4. Descriptive Statistics: Two or More Variates. 4.1 Multi-valued Variables. 4.2 Interval-valued Variables. 4.3 Modal Multi-valued Variables. 4.4 Modal Interval-valued Variables. 4.5 Baseball Interval-valued Dataset. 4.6 Measures of Dependence. 5. Principal Component Analysis. 5.1 Vertices Method. 5.2 Centers Method. 5.3 Comparison of the Methods. 6. Regression Analysis. 6.1 Classical Multiple Regression Model. 6.2 Multi-valued Variables. 6.3 Interval-valued Variables. 6.4 Histogram-valued Variables. 6.5 Taxonomy Variables. 6.6 Hierarchical Variables. 7. Cluster Analysis. 7.1 Dissimilarity and Distance Measures. 7.2 Clustering Structures. 7.3 Partitions. 7.4 Hierarchy-Divisive Clustering. 7.5 Hierarchy-Pyramid Clusters. Data Index. Author Index. Subject Index.

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Book SynopsisPLATINUM WINNER - 2006 MarCom Creative Awards Postgraduate students require a variety of skills in addition to the specialist knowledge of their area of research, including organisation, time management, preparation and presentation of a seminar, and writing a thesis and a research paper.This outstanding title provides PhD and MSc students with advice on key issues relating to the organisation and presentation of their research. Helps students to deal with an increasingly competitive marketplace after completing their studies Clearly written and illustrated by professional lecturers Covers the skills that the Research Councils expect students to develop during their doctoral training Features handy quick tips, checklists and key remember' points so that students can dip into it in any order throughout their research or read in stages as their work develops This easy-to-use guide on study skills is also of practical value Table of ContentsPreface. Foreword by Clare Isacke. Introduction by Kathryn Allen. List of contributors. SECTION ONE: PERSONAL EFFECTIVENESS. Chapter 1: Effective Organisation and Time Management (Professor Steve Webb and Professor Bob Ott). Chapter 2: Personal and Interpersonal Skills (Mr Neil Walford). SECTION TWO: FINDING AND USING INFORMATION. Chapter 3: Information Retrieval (Barry Jenkins) Chapter 4: Critical Reading (Dr Stan Venitt). SECTION THREE: COMMUNICATION SKILLS. Chapter 5: Oral and Poster Presentations (Dr Maggie Flower). Chapter 6: Writing a Paper (Dr Jeff Bamber). Chapter 7: Writing and Defending Your Thesis (Dr Stan Venitt). Index.

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Book SynopsisIntegrated Genomics: A Discovery-Based Laboratory Course introduces the excitement of discovery to the basic molecular biology laboratory. Utilizing up-to-date molecular biology protocols and a basic experimental design, this text offers experience with three different model systems.Trade Review"I greatly admire the efforts of the authors. Their goals are praiseworthy and this manual is well written." (The Quarterly Review of Biology, September 2007) "…an excellent tool for introducing a wide range of students to modern concepts in molecular biology, genomics, proteomics, and bioinformatics in an integrated discovery-based format…" (The Annals of Pharmacotherapy, March 2007)Table of ContentsPreface. Author biographies. Acknowledgments. List of figures. 1 Introduction to basic laboratory genetics. 1.1 Transferring and handling C. elegans. 1.2 Introduction to laboratory genetics. 2 Gene expression analysis using transgenic animals. 2.1 Transgenic gene expression analysis in C. elegans: lacZ staining. 2.2 Transgenic gene expression analysis in C. elegans: GFP analysis. 3 Creation and testing of transgenic yeast for use in protein–protein interaction screening. 3.1 Small-scale transformation of S. cerevisiae. 3.2 Transformation of S. cerevisiae to test for non-specific interaction. 3.3 Assaying for protein–protein interaction by reporter gene expression. 4 Yeast two-hybrid screening. 4.1 Protein–protein interaction screening of a C. elegans cDNA library. 4.2 Assaying for protein–protein interaction by reporter gene expression. 5 Isolation and identification of interacting proteins. 5.1 Preparation of electrocompetent E. coli. 5.2 Isolation of DNA from yeast and electroporation of E. coli. 5.3 Small-scale isolation of plasmid DNA from E. coli: the mini-prep. 5.4 Sequencing of two-hybrid library plasmid DNA vectors. 6 Using bioinformatics in modern science. 6.1 DNA sequence chromatogram. 6.2 BLASTing your sequence. 6.3 Evaluating sequence results and choosing an RNAi target. 6.4 Bioinformatics practice questions. 7 Generation of an RNAi vector. 7.1 Small-scale isolation of genomic DNA from C. elegans. 7.2 PCR amplification of target gene sequence from C. elegans genomic DNA. 7.3 Preparations for cloning to generate RNAi vector. 7.3.1 Agarose gel electrophoresis. 7.3.2 Removal of dNTPs from PCR reaction. 7.3.3 Restriction enzyme digestion of PCR product and C. elegans RNAi vector. 7.4 Gel purification of DNA and ligation of vector and PCR-amplified DNA. 7.4.1 Preparative agarose gel electrophoresis. 7.4.2 Gel purification of DNA from agarose gel. 7.4.3 Ligation of vector and PCR-amplified DNA. 7.5 Transformation of ligation reactions. 7.6 PCR screening of transformation colonies. 7.7 Small-scale isolation of plasmid DNA from E. coli: the mini-prep. 7.8 Verifying successful ligation by restriction digestion. 8 RNA-mediated interference by bacterial feeding. 8.1 Preparation of RNAi-feeding bacteria for transformation. 8.2 Media preparation for RNAi feeding. 8.3 Transformation of RNAi-feeding strain HT115(DE3). 8.4 RNA interference by bacterial feeding of C. elegans. 8.5 Analyzing effects of dsRNAi. 8.5.1 Assaying for sterility (Ste) or embryonic lethality (Emb). 8.5.2 Assaying for growth effect. 8.5.3 Assaying for morphological effects. 8.5.4 Assaying for general neuromuscular effects. 8.5.5 Assaying for specific neuronal effects. 8.5.6 Assaying for dauer formation. Appendix I Recombinational cloning. AI.1 Isolation of genomic DNA from C. elegans. AI.2 PCR amplification of target gene sequence from C. elegans genomic DNA. AI.3 Agarose gel electrophoresis and clean-up of PCR reaction. AI.4 Entry vector cloning. AI.5 Small-scale isolation of plasmid DNA from E. coli: the mini-prep. AI.6 Destination vector cloning. AI.7 Small-scale isolation of plasmid DNA from E. coli: the mini-prep. Appendix II Recipes and media preparation. Solution recipes. Media preparation. Appendix III Sterile techniques and worm protocols. Sterile techniques. Worm protocols. Appendix IV Mutant C. elegans phenotypes. Appendix V Vector maps. Subject index.

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Book SynopsisMachine learning techniques such as Markov models, support vector machines, neural networks, graphical models, etc. , have been successful in analyzing life science data because of their capabilities of handling randomness and uncertainties of data and noise and in generalization.Table of ContentsForeword. Preface. Contributors. 1 Feature Selection for Genomic and Proteomic Data Mining (Sun-Yuan Kung and Man-Wai Mak). 2 Comparing and Visualizing Gene Selection and Classification Methods for Microarray Data (Rajiv S. Menjoge and Roy E. Welsch). 3 Adaptive Kernel Classifiers Via Matrix Decomposition Updating for Biological Data Analysis (Hyunsoo Kim and Haesun Park). 4 Bootstrapping Consistency Method for Optimal Gene Selection from Microarray Gene Expression Data for Classification Problems (Shaoning Pang, Ilkka Havukkala, Yingjie Hu, and Nikola Kasabov). 5 Fuzzy Gene Mining: A Fuzzy-Based Framework for Cancer Microarray Data Analysis (Zhenyu Wang and Vasile Palade). 6 Feature Selection for Ensemble Learning and Its Application (Guo-Zheng Li and Jack Y. Yang). 7 Sequence-Based Prediction of Residue-Level Properties in Proteins (Shandar Ahmad, Yemlembam Hemjit Singh, Marcos J. Araúzo-Bravo, and Akinori Sarai). 8 Consensus Approaches to Protein Structure Prediction (Dongbo Bu, ShuaiCheng Li, Xin Gao, Libo Yu, Jinbo Xu, and Ming Li). 9 Kernel Methods in Protein Structure Prediction (Jayavardhana Gubbi, Alistair Shilton, and Marimuthu Palaniswami). 10 Evolutionary Granular Kernel Trees for Protein Subcellular Location Prediction (Bo Jin and Yan-Qing Zhang). 11 Probabilistic Models for Long-Range Features in Biosequences (Li Liao). 12 Neighborhood Profile Search for Motif Refinement (Chandan K. Reddy, Yao-Chung Weng, and Hsiao-Dong Chiang). 13 Markov/Neural Model for Eukaryotic Promoter Recognition (Jagath C. Rajapakse and Sy Loi Ho). 14 Eukaryotic Promoter Detection Based on Word and Sequence Feature Selection and Combination (Xudong Xie, Shuanhu Wu, and Hong Yan). 15 Feature Characterization and Testing of Bidirectional Promoters in the Human Genome—Significance and Applications in Human Genome Research (Mary Q. Yang, David C. King, and Laura L. Elnitski). 16 Supervised Learning Methods for MicroRNA Studies (Byoung-Tak Zhang and Jin-Wu Nam). 17 Machine Learning for Computational Haplotype Analysis (Phil H. Lee and Hagit Shatkay). 18 Machine Learning Applications in SNP–Disease Association Study (Pritam Chanda, Aidong Zhang, and Murali Ramanathan). 19 Nanopore Cheminformatics-Based Studies of Individual Molecular Interactions (Stephen Winters-Hilt). 20 An Information Fusion Framework for Biomedical Informatics (Srivatsava R. Ganta, Anand Narasimhamurthy, Jyotsna Kasturi, and Raj Acharya). Index.

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Book SynopsisUnderstanding the dopamine transporter can lead to new therapies for neurological disorders This book consolidates current information on the dopamine transporter (DAT) in relationto medicinal chemistry and synthesis, biology and pathology, and pharmacology. Because of DAT''s role in diseases such as Parkinson''s, schizophrenia, attention deficit hyperactivity disorder (ADHD), Tourette syndrome, and drug abuse (in particular, cocaine addiction), DAT research is an exploding field. Tremendous advances have been made toward understanding how it impacts a variety of neurological disease states and disorders. This reference provides a broad overview of current knowledge that is detailed enough to furnish a basic understanding of the biological, chemical, and pharmacological aspects of DAT in one comprehensive reference. With contributions from eminent scientists who are experts in their particular areas, Dopamine Transporters: Chemistry, Biology, and Pharmacology:Trade Review"Much of what will be accomplished in the coming years will require an understanding of the issues and tools presented here. No doubt, those focused on other synaptic transporters will be jealous of this resource and should demand companion volumes." (The Quarterly Review of Biology, March 2010) "The book is well written and the chapters are well illustrated where appropriate. It is a valuable addition to the bookshelf of anyone interested in dopaminergic neurotransmission." (Journal of Medicinal Chemistry, March 2009)Table of ContentsContributors. Preface. Part I: Biochemistry and Molecular Biology. Chapter 1: The Dopamine Transporter: An Anatomical Perspective (Hilary R. Smith, Thomas J. Beveridge, Colleen A. Hanlon, Linda J. Porrino). Chapter 2: Dopamine Transporter, Disease States and Pathology (Deborah C. Mash). Chapter 3: Cloning and Genetic Analysis of Dopamine Transporters (David J. Vandenbergh). Chapter 4: Molecular Structure and Composition of Dopamine Transporters (M. Laura Parnas and Roxanne A. Vaughan). Chapter 5: Electrochemical Characterization of Dopamine Transporters (Evgeny A. Budygin and Sara R. Jones). Part II: Medicinal Chemistry. Chapter 6: Tropane-Based Dopamine Transporter-uptake Inhibitors (Scott P. Runyon and F. Ivy Carroll). Chapter 7: The Benztropines: Atypical Dopamine-Uptake Inhibitors that Provide Clues About Cocaine's Mechanism at the Dopamine Transporter (Amy Hauck Newman and Jonathan L. Katz). Chapter 8. Structure-Activity Relationship of GBR 12909 Ligands (Thomas E. Prisinzano and Kenner C. Rice). Chapter 9: Structure-Activity Relationship Study of Piperidine Derivatives for Dopamine Transporters (Prashant S. Kharkar, Maarten E. A. Reith, and Aloke K. Dutta). Chapter 10: Non-Nitrogen-Containing Dopamine Transporter-Uptake Inhibitors (Peter C. Meltzer). Chapter 11: Dopamine-Releasing Agents (Bruce E. Blough). Part III: Pharmacology. Chapter 12: PET/SPECT Imaging Studies of the Plasma Membrane Dopamine Transporter. (Paul Cumming, Weiguo Ye, Dean F. Wong). Chapter 13: In Vitro Studies of Dopamine Transporter Function and Regulation (Brian R. Hoover, Bruce H. Mandt and Nancy R. Zahniser). Chapter 14: In Vivo Studies of Dopamine Transporter Function (Jane B. Acri). Index.

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Book SynopsisThis book introduces the methodology for collection and identification of herbal materials, extraction and isolation of compounds from herbs, in vitro bioassay, in vivo animal test, toxicology, and clinical trials of herbal research. To fully understand and make the best use of herbal medicines requires the close combination of chemistry, biochemistry, biology, pharmacology, and clinical science. Although there are many books about traditional medicines research, they mostly focus on either chemical or pharmacological study results of certain plants. This book, however, covers the systematic study and analysis of herbal medicines in general including chemical isolation and identification, bioassay and mechanism study, pharmacological experiment, and quality control of the raw plant material and end products.Trade Review"This book is neither a set of herbal monographs nor a cursory discussion of research mixed with rhetoric; instead it offers concrete and insightful discussion of research methodology in traditional herbal medicine. While it does not replace reference books containing complete scientific monographs on specific herbal medicines, it is complementary, providing the research framework required to develop scientifically sound, quality products. For this important role, it is highly recommended." (Doody's, 5 August 2011) Table of ContentsPreface. Contributors. Abbreviations. 1. Introduction to Traditional Herbal Medicines and Their Study (Willow J.H. Liu). 1.1 Definition and Trends of Traditional Herbal Medicines. 1.2 Research and Development of Herbal Medicines. 1.3 Common Mistakes Seen in Research on Traditional Herbal Medicines. 1.4 Research on Traditional Herbs Should Refer to Theories and Clinical Application of Traditional Medicine. 1.5 Brief Introduction of Different Systems of Traditional Medicine. 1.6 Regulation of Herbal Medicines and Their Products. 1.7 Achievements and Challenges of Research on Chinese Herbal Medicines. References. 2. Collection and Identification of Raw Herbal Materials (Ping Li, Ling Yi, and Hui-Juan Liu). 2.1 Collection of Herbal Materials. 2.2 Methods for Species Identification of Herbal Materials. References. 3. Extraction and Isolation of Compounds from Herbal Medicines (Hong-Wei Liu). 3.1 Compounds in Plants and Their Structures and Properties. 3.2 Methods for Extraction of Herbal Medicines. 3.3 Methods for Isolation of Compounds from Herbal Extracts. 3.4 An Example of Extraction and Compound Isolation from Herbal Medicine. References. 4. Identification and Structure Elucidation of Compounds from Herbal Medicines (Xin-miao Liang, Yu Jin, Jia-tao Feng, and Yan-xiong Ke). 4.1 Structural Characteristics and Chemical Identification of Compounds in Herbal Medicines. 4.2 Brief Introduction of UV, IR, NMR, MS, and other Spectra. 4.3 Identification of Compounds by HPLC and TLC. 4.4 Identification of Compounds By Spectra. 4.5 Structure Elucidation of Unknown Compounds by Hyphenated Technique. References. 5. Bioassays for Screening and Functional Elucidation of Herbal Medicines (Willow J.H. Liu). 5.1 History of Screening Compounds from Natural Products for Drug Development. 5.2 Brief Introduction of Enzymes, Receptors, Cells, and Gene Expression. 5.3 Selection of Bioassay. 5.4 Evaluation of Bioassay Results of Herbal Samples. 5.5 Enzyme Binding Assay. 5.6 Receptor Binding Assay. 5.7 Gene Expression Assays. 5.8 New Technologies and other Bioassays for Screening and Mechanism Study. 5.9 Keys to Functional Mechanism Study of Herbal Medicines. 5.10 Example 1. Screening and Evaluation of Estrogenic Activity of Herbal Medicines. 5.11 Example 2. Functional Elucidation of Black Cohosh for Menopause Symptoms. References. 6. Functional Evaluation of Herbal Medicines by Animal Experiments (Chun-fu Wu, Fang Wang, and Chun-li Li). 6.1 Purposes and Significance of Pharmacological Research for Herbal Medicines. 6.2 Characteristics of Pharmacological Research of Herbal Medicines. 6.3 Design of Pharmacological Study on Herbal Medicines. 6.4 Examples of In Vivo Experiments for Herbal Extracts. References. 7. Safety Pharmacology and Toxicity Study of Herbal Medicines (Jing-yu Yang and Li-hui Wang). 7.1 Safety Pharmacology. 7.2 Acute Toxicity Study. 7.3 Chronic Toxicity Study. 7.4 Special Toxicity Study. 7.5 Examples of In Vivo Toxicological Experiments for Compounds or Extracts from Herbal Medicines. References. 8. Clinical Study of Traditional Herbal Medicine (Hong Yuan, Guo-ping Yang, and Zhi-jun Huang). 8.1 Introduction to Clinical Trials and Challenge of Clinical Trials on Herbal Medicines. 8.2 Essential Elements and Principles of Clinical Trial Design. 8.3 Design of Clinical Trials. 8.4 Examples of Clinical Trials. References. 9. Standardization and Quality Control of Herbal Extracts and Products (Jian-guo Zeng, Man-liang Tan, Xuan Peng, and Qi Luo). 9.1 Introduction of QA, QC, and GMP. 9.2 Standardizations and SOP of Herbal Extracts. 9.3 Equipment for Quality Control of Herbal Extracts and Products. 9.4 Qualitative Analysis of Herbal Extracts and Products. 9.5 Quantitative Analysis of Herbal Extracts and Products. References. 10. Understanding Traditional Chinese Medicine and Chinese Herbs (Willow J.H. Liu). 10.1 Understanding TCM Theories with Modern Medical Terminology. 10.2 Chemicals are Fundamental Substances Refl ecting Functions of Chinese Herbs. 10.3 Brief Introduction to the Properties of Chinese Herbs. 10.4 Modern Pharmacology of Chinese Herbal Medicine. 10.5 Chinese Herbal Formulas. References. Index.

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Book SynopsisThis comprehensive reference presents cutting-edge and long-ranging research in computational systems biology. It is written by leading experts and covers a range of topics from modeling and learning biological systems to the impact of computational systems biology on drug design and medicine.Trade Review“The book should serve well as a resource for anyone interested in learning about computational systems biology.” (The Quarterly Review of Biology, 1 March 2012) Table of ContentsPreface. Contributors. PART I: OVERVIEW. 1 Advances in Computational Systems Biology (Huma M. Lodhi). PART II: BIOLOGICAL NETWORK MODELING. 2 Models in Systems Biology: The Parameter Problem and the Meanings of Robustness (Jeremy Gunawardena). 3 In Silico Analysis of Combined Therapeutics Strategy for Hearth Failure (Sung-Young Shin, Tae-Hwan Kim, Kwang-Hyun Cho, and Sang-Mok Choo). 4 Rule-Based Modeling and Model Refinement (Elaine Murphy, Vincent Danos, Jerome Feret, Jean Krivine, and Russell Harmer). 5 A (Natural) Computing Perspective on Cellular Processes (Mateo Cavaliere and Tommaso Mazza). 6 Simulating Filament Dynamics in Cellular Systems (Wilbur E. Channels and Pablo A. Iglesias). PART III: BIOLOGICAL NETWORK INFERENCE. 7 Reconstruction of Biological Networks by Supervised Machine Learning Approaches (Jean-Philippe Vert). 8 Supervised Inference of Metabolic Networks from the Integration of Genomic Data and Chemical Information (Yoshihiro Yamanishi). 9 Integrating Abduction and Induction in Biological Inference Using CF-Induciton (Yoshitaka Yamamoto, Katsumi Inoue, and Andrei Doncescu). 10 Analysis and Control of Deterministic and Probabilistic Boolean Networks (Tatsuya Akutsu and Wai-Ki Ching). 11 Probabilistic Methods and Rate Heterogeneity (Tal Pupko and Itay Mayrose). PART IV: GENOMICS AND COMPUTATIONAL SYSTEMS BIOLOGY. 12 From DNA Motifs to Gene Networks: A Review of Physical Interaction Models (Panayiotis V. Benos and Alain B. Tchagang). 13 The Impact of Whole Genome In Silico Screening for Nuclear Receptor-Binding Sites in Systems Biology (Carsten Carlberg and Merja Heinaniemi). 14 Environmental and Physiological Insights from Microbial Genome Sequences (Alessandra Carbone and Anthony Mathelier). PART V: SOFTWARE TOOLS FOR SYSTEMS BIOLOGY. 15 Ali Baba: A Text Mining Tool for Systems Biology (Jorg Hakenberg, Conrad Plake, and Ulf Leser). 16 Validation Issues in Regulatory Module Discovery (Alok Mishra and Duncan Gillies). 17 Computational Imaging and Modeling for Systems Biology (Ling-Yun Wu, Xiaobo Zhou, and Stephen T.C. Wong). Index. Series Information.

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Book SynopsisThis book comprehensively covers the mechanisms of action and inhibitor design for HIV-1 integrase. It serves as a resource for scientists facing challenging drug design issues and researchers in antiviral drug discovery.Trade Review“This book will be certainly a valuable reference source for all those who are interested in antiviral drug discovery. All of the information contained in this text offers a rich scientific support for researchers in academia and industry at any level who are interested in enhancing their knowledge on a very fascinating scientific topic.” (ChemMedChem, 2012) Table of ContentsChapter 1. HIV life cycle: Targets for anti-HIV agents (Erik De Clercq (Rega Institute)). Chapter 2. PP32 is hot (Duane P. Grandgenett (SLU)). Chapter 3. Integrase mechanism and function (Robert Craigie (NIDDK, NIH)). Chapter 4. Structural studies of retroviral integrases (Mariusz Jaskolski, Jerry N. Alexandratos, Grzegorz Bujacz and Alexander Wlodawer (NIDDK, NCI, NIH)). Chapter 5. Retroviral integration target site selection (Angela Ciuffi and Frederick Bushman (U. Penn)). Chapter 6. The pleiotropic nature of human immunodeficiency virus type 1 integrase mutations (Alan Engelman (Harvard)). Chapter 7. Insights into HIV-1 integrase-DNA interaction (Allison Johnson, Christopse Marchand, and Yves Pommier (NCI, NIH)). Chapter 8. Functional interaction between human immunodeficiency virus type 1 reverse transcriptase and integrase (Thomas Wilkinson and Samson A. Chow (UCLA)). Chapter 9. Cellular cofactors of HIV integration (Wannes Thys, Koen Bartholomeeusen, Zeger Debyser and Jan De Rijck (KULeuven)). Chapter 10. Structural aspects of the lentiviral integrase - LEDGF interaction (Steve Hare, Alan Engelman and Peter Cherepanov (Imperial College London and Harvard)). Chapter 11. Host factors that affect provirus stability and silencing (Richard A. Katz, René Daniel and Anna Marie Skalka (Fox Chase)). Chapter 12. Assays for the evaluation of HIV-1 integrase enzymatic activity, DNA-binding and co-factor interaction (Frauke Christ, Katrien Busschots, Jelle Hendrix, Melissa McNeely, Yves Engelborghs, Zeger Debyser (KU Leuven, Belgium)). Chapter 13. HIV-1 integrase inhibitor design: Overview and historical perspectives (Nouri Neamati (USC)). Chapter 14. HIV integrase inhibitors: from diketoacids to heterocyclic templates: A history of HIV integrase medicinal chemistry at Merck West Point and Merck Rome (IRBM) leading to the discovery of raltegravir (Melissa S. Egbertson, Neville J. Anthony and Vincenzo Summa). Chapter 15. Elvitegravir, a novel quinolone HIV-1 integrase strand transfer inhibitor (Hisashi Shinkai, Motohide Sato, and Yuji Matsuzaki, Central Pharmaceutical Research Institute, JT Inc., Takatsuki, Japan). Chapter 16. Conformationally constrained tricyclic HIV integrase inhibitors (Maria Fardis, Haolun Jin, Xiaowu Chen, Manuel Tsiang, James Chen, Choung Kim, Matthew Wright (Gilead)). Chapter 17. Slow onset kinetics of HIV integrase inhibitors and proposed molecular model (Edward P. Garvey and Benjamin Schwartz). Chapter 18. Azaindole hydroxamic acids are hiv-1 integrase inhibitors (Michael B. Plewe, Ted W. Johnson). Chapter 19. A simple and accurate in vitro method for predicting serum protein binding of hiv integrase strand transfer inhibitors (Ira B. Dicker, Michael A. Walker, Zeyu Lin, Brian Terry, Lori Pajor, Ming Zheng, B. Narasimhulu Naidu, Jacques Banville, Nicholas A. Meanwell and Mark Krystal (BMS)). Chapter 20. Role of metals in HIV-1 integrase inhibitor design (Mario Sechi, Mauro Carcelli, Dominga Rogolino and Nouri Neamati). Chapter 21. Discovery and development of natural product inhibitors of HIV-1 integrase (Sheo B. Singh (Merck)). Chapter 22. Development of styrylquinoline integrase inhibitors (Jean-Francois Mouscadet, Eric Deprez, Didier Desmaele, Jean d'Angelo (CNRS, France)). Chapter 23. Dicaffeoyltartaric acid and dicaffeoylquinic acid HIV integrase inhibitors (David c. Crosby and W. Edward Robinson, Jr. (UCI)). Chapter 24. Design and discovery of peptide-based inhibitors (Ya-Qiu Long and Nouri Neamati (Shanghai & USC)). Chapter 25. Nucleotide-Based Inhibitors of HIV Integrase (Vasu Nair and Guochen Chi (U. Georgia)). Chapter 26. Design of HIV-1 Integrase Inhibitors Using Computer-aided techniques (Erik Serrao, Rambabu Gundla, Jinxia Deng, Srinivas Odde, Nouri Neamati (USC)). Chapter 27. Application of protein covalent modification to studying the structure and function of HIV-1 integrase and its inhibitors (Xue Zhi Zhao and Terrence R. Burke, Jr.). Chapter 28. HIV-1 intergase-DNA models (Chenzhong Liao, Marc C. Nicklaus (NCI)). Chapter 29. A new paradigm for integrase inhibition: blocking enzyme function without directly targeting the active site (Laith Q. Al-Mawsawi and Nouri Neamati). Chapter 30. Resistance to integrase inhibitors (Leen Hombrouck, Zeger Debyser and Myriam Witvrouw (KU Leuven, Belgium)).

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Book Synopsis* Focuses on learning patterns and knowledge from data generated by mobile users and mobile technology. * Covers research and application issues in applying computational intelligence applications to mobile computing * Delivers benefits to a wide range of applications * Introduces the state of the art of computational intelligence to the mobile paradigmTable of ContentsPreface ix Contributors xv Part I Mobile Data and Intelligence 1. A Survey of State-of-the-Art Routing Protocols for Mobile Ad Hoc Networks 3 2. Connected Dominating Set for Topology Control in Ad Hoc Networks 26 3. An Intelligent Way to Reduce Channel Under-utilization in Mobile Ad Hoc Networks 43 4. Mobility in Publish/Subscribe Systems 62 5. Cross-Layer Design Framework for Adaptive Cooperative Caching in Mobile Ad Hoc Networks 87 6. Recent Advances in Mobile Agent-Oriented Applications 106 Part II Location-Based Mobile Information Services 7. KCLS: A Cluster-Based Location Service Protocol and Its Applications in Multihop Mobile Networks 143 8. Predictive Location Tracking in Cellular and in Ad Hoc Wireless Networks 163 9. An Efficient Air Index Scheme for Spatial Data Dissemination in Mobile Computing Environments 191 10. Next Generation Location-based Services: Merging Positioning and Web 2.0 213 Part III Mobile Mining 11. Data Mining for Moving Object Databases 239 12. Mobile Data Mining on Small Devices through Web Services 264 Part IV Mobile Context-Aware and Applications 13. Context Awareness: A Formal Foundation 279 14. Experiences with a Smart Office Project 294 15. An Agent-Based Architecture for Providing Enhanced Communication Services 320 Part V Mobile Intelligence Security 16. MANET Routing Security 345 17. An Online Scheme for Threat Detection within Mobile Ad Hoc Networks 380 18. SMRTI: Secure Mobile Ad Hoc Network Routing with Trust Intrigue 412 19. Managing Privacy in Location-based Access Control Systems 437 Part VI Mobile Multimedia 20. VoiceXML-Enabled Intelligent Mobile Services 471 21. User Adaptive Video Retrieval on Mobile Devices 488 22. A Ubiquitous Fashionable Computer with an i-Throw Device on a Location-based Service Environment 510 23. Energy Efficiency for Mobile Multimedia Replay 530 Part VII Intelligent Network 24. Efficient Data-Centric Storage Mechanisms in Wireless Sensor Networks 549 25. Tracking in Wireless Sensor Networks 573 26. DDoS Attack Modeling and Detection in Wireless Sensor Networks 595 27. Energy-Efficient Pattern Recognition for Wireless Sensor Networks 627 Index 661

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Book SynopsisThis is the first comprehensive systems biology book to focus on its applications in drug discovery and development. It covers all phases of drug discovery and development, discussing their interaction with systems biology. Using real-world examples, the book shows how systems biology can enhance pharmaceutical research.Trade Review“I enjoyed reading this book as it should be essential reading for those involved in drug discovery and development for all others who share an interest in this field.” (International Society for the Study of Xenobiotics, 2012) "In short, this is an indispensable tool for both experienced and early stage investigators and others to understand the current and future impact of systems biology on the drug discovery and development process." (Doody's, 6 January 2012) Table of ContentsPart I: Introduction to Systems Biology Approach. Chapter 1. Introduction to systems biology in drug discovery and development. 1.1 Introduction. Chapter 2. Methods for In Silico Biology: Model Construction and Analysis. 2.1 Introduction. 2.2 Model building. 2.3 Parameter estimation. 2.4. Model analysis. 2.5 Conclusions. Chapter 3. Methods in In Silico Biology: Modeling Feedback Dynamics in Pathways. 3.1 Introduction. 3.2 Statistical modeling. 3.3 Mathematical modeling. 3.4 Feedback and feedforward. 3.5 Conclusions. Chapter 4. Simulation of Population Variability in Pharmacokinetics. 4.1 Introduction. 4.2 PBPK modeling. 4.3 Simulation of pharmacokinetic variability. 4.4 Conclusions and future directions. Part II: Applications to Drug Discovery. Chapter 5. Applications of Systems Biology Approaches to Target Identification and Validation in Drug Discovery. 5.1 Introduction. 5.2 Typical drug discovery paradigm. 5.3 Integrated drug discovery. 5.4 Drivers of the disease phenotype: clinical endpoints and hypotheses. 5.5 Extracellular disease drivers: mechanistic biotherapeutic models. 5.6 Relevant cell models for clinical endpoints. 5.7 Intracellular disease drivers: signaling pathway quantification. 5.8 Target selection: dynamic pathway modeling. 5.9 Conclusions. Chapter 6. Lead Identification and Optimization. 6.1 Introduction. 6.2 The systems biology toolkit. 6.3 Conclusions. Chapter 7. The role of core biological motifs in dose-response modeling: an example with switch-like circuits. 7.1 Introduction: systems perspective in drug discovery. 7.2 Systems biology and toxicology. 7.3 Mechanistic/computational concepts in a molecular/cellular context. 7.4 Response motifs in cell signaling and their role in dose response. 7.5 Discussion and conclusions. Chapter 8. Mechanism Based Pharmacokinetic-Pharmacodynamic Modeling During Discovery and Early Development. 8.1 Introduction. 8.2 Challenges in drug discovery and development: the need to bring together PK and PD. 8.3 Methodological aspects and concepts. 8.4 Application during lead optimization. 8.5 Application during clinical candidate selection. 8.6 Entry into human (EIH) preparation and translational PK/PD modeling. 8.7 PK/PD for toxicology study design and evaluation. 8.8 Justification of starting dose, calculation of safety margins, and support of phase I design. 8.9 Phase I and beyond. 8.10 Support of early formulation development. 8.11 Outlook and conclusions. Part III: Applications to Drug Development. Chapter 9. Developing Oncology Drugs Using Virtual Patients of Vascular Tumor Diseases. 9.1 Introduction. 9.2 Modeling angiogenesis. 9.3 Use of rigorous mathematical analysis for gaining insight on drug development. 9.4 Use of angiogenesis models in theranostics. 9.5 Use of angiogenesis models in drug salvage: the virtual patient technology. 9.6 Summary and conclusions. Chapter 10. Systems Modeling Applied to Candidate Biomarker Identification. 10.1 Introduction. 10.2 Biomarker discovery approaches. 10.3 Examples of systems modeling approaches for identification of candidate biomarkers. 10.4 Conclusions. Chapter 11. Simulating Clinical Trials. 11.1 Introduction. 11.2 Types of models used in clinical trial design. 11.3 Sources of prior information for designing clinical trials. 11.4 Aspects of a trial to be designed and optimized. 11.5 Trial simulation. 11.6 Optimizing designs. 11.7 Real world examples. 11.8 Conclusions. Part IV: Synergies with other technologies. Chapter 12. Pathway Analysis in Drug Discovery. 12.1 Introduction: pathway analysis, dynamic modeling, and network analysis. 12.2 Software systems for pathway analysis. 12.3 Pathway analysis in modern drug development pipeline. 12.4 Conclusions. Chapter 13. Functional mapping for predicting drug response and enabling personalized medicine. 13.1 Introduction. 13.2 Functional mapping. 13.3 Predictive modeling. 13.4 Future directions. Chapter 14. Future Outlook of Systems Biology. 14.1 Introduction. 14.2 Systems complexity in biological systems. 14.3 Models for quantitative integration of data. 14.4 Changing requirements for systems approaches during drug discovery and development. 14.5 Better models for better decisions. 14.6 Advancing personalized medicine. 14.7 Improving clinical trials and enabling more complex treatment approaches. 14.8 Collaboration and training for systems biologists. 14.9 Conclusions.

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Book SynopsisThe concepts, applications, and practical issues of Quality by Design Quality by Design (QbD) is a new framework currently being implemented by the FDA, as well as EU and Japanese regulatory agencies, to ensure better understanding of the process so as to yield a consistent and high-quality pharmaceutical product. QbD breaks from past approaches in assuming that drug quality cannot be tested into products; rather, it must be built into every step of the product creation process. Quality by Design: Perspectives and Case Studies presents the first systematic approach to QbD in the biotech industry. A comprehensive resource, it combines an in-depth explanation of basic concepts with real-life case studies that illustrate the practical aspects of QbD implementation. In this single source, leading authorities from the biotechnology industry and the FDA discuss such topics as: The understanding and development of the product''s critical quality atTable of ContentsForeword xiii Preface xv Preface to the Wiley Series on Biotechnology and Related Topics xvii Contributors xix 1 QUALITY BY DESIGN: AN OVERVIEW OF THE BASIC CONCEPTS 1 Rohin Mhatre and Anurag S. Rathore 1.1 Introduction 1 1.2 Critical Quality Attributes 2 1.3 An Overview of Design Space 3 1.4 Raw Materials and their Impact on QbD 4 1.5 Process Analytical Technology 4 1.6 The Utility of Design Space and QbD 5 1.7 Conclusions 7 2 CONSIDERATIONS FOR BIOTECHNOLOGY PRODUCT QUALITY BY DESIGN 9 Steven Kozlowski and Patrick Swann 2.1 Introduction 9 2.2 Quality by Design 10 2.3 Relevant Product Attributes 11 2.4 Manufacturing Process 14 2.5 Developing a Design Space 18 2.6 Uncertainty and Complexity 22 2.7 Future Horizons 23 2.8 QbD Submission Thoughts 25 2.9 Implementation Plans 26 2.10 Summary 27 3 MOLECULAR DESIGN OF RECOMBINANT MALARIA VACCINES EXPRESSED BY Pichia pastoris 31 David L. Narum 3.1 Introduction 31 3.2 The Malaria Genome and Proteome 34 3.3 Expression of Two Malaria Antigens in P. pastoris 34 3.4 Summary 46 4 USING A RISK ASSESSMENT PROCESS TO DETERMINE CRITICALITY OF PRODUCT QUALITY ATTRIBUTES 53 Mark A Schenerman, Milton J. Axley, Cynthia N. Oliver, Kripa Ram, and Gail F. Wasserman 4.1 Introduction 53 4.2 Examples of Criticality Determination 60 4.3 Conclusion 81 5 CASE STUDY ON DEFINITION OF PROCESS DESIGN SPACE FOR A MICROBIAL FERMENTATION STEP 85 Pim van Hoek, Jean Harms, Xiangyang Wang, and Anurag S. Rathore 5.1 Introduction 85 5.2 Approach Toward Process Characterization 87 5.3 Risk Analysis 88 5.4 Small-Scale Model Development and Qualification 89 5.5 Design of Experiment Studies 94 5.6 Worst Case Studies 96 5.7 Definition of Design Space 99 5.8 Definition of Validation Acceptance Limits 103 5.9 Regulatory Filing, Process Monitoring, and Postapproval Changes 106 6 APPLICATION OF QbD PRINCIPLES TO TANGENTIAL FLOW FILTRATION OPERATIONS 111 Peter K. Watler and John Rozembersky 6.1 Introduction 111 6.2 Applications of TFF in Biotechnology 113 6.3 Tangential Flow Filtration Operating Principles 113 6.4 TFF Design Objectives 115 6.5 Membrane Selection 115 6.6 TFF Operating Parameter Design 118 6.7 TFF Diafiltration Operating Mode Design 122 6.8 Summary 125 7 APPLICATIONS OF DESIGN SPACE FOR BIOPHARMACEUTICAL PURIFICATION PROCESSES 127 Douglas J. Cecchini 7.1 Introduction 127 7.2 Establishing Design Space for Purification Processes during Process Development 128 7.3 Applications of Design Space 131 7.4 Cell Harvest and Product Capture Steps 131 7.5 Protein A Capture Column 136 7.6 Hydrophobic Interaction Chromatography 137 7.7 Anion Exchange Chromatography 138 7.8 Summary 141 8 VIRAL CLEARANCE: A STRATEGY FOR QUALITY BY DESIGN AND THE DESIGN SPACE 143 Gail Sofer and Jeffrey Carter 8.1 Introduction 143 8.2 Current and Future Approaches to Virus Clearance Characterization 143 8.3 Benefits of Applying Design Space Principles to Virus Clearance 144 8.4 Technical Limitations Related to Adoption of QdB/Design Space Concepts in Virus Clearance 145 8.5 Developing a Virus Clearance Design Space 148 8.6 Staying in the Design Space 156 8.7 Conclusion 157 9 APPLICATION OF QUALITY BY DESIGN AND RISK ASSESSMENT PRINCIPLES FOR THE DEVELOPMENT OF FORMULATION DESIGN SPACE 161 Kingman Ng and Natarajan Rajagopalan 9.1 Introduction 161 9.2 Quality by Design (QbD) Approach 162 9.3 Target Product Profile (TPP) 163 9.4 Molecular Degradation Characterization 164 9.5 Active Pharmaceutical Ingredient (API) Critical Properties 166 9.6 Preformulation Characterization 167 9.7 Initial Formulation Risk Assessments 168 9.8 Formulation Optimization and Design Space 169 9.9 Selection of Solution Formulation Composition 171 9.10 Summary 173 10 APPLICATION OF QbD PRINCIPLES TO BIOLOGICS PRODUCT: FORMULATION AND PROCESS DEVELOPMENT 175 Satish K. Singh, Carol F. Kirchhoff, and Amit Banerjee 10.1 Introduction: QbD in Biologics Product Development 175 10.2 Risk Assessment Process 177 10.3 Examples 178 10.4 Conclusions 191 11 QbD FOR RAW MATERIALS 193 Maureen Lanan 11.1 Introduction 193 11.2 Background 194 11.3 Current Practice for Raw Materials 195 11.4 QbD in Development 195 11.5 QbD in manufacturing 196 11.6 QbD for organizations 197 11.7 Tests Available 197 11.8 Conclusions and Future Prospects 207 12 PAT TOOLS FOR BIOLOGICS: CONSIDERATIONS AND CHALLENGES 211 Michael Molony and Cenk Undey 12.1 Introduction 211 12.2 Cell Culture and Fermentation PAT Tools 214 12.3 Purification PAT Tools 223 12.4 Formulation PAT Tools 228 12.5 PAT Tools for Bioprocess Starting Materials, Defined Media, and Complex Raw Materials 230 12.6 Chemometrics and Advanced Process Control Tools 232 12.7 The power of PLS and PCA 233 12.8 "Relevant Time"Column Integrity Monitoring (Moments Analysis versus HETP) 240 12.9 Challenges for Implementation of PAT Tools 244 12.10 Future PAT Tools 247 13 EVOLUTION AND INTEGRATION OF QUALITY BY DESIGN AND PROCESS ANALYTICAL TECHNOLOGY 255 Duncan Low and Joseph Phillips 13.1 Introduction 255 13.2 Evolution of PAT and Quality by Design (QbD): Emerging Guidelines and Standards 256 13.3 Process Analytical Technology (PAT) 261 13.4 Quality by Design 263 13.5 Implementing QbD and PAT 266 13.6 Conclusions 282 Acknowledgments 283 References 283 Index 287

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