Genetics (non-medical) Books

Book SynopsisEpigenetics, the study of heritable changes in gene expression, has been heralded as one of the most promising new fields of scientific inquiry. Current large-scale studies selectively draw on epigenetics to connect behavioral choices made by pregnant people, such as diet and exercise, to health risks for future generations. As the first ethnography of its kind, Weighing the Future examines the sociopolitical implications of ongoing pregnancy trials in the United States and the United Kingdom, illuminating how processes of scientific knowledge production are linked to capitalism, surveillance, and environmental reproduction. Natali Valdez argues that a focus on individual behavior rather than social environments ignores the vital impacts of systemic racism. The environments we imagine to shape our genes, bodies, and future health are intimately tied to race, gender, and structures of inequality. This groundbreaking book makes the case that science, and how we translate it, is a reproductive project that requires feminist vigilance. Instead of fixating on a future at risk, this book brings attention to the present at stake.Trade Review"A ground-breaking book, both subtle and razor-sharp in its analysis. It provides an immensely valuable critique of the workings of epigenetic foreclosure in pregnancy trials." * Medical Anthropology Quarterly *Table of ContentsContents List of Illustrations Acknowledgments Introduction: Weighing the Future Part I 1. Epistemic Environments: Reproducing Solutions to Past, Present, and Future Maternal Health 2. Un/Altered: The Durability of Individualized Interventions for Multidimensional Illness Part II 3. Politics of Recruitment: How Fatness, Race, and Risk Shape Contemporary Pregnancy Trials 4. Pregnant Narratives: Experiencing Lifestyle Interventions Part III 5. Environmental Animations: What Counts as the Maternal Environment? 6. Prospecting Pregnancies: Data, Time, and Speculative Value Conclusion: The Afterbirth of Foreclosure Epilogue: [The Future] Is Composed of Nows Notes References Index

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Book SynopsisEpigenetics, the study of heritable changes in gene expression, has been heralded as one of the most promising new fields of scientific inquiry. Current large-scale studies selectively draw on epigenetics to connect behavioral choices made by pregnant people, such as diet and exercise, to health risks for future generations. As the first ethnography of its kind, Weighing the Future examines the sociopolitical implications of ongoing pregnancy trials in the United States and the United Kingdom, illuminating how processes of scientific knowledge production are linked to capitalism, surveillance, and environmental reproduction. Natali Valdez argues that a focus on individual behavior rather than social environments ignores the vital impacts of systemic racism. The environments we imagine to shape our genes, bodies, and future health are intimately tied to race, gender, and structures of inequality. This groundbreaking book makes the case that science, and how we translate it, is a reproduTrade Review"A ground-breaking book, both subtle and razor-sharp in its analysis. It provides an immensely valuable critique of the workings of epigenetic foreclosure in pregnancy trials." * Medical Anthropology Quarterly *Table of ContentsContents List of Illustrations Acknowledgments Introduction: Weighing the Future Part I 1. Epistemic Environments: Reproducing Solutions to Past, Present, and Future Maternal Health 2. Un/Altered: The Durability of Individualized Interventions for Multidimensional Illness Part II 3. Politics of Recruitment: How Fatness, Race, and Risk Shape Contemporary Pregnancy Trials 4. Pregnant Narratives: Experiencing Lifestyle Interventions Part III 5. Environmental Animations: What Counts as the Maternal Environment? 6. Prospecting Pregnancies: Data, Time, and Speculative Value Conclusion: The Afterbirth of Foreclosure Epilogue: [The Future] Is Composed of Nows Notes References Index

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Book SynopsisThe 11th Hour Series is designed to be used when a textbook doesn''t make sense, when the course content is tough, or when you just want a better grade in the course. The authors cut through the fluff, get to what you need to know, and then help you understand it. Clinical correlations or everyday applications include examples from the real world to help students understand key concepts more readily. Dedicated web page, there 24 hours a day, will give extra help, tips, warnings of trouble spots, extra visuals and more. A quick check on what background students will need to apply helps equip them to conquer a topic. The most important information is highlighted and explained, showing the big picture and eliminating the guesswork. After every topic and every chapter, lots of opportunity for drill is provided in every format, multiple choice, true/false, short answer, essay. An easy trouble spot identifier dTable of Contents11th Hour Guide to Success. Preface. DNA: The Genetic Material. From DNA to RNA: The Process of Transcription. From Messenger RNA to Protein: The Process of Translation. Mutations.. MIDTERM EXAM. Regulation of Gene Expression in Bacteria. Regulation of Gene Expression in Eukaryotes. Recombinant DNA.. FINAL EXAM. Index.

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Book SynopsisIn a book that promises to change the way we think and talk about genes and genetic determinism, Evelyn Fox Keller, one of our most gifted historians and philosophers of science, provides a powerful, profound analysis of the achievements of genetics and molecular biology in the twentieth century, the century of the gene.Trade ReviewSometimes, with great luck, you happen on a book that is wondrous in its ability to take a topic apart and explain it lucidly. Sometimes, the joy is to be found in the way an author is able to put those pieces back together. And sometimes, it is the elegance both of analysis and synthesis that makes a book truly great. The Century of the Gene, by Evelyn Fox Keller, reaches that level and then vaults past it into the category of rare volumes that are unforgettable. This is the sort of book that, once found, can never be relinquished. The breadth of intellect is so strong, the importance of the subject so acute, the language so beautifully wrought, that you find yourself drawn to read it again and again, only to find a new dimension each time… In fact—and this is one of the most intense pleasures of the book—Fox Keller’s explanation of how the thinking about the gene has evolved over the past century is both as simple and as complex as the gene itself. Her topic is also her metaphor. -- Alanna Mitchell * Globe and Mail *[Keller] is at the same time enthusiastic about the light that has been shed on the nature of life and critical of the oversimplifications that she feels have been made… She is well qualified to draw [her conclusions]. She has an admirable grasp of recent research in molecular genetics…and has read widely in the history of genetics… She has also thought hard about both the history and the current state of the subject… We need Keller’s voice. -- John Maynard Smith * New York Review of Books *[Keller writes] with a peculiar, elegant blend of linguistic skill, historical reflection, conceptual analysis and synthetic outlook, and with the generously encompassing gesture of someone who participated in and followed the developments of molecular biology and genetics over several decades… Keller sees her book as a plea for scientific and political realism. Indeed it is. But it is more than just that. It engages historians, philosophers, scientists and the educated lay public alike in a discussion that self-consciously resists the temptation of polemics…about the conceptual and experimental developments in life sciences during the course of the twentieth century. -- Hans-Jorg Rheinberger * American Scientist *[In] a lucid analysis of the mind-boggling advances in genetics and molecular biology in the twentieth century, Keller says it’s time to change the way we think about the gene. * Atlanta Journal-Constitution *The Century of the Gene is unusual among popular histories of science in that it largely avoids both technical minutiae and sociological or historical background. Rather, it is almost exclusively a history of ideas, even a history of just one idea—the concept of the gene. Keller’s aim, one that she achieves admirably, is to give readers just enough information about discoveries in molecular biology so that they can appreciate the consequence of those discoveries for our understanding of what genes are. -- Austin L. Hughes * Commonweal *The very word ‘gene’ symbolizes our self-obsessed culture. All we do, know, learn, and sacrifice is somehow explained away by appealing to this tiny and elusive biological structure. Yet according to at least one scientist, it’s time for us to shift our focus and branch out to other possible, and perhaps more suitable, interpretations of our natures. In The Century of the Gene, Evelyn Fox Keller urges the genomic society to break free of the linguistic (and therefore conceptual) restraints and the historical baggage inherent in the use of the term ‘gene’—a break she sees as imperative and, ultimately, inevitable. * Rain Taxi *The Century of the Gene, by Evelyn Fox Keller, not only provides an insightful overview of the role of a gene in the creation of an organism but also traces the history of our perception of the gene’s role in that creation… Keller provides several concise figures that allow a person with minimal knowledge of molecular biology to understand the basics of what a gene is and how it functions within the body. This book also captures past and present thought from critical scientists and philosophers who have contributed to our current understanding of molecular biology… [The] overall outlook provides a new understanding of the dynamics of gene regulation and predicts that a new era in which we can understand how to control our own evolution is approaching. From a research perspective, we hope to be able to use this knowledge to help correct medical disorders. However, from a moral and religious perspective, many new boundaries are being crossed. Read this book. You will challenge yourself in trying to figure out what the future will be. -- Dr. John J. Nemunaitis * Baylor University Medical Center Proceedings *Evelyn Fox Keller’s The Century of the Gene is a clear, concise and challenging contribution to our understanding of the history of genetics and of modern biology more generally. There can be no doubt that Keller’s analysis of ‘gene talk,’ that is, her analysis of the variety of contexts and ways in which biologists have deployed the word ‘gene’, is more than timely. -- Paolo Palladino * British Journal for the History of Science *The notes…are detailed and useful… Her book is a thought-provoking review of the history and philosophy of genetics and genomics. -- Victor A. McKusick * Bulletin of the History of Medicine *Among the many books on cloning and genetic therapy, The Century of the Gene, an overview of current research and thought by philosopher of science Evelyn Fox Keller, seems especially promising. -- Martin Levin * Globe and Mail *Although brief, this book is packed with good things. The historical analysis is unfailingly interesting, the scientific reportage lucid. Best of all, perhaps, is the sheer excitement the book communicates about the state of genetics and the need to get that state into proper focus, using all the intellectual resources going… I am impressed by the diversity of gene concepts within what Keller sees…as a single concept… Her own contribution to the case for conceptual unity is an important one. -- Gregory Radick * Heredity *[This] book opens up exciting possibilities of new ways of thinking about biological organization, which are not overshadowed by traditional language or by ‘historical baggage’… Evelyn Fox Keller has put down a marker in this important book. The time has come for us to take on a richer understanding of genetics and with it some new language and concepts. -- Sue Weldon * New Genetics and Society *Once again, with the prescience her readers have come to expect from her, Evelyn Fox Keller is ahead of the curve in identifying and illuminating new questions for our attention… [Keller] addresses myths and misunderstandings that surround the concept of a gene… [Her] informed and entertaining volume takes the reader on a quick historical tour through the gestation and birth of molecular genetics and then, with a few helpful illustrations, into current perceptions of gene structure and function in sufficient detail to explain her critical arguments… Her fascinating tale should raise your interest in the biological mysteries that remain. -- Cecily Cannan Selby * Radcliffe Quarterly *For anyone fascinated by biology, the technology used to explore it, and the medical promises implicit in the information contained within our genetic material, Keller’s overview makes for clear, engaging, and exciting reading. -- Tom Bowden * Tech Directions *Keller traces the evolution of genetic science over the course of the twentieth century, during which Gregor Mendel’s theories of inheritance were rediscovered, the structure of DNA revealed, and the human genome mapped—world-changing achievements that have taken our understanding of genetics far beyond the level at which the now too-simple word gene was coined. -- Donna Seaman * Booklist *Top-drawer science reading. -- Ray Olson * Booklist *In this tight, clearly written survey, Keller does a wonderful job of explaining and demonstrating how our knowledge of genetics has accumulated… In her articulate and insightful…history of genetics and molecular biology, she suggests that most of our common assumptions about genes are either too simplistic or simply incorrect. * Publishers Weekly *In The Century of the Gene, Evelyn Keller gathers together her considerable skills as a mathematician, physicist, historian and philosopher and applies them to the central problem of the last 100 years of biology, namely the relation of the genes to the building of an organism. The scholarship is masterly, not only because of her wide reading of the literature, but her deep, penetrating understanding of what she reads. To cap it all she writes clearly and elegantly so that the book is a pleasure to read. This is a conspicuously intelligent book. -- John Bonner, Princeton UniversityEvelyn Keller has the disturbing ability to make you think again from scratch about things you thought you had already understood. It is a long time since I have thought so hard about fundamental problems in genetics as I did when reading The Century of the Gene. -- Richard Lewontin, Harvard UniversityGenes have captured the scientific and popular imagination. But in The Century of the Gene, Evelyn Fox Keller provides us with a powerful analysis of the limits of the gene as an explanatory concept. Indeed, the success of molecular biology and greater understanding of biological development have exposed the wide gap between genetic information and biological meaning, undermining the very concept of the gene. Yet gene talk with all its historical baggage persists in shaping both science and popular perceptions. Keller argues convincingly for a new language, for new concepts that will enable us to deal with the real complexity of biological organization. This is a critically important book to be very widely read. -- Dorothy Nelkin, New York UniversityIn this elegantly written book, Evelyn Fox Keller tells the fascinating story of how the heuristic power of genetic experimentation interacts with the narrative power of the word ‘gene.’ Both are built on and reinforce each other. I never saw an equally convincing and well informed narrative on how language mediates the interaction between experimental research and its social context. -- Günter P. Wagner, Yale UniversityTable of Contents* Introduction: The Life of a Powerful Word *1. Motors of Stasis and Change: The Regulation of Genetic Stability *2. The Meaning of Gene Function: What Does a Gene Do? *3. The Concept of a Genetic Program: How to Make an Organism *4. Limits of Genetic Analysis: What Keeps Development on Track? * Conclusion: What Are Genes For? * Notes * References * Acknowledgments * Index

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Book SynopsisRepresents an original look at the biotechnology research in the wake of the mapping of the human genome. Presenting a series of interviews with various key players in Celera Diagnostics, this title opens a window on the complexity of corporate scientific innovation.Trade Review"The strength of Rabinow's approach is that we hear the voices of scientists at work. Not only do they describe the science itself, but they also provide their perception of its importance. Rabinow is a skillful interviewer who elicits motivation from his subjects. We are given a rare glimpse into the professional lives of the participants and the energy that drives their scientific and personal decisions."--William A. Haseltine, Science "Paul Rabinow is the leading anthropologist of contemporary biotechnology... It would be easy for him to use his authority to apportion praise and blame, or to develop a magisterial contribution to anthropological theory. But [he] resists coming to artificially neat conclusions... This book's compelling insights should be required reading for everyone who pictures themselves a scientific entrepreneur, or who cares about the state of contemporary science."--Christine Hine, New Scientist "A Machine to Make a Future by Paul Rabinow and Talia Dan-Cohen, a book as impressive as the previous two works in Rainbow's biotechnology trilogy ... Is an in-depth and well-constructed anthropological chronicle of this new Californian scientific enterprise. With his student Talia Dan-Cohen, Rabinow has provided a highly readable account of Celera Diagnostics' formative period ... through a series of lengthy but insightful interviews with the original researchers."--Xuefeng Bruce Ling, The Journal of Clinical Investigation "This book is a good choice for even a layperson to get a grip on the current developments in the world of genomics and how these diagnostics can help health and health care."--Rukmini Rajagopalan, Current Science "This book may signal an entirely new way of viewing scientific innovation in a globalized, competitive environment, integrating new technologies and methodological insights."--Biology Digest "[Paul Rabinow's] interviews are expertly conducted and provide a rich resource that can be mined from a variety of perspectives--including scientific, business, legal, ethical, and philosophical."--George Jannas, Quarterly Review of BiologyTable of ContentsOverture: A MACHINE TO MAKE A FUTURE 1 Chapter One: ENDING AND BEGINNING 13 Chapter Two: THE STATE OF THINGS AT CELERA DIAGNOSTICS, EXPLAINED TO INVESTORS AND TO ANTHROPOLOGISTS 38 Chapter Three: THE MACHINERY AND ITS STEWARDS 62 Chapter Four: ETHICAL AND SOCIAL CONSULTANCY 97 Chapter Five: CONFIDENCE AND TRUST 111 Chapter Six: MODELS ORIENT, TECHNOLOGIES PERFORM, SAMPLES SPEAK (OR VICE VERSA) 144 Chapter Seven: SUMMER 2003 169 Illustrations 187 Appendix: A CORPORATE HISTORY 189 Notes 191 Glossary 195

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Book SynopsisJohn Tyler Bonner, one of our most distinguished and insightful biologists, here challenges a central tenet of evolutionary biology. In this concise, elegantly written book, he makes the bold and provocative claim that some biological diversity may be explained by something other than natural selection. With his customary wit and accessible style,Trade Review"[I]ncredibly useful ... refreshingly honest ... witty and engaging."--Tiffany Taylor, Times Higher Education "[F]orthright, informal, and humorous. His reminder that not every trait has a biologically adaptive function is a welcome lesson, as is his self-deprecating description of his ideas as just another 'just-so' story... [A] call to the biologists who take over from him to do more research to confirm or to refute the often surprising ideas here."--Rob Hardy, Commercial Dispatch "[Bonner] provides a well-written, well-documented collection of evidence suggesting randomness as a primary engine behind natural selection... This is an excellent essay, valuable to a wide audience. Evolution is an important, timely topic, making Bonner's work a worthy contribution."--Choice "[T]he book provides a careful analysis of the relationship between randomness and size in evolution and makes a good case for neutral morphologies."--James Bradley, Quarterly Review of Biology "The main strength of this provocative book is that it undoubtedly provides a successful argument against the widespread tendency to give an adaptive explanation for any biological trait, and, above all, it opens the door to a fruitful way to reconsider the traditional view of evolution as mainly driven by natural selection."--Francesca Merlin, Biol TheoryTable of ContentsIllustrations vii Preface ix 1 Life and the Riddle of Randomness 1 2 Time, Size, and Complexity 17 3 Small Organisms and Neutral Morphologies 40 4 The Evolution of the Decrease of Randomness 63 5 An Exception: Where Small Organisms Suppress Randomness 93 6 The Division of Labor: Two Cases of the Return of Randomness in Higher Forms 101 7 Envoi 118 Acknowledgments 121 Bibliography 125 Index 131

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Book SynopsisTrade Review"Co-Winner of the 2018 Best Book Award, Evolution, Biology, and Society Section, American Sociological Association""Winner of the 2018 Otis Dudley Duncan Award, Section on Population of the American Sociological Association"

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Book SynopsisThis third, fully revised edition, brings the reader up to date with recent advances made in the study of disease at the molecular and cellular level, and examines the new possibilities for treatment. Subjects covered include methods used in molecular medicine and the polymerase chain reaction.Table of ContentsMolecular and cell biology in clinical medicine; methods in molecular medicine; the polymerase chain reaction - a tool for molecular medicine; an introduction to cells; stem cells in normal growth and disease; cell reproduction; apoptosis (programmed cell death); cell to cell and cell to matrix adhesion; how do receptors at the cell surface transmit signals to the cell interior?; membrane traffic, from cell to clinic; cytoskeleton and disease; the cell nucleus' gene regulation and transcription factors; genes and cancer; human congenital malformations - insights from molecular genetics; molecular genetics of common diseases; impact of molecular biology on clinical genetics; monoclonal antibodies in medicine; production and use of therapeutic agents; gene therapy.

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Book SynopsisEdited by leaders in the field, written by experts from around the globe, and brimming with full-color illustrations, Genomic Medicine is an indispensable guide to the full potential of the DNA-based transformation of medicine.Trade ReviewAn indispensable guide to the full potential of the DNA-based transformation of medicine. Human Reproduction and Genetic Ethics The editors have assembled a fine set of short, readable and highly authoritative articles by eminent authors. The book is beautifully produced and will give an accessible entry into genetic medicine to its target audience of non-specialist clinicians. Readers of this journal will need no persuading of the fascination and ever growing importance of genetic medicine and these themes are well communicated. -- Andrew P. Read Human Genetics 2004Table of ContentsForewordPrefaceList of Contributors GlossaryChapter 1. Getting Ready for Gene-Based MedicineChapter 2. Genomic Medicine – A PrimerChapter 3. Genetic TestingChapter 4. Population Screening in the Age of Genomic Medicine Chapter 5. Inheritance and Drug Response Chapter 6. Pharmacogenomics – Drug Disposition, Drug Targets, and Side EffectsChapter 7. Pharmacogenetics in the Laboratory and the Clinic Chapter 8. Hereditary Colorectal CancerChapter 9. Alzheimer's Disease and Parkinson's DiseaseChapter 10. Molecular Diagnosis of the Hematologic CancersChapter 11. Breast and Ovarian CancerChapter 12. Cardiovascular DiseaseChapter 13. Ethical, Legal, and Social Implications of Genomic MedicineChapter 14. Genomics as a Probe for Disease Biology Chapter 15. Welcome to the Genomic EraIndex

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Book SynopsisTrade Review"An impressive, timely, and critically important book and the first scholarly work to take stock of what the genomics turn means for the social sciences. With uncommon interpretive clarity and dazzling interdisciplinary range, Bliss takes us behind the scenes of the emergent field of sociogenomics. Social by Nature forcefully reveals how genetic social science may share a genealogy with earlier eugenics research—even if unwittingly—and urgently points us to the dangers that may arise from this twenty-first century attempt to link deeply-complex social concerns to narrow genetic causes." -- Alondra Nelson * Columbia University *"Catherine Bliss's Social by Nature is critical to understanding the social dangers of over-interpreting genomic data." -- J. Craig Venter, Founder, Chairman, and CEO * J. Craig Venter Institute *"Social by Nature is an insightful, in-depth investigation of the scientific, ethical and political stakes in the emerging field of social genomics. As social scientists and policymakers are urged to jump on the sociogenomics band wagon, Catherine Bliss sounds an urgently needed note of caution and call for more meaningful public engagement." -- Dorothy Roberts * Author, Fatal Invention: How Science, Politics, and Big Business Re-create Race in the Twenty-first Century. *"[Social by Nature] is a brilliant book—dense at times, but insightful and filled with illustrative anecdotes and case studies. It's one you should read if you care about what drives academic research, scientific racism or genetic futurism." -- Nathaniel Comfort * Nature *Table of ContentsContents and Abstracts1Genes and Their Environments chapter abstractChapter 1 provides a social history of the "nature-nurture" divide. Starting with protobiological notions at work in early modern thought and moving forward to modern and late modern biology, this chapter reveals the roots of today's gene-environment emphasis. Situating social genomics amid long-standing sciences such as sociobiology and behavior genetics, and more recent fields such as evolutionary psychology and neuropolitics, it examines the features specific to today's sociogenomic paradigm. 2Science without Borders chapter abstractChapter 2 takes us into the world of social genomics, exposing the who, what, when, and where of the emerging science. It shows that social genomics is not a loose network of independent scientists who are working to benefit the greater good of the sciences more broadly and who have been stochastically drawn into genetic research as a result of shared concepts, methods, and expertise. Rather, it is a fast-evolving field with a great deal of unexamined influence due to its irreverence for discipline. 3Toward the "Deeper Descriptions" chapter abstractChapter 3 shines a light on social genomics' foundational theory and methodology, including novel approaches like the multicohort GWAS and multivariate risk analysis, to show the ways the science innovates genetic explanantia and evolutionary theory. Scientists are currently training their attention on broader natural science debates, even in their attempts to usher in their methodology in the social sciences and to interpret the relevance of their findings for policy. Their focus is less on tackling deep social science conundrums or participating in policy analysis, and more on aligning with health and medical science. 4Determining Difference chapter abstractChapter 4 reveals how sociogenomics is remaking societal notions of human difference in terms of the media as well as basic science characterizations of race, gender, and sexuality. This chapter builds on prior analyses of genome science to evince the ways that new avenues in sociogenomics privilege and perpetuate a genetically deterministic lens for human difference. It shows that troubling, biologically reductive definitions of race, gender, and sexuality thrive in a sociogenomic world. 5The Breakthrough chapter abstractChapter 5 uncovers the central "positions and dispositions" of social genomics, including how participating scientists see their mandate vis-à-vis science writ large. It shows the ways researchers have formed a flexible matrix of specialized knowledge in an attempt to produce credible research innovations and conclusions about the genomics of behavior that can have an impact on bioscience and the wider public. As scientists have invested in the notion of moving theory and methods forward for all sciences, they have formed a confrontational style of practice that is characterized by a unique brand of pioneerism and optimism. 6A Bigger, Better Science chapter abstractChapter 6 examines the impact social genomics is having on the wider world of science. It shows how the field is being received and interpreted by its vast array of collaborator fields, and prioritized by the major funding agencies of our time. This chapter similarly discusses key successes and challenges the field faces going forward, pertaining to funding, governmental support, and scientific publication. 7Applied Science chapter abstractChapter 7 explores the uptake of sociogenomic applications by experts working in the public domain. Whereas use of genomic applications has largely been reserved for biomedical settings, sociogenomic applications have enjoyed adoption in criminal justice, education, and other legal arenas. This chapter presents the salience of sociogenomics for these domains, including how experts in the wider public understand and utilize it, and how the organizations, institutions, and fields they work in perceive its value. The chapter further uncovers key policy issues that scientists see as relevant in sociogenomics' expansion to new public arenas. 8The Business of Sociogenomics chapter abstractChapter 8 presents the array of technologies and therapeutics that have arisen in the commercial domain of genes and behavior. From inborn talent tests to genomic matchmaking, a cottage industry in sociogenomic science has arisen to serve the rising Genome Generation. While only some of these tests have been a direct result of sociogenomic efforts, their usage contributes to the popularization of the sociogenomic paradigm in the mass public. This chapter details the ways the bullish strength of broader markets in personal genomic technology is spurring on sociogenomics as a valuable set of personal predictive indicators. Conclusion chapter abstractThe Conclusion draws together analyses from the preceding chapters to consider the meaning of the sociogenomic paradigm in society. Not only is sociogenomics a scientific orientation, a governmental framework, and a tool in the expert's toolkit; it is a popular lens for deciphering the individual, and a game-changer in public notions of human difference. The analysis ends by signaling meaningful ways that we can critically engage with sociogenomics so that socially responsible frameworks may take hold.

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Book SynopsisThe complete mapping of the horse genome sequence makes a significant contribution to understanding equine biology. This book provides a timely comprehensive overview of equine genomic research.Trade Review“Equine Genomicsis an excellent text that compiles historical accomplishments in equine genetics and molecular biology, describes state-of-theart approaches to understanding the equine genome, and provides glimpses of where the field may go in the future . . . It is our responsibility to try to keep up, and I believe this book will help us do that.” (Journal of the American Veterinary Medical Association, 15 June 2014)Table of ContentsContributors ix Preface xi Chapter 1 Defining the equine genome: The nuclear genome and the mitochondrial genome 1Bhanu P. Chowdhary Chapter 2 Genetic linkage maps 11June Swinburne and Gabriella Lindgren Chapter 3 Physical and comparative maps 49Terje Raudsepp and Bhanu P. Chowdhary Chapter 4 The Y-chromosome 73Terje Raudsepp, Nandina Paria, and Bhanu P. Chowdhary Chapter 5 Unexpected structural features of the equine major histocompatibility complex 93Loren C. Skow and Candice L. Brinkmeyer-Langford Chapter 6 Assembly and analysis of the equine genome sequence 103Claire M. Wade Chapter 7 Genomic tools and resources: Development and applications of an equine SNP genotyping array 113Molly McCue and Jim Mickelson Chapter 8 Functional genomics 125Stephen J. Coleman, Michael J. Mienaltowski, and James N. MacLeod Chapter 9 Coat color genomics 143Samantha A. Brooks and Rebecca R. Bellone Chapter 10 Genomics of skin disorders 155Amy E. Young, Stephen D. White, and Danika L. Bannasvch Chapter 11 Genomics of muscle disorders 171James R. Mickelson, Stephanie J. Valberg, Carrie J. Finno, and Molly E. McCue Chapter 12 Genomics of skeletal disorders 187Ottmar Distl Chapter 13 Genomics of reproduction and fertility 199Terje Raudsepp, Pranab J. Das and Bhanu P. Chowdhary Chapter 14 Genetics of equine neurologic disease 217Carrie J. Finno and Monica Aleman Chapter 15 Molecular genetic testing and karyotyping in the horse 241M. C. T. Penedo and Terje Raudsepp Chapter 16 Genomics of laminitis 255Jim K. Belknap Chapter 17 Genomics of performance 265Emmeline W. Hill, Lisa M. Katz, and David E. MacHugh Chapter 18 Genomics of the circadian clock 285Barbara A. Murphy Chapter 19 Mitochondrial genome: Clues about the evolution of extant equids and genomic diversity of horse breeds 311Cynthia C. Steiner, Kateryna D. Makova, and Oliver A. Ryder Index 323

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Book SynopsisThoroughly covers genetic and genomics research in weedy and invasive plants Identifies future areas of research necessary to managing weedy and invasive species Applies advances in genomics to these specific plants Written by an international team of experts in the field.Table of ContentsContributors xi Preface xv Chapter 1 Why Should Weed Scientists Care About Genomics? 3WILLIAM K. VENCILL Genomics To A Weed Scientist 3 Resistance 4 Better Use Of Existing Herbicides 8 Chapter 2 An Introduction To Molecular Genetic And Genomic Techniques 11CHHANDAK BASU AND SAM R. ZWENGER Weeds As A Source Of Genes For Crop Improvement 11 Tools And Approaches For Understanding Weediness At The Molecular Level 12 Chapter 3 Arabidopsis Is Not A Weed, And Mostly Not A Good Model For Weed Genomics; There Is No Good Model For Weed Genomics 25JONATHAN GRESSEL Introduction: Arabidopsis And Weediness 25 Questions About Weeds—Can Arabidopsis Genomics Answer Them? 27 The Misdirected Approach In Using Arabidopsis To Elucidate New Herbicide Targets 28 Arabidopsis Genomics Can Help In Dealing With Transgene Flow—In A Limited Manner 29 Lessons To Be Learned 30 Chapter 4 Model Weeds For Genomics Research 33WUN S. CHAO AND DAVID P. HORVATH What Makes A Good Model Species? 34 Leveraging From Other Models 36 Genomics Tools For Weeds That Are Under Development 44 Chapter 5 21st-Century Weed Science: A Call For Amaranthus Genomics 53PATRICK J. TRANEL AND FEDERICO TRUCCO The Amaranthus Genus 53 Hybridization And Adaptive Evolution 61 Herbicide Resistance 64 Currently Available Genomic Resources 71 Needs And Opportunities 75 Chapter 6 Evolutionary Genomics Of Weedy Rice 83BRIANA L. GROSS AND KENNETH M. OLSEN Phenotypic Diversity Of Weedy Rice 84 Genomic Diversity Of Weedy Rice 85 The Origin(s) And Evolution Of Weedy Rice 89 The Genetic Basis Of Weediness And Use Of Weedy Rice In Crop Breeding 94 Chapter 7 Rhizomatousness: Genes Important For A Weediness Syndrome 99ANDREW H. PATERSON Developmental Context 100 An Exemplary Case: Johnsongrass 101 Dissecting The Genetic Control Of Rhizomatousness 103 Early Insights Into The Sorghum Rhizo-Transcriptome 105 Future Work And Potential Applications 107 Synthesis 109 Chapter 8 Leafy Spurge: An Emerging Model To Study Traits Of Perennial Weeds 113DAVID P. HORVATH AND JAMES V. ANDERSON Regulation Of Shoot Development And Growth 113 Regulation Of Bud Dormancy 116 Case Study: Leafy Spurge 117 Future Work 122 Chapter 9 Herbicide Resistance: Target Site Mutations 127CHRISTOPHER PRESTON Resistance To Photosystem II-Inhibiting Herbicides 128 Resistance To Acetohydroxyacid Synthase-Inhibiting Herbicides 131 Resistance To Acetyl Coenzyme A Carboxylase-Inhibiting Herbicides 136 Resistance To Glyphosate 138 Resistance To Microtubule Assembly Inhibitors 140 Resistance To Phytoene Desaturase Inhibitors 141 Chapter 10 Molecular and Genomic Mechanisms Of Non-Target-Site Herbicide Resistance 149JUN HU, PATRICK J. TRANEL, C. NEAL STEWART JR., AND JOSHUA S. YUAN Herbicide Application And Resistance 149 Herbicide Classification And Resistance 150 Non-Target Herbicide Resistance 150 Signal Transduction 150 Detoxification and Modification 151 Chapter 11 A Herbicide Defense Trait That Is Distinct From Resistance: The Evolutionary Ecology And Genomics Of Herbicide Tolerance 163REGINA S. BAUCOM Resistance Versus Tolerance In Weed Science 163 Tolerance In Evolutionary Ecology 166 Tolerance Traits And The Genomics Of Tolerance 171 Why Again Should We Focus On Tolerance, Tolerance Traits, And The Genomics Of Tolerance? 172 Chapter 12 The Genomics of Plant Invasion: A Case Study In Spotted Knapweed 177AMANDA K. BROZ AND JORGE M. VIVANCO Why Study Invasive Plant Genomics? 177 Spotted Knapweed Life History 178 Allelopathy And The Novel Weapons Hypothesis 180 Genomics Resources And Approaches For Studying Spotted Knapweed 185 Chapter 13 Molecular Ecology Of Plant Competition 197DOMINIK D. SCHMIDT, MERIJN R. KANT, AND IAN T. BALDWIN Competition Signals And Their Perception By Plants 198 Molecular Basis Of Competitively Important Traits 207 Transcriptomic Insights Into Competitive Interactions Of Weedy Plants 211 Chapter 14 Genomics And Weeds: A Synthesis 221STEPHEN O. DUKE, SCOTT R. BAERSON, AND JONATHAN GRESSEL From Fundamental Information To Practical Solutions 222 Where Do We Go From Here? 241 Index 249

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Book SynopsisExplores the debate on the biological significance and cultural meaning of genes in the development of organisms - the molecular paradigmTrade Review“The rich scientific knowledge about the genetic basis of life and it complex involvement in the life of individuals and populations is highly relevant to our worldview. Genes in Development helps to bring understandings of the conceptual and philosophical implications of molecular genetics up to date.”—Werner Arber, Nobel Laureate in Medicine and Emeritus Professor of Molecular Microbiology, University of Basel“Together the essays in Genes in Development give lively voice to many of the current alternatives to genetic reductionism. Well-known figures from the debates of the past two decades are represented alongside a good number of emerging scholars.”—Hans-Jörg Rheinberger, Max Planck Institute for the History of Science, BerlinTable of ContentsIntroduction / Eva M. Neumann-Held and Christoph Rehmann-Sutter 1 I. Empirical Approaches 1. Genome Analysis and Developmental Biology: The Nematode Caenorhabditis elegans as a Model System / Thomas R. Burglin 15 2. Genes and Form: Inherency in the Evolution of Developmental Mechanisms / Stuart A. Newman and Gerd B. Muller 38 II. Looking Back into History 3. From Genes as Determinants to DNA as Resource: Historical Notes on Development and Genetics / Sahotra Sarkar 77 III. Theorizing Genes 4. The Origin of Species: A Structuralist Approach / Gerry Webster and Brian C. Goodwin 99 5. On the Problem of the Molecular versus the Organismic Approach in Biology / Ulrich Wolf 135 6. Genes, Development, and Semiosis / Jesper Hoffmeyer 152 7. The Fearless Vampire Conservator: Philip Kitcher, Genetic Determinism, and the Informational Gene / Paul E. Griffiths 175 8. Genetics from an Evolutionary Process Perspective / James Griesemer 199 9. Genes-Causes-Codes: Deciphering DNA’s Ontological Privilege / Eva M. Newmann-Held 238 10. Boundaries and (Constructive) Interaction / Susan Oyama 272 11. Beyond the Gene but Beneath the Skin / Evelyn Fox Keller 290 12. Poiesis and Praxis: Two Modes of Understanding Development / Christoph Rehmann-Sutter 313 IV. Social and Ethical Implications 13. Developmental Emergence, Genes, and Responsible Science / Brian C. Goodwin 337 14. Nothing Like a Gene / Jackie Leach Scully 349 Contributors 365 Index 369

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Book SynopsisA case study of the development and reception of genomics in the Netherlands.Trade Review“Taussig’s monograph provides a counter-weight not only to the bold universal truths declared in the field of science, but also to representations of ‘the west’ as a monolith, because the forces that shape genetic science and biomedicine are, in all their complexity, distinctly Dutch. . . . I encourage a reading of Ordinary Genomes because of its analysis, and also as an exercise in analytical departure, and unstructured flight.” - Abigail Baim-Lance, Somatosphere“. . . [A]n interesting case study of the interplay between science, culture and society. The book will be of particular relevance to scholars in medical anthropology, science and technology studies and health studies. This book will be of use to anyone seeking to explore the dynamics of history, religion, culture and their impact on the making of knowledge in natural science.” - Masae Kato, Genomics, Society and Policy“This well-written book provides an interesting and insightful analysis of genetic knowledge and biosocial practices. The cultural and social connection she uncovers between genetics and the nation is particularly useful.” - Casmir Macgregor, Society and Culture“Ordinary Genomes is a thoughtful, nuanced book. Among its many virtues are the clarity of Karen-Sue Taussig’s prose and her admirably fair and sympathetic presentation and analysis of the geneticists. With her close and careful readings of geneticists at work in the multiple spaces of the laboratory, the field, and the clinic, we get an all too rare ethnographic look at genetics-in-practice. Here we have fleshed out, complex figures who negotiate diagnoses, reflect on their own practices and knowledge, and allow us to enter a professional life that is probably far different from what we might have imagined. I cannot stress enough what an important achievement this is.”—Michael Fortun, editor of the journal Cultural Anthropology“Ordinary Genomes is a timely, provocative, compelling account of how research in the genome sciences at once challenges the norms of national culture and is made meaningful through those norms.”—Priscilla Wald, author of Contagious: Cultures, Carriers, and the Outbreak Narrative“What might suspicions of religious inbreeding; Herman the Bull; anxiety about continued influence of Nazi eugenics; and the quest to be normal all have in common? These themes are skilfully woven together in Karen-Sue Taussig's thoughtful and provocative Ordinary Genomes which makes a very important case for the specificity of Dutch genetic perceptions and practices. Her account convinces us to rethink the meaning of ‘Western’ in light of Taussig's excellent ethnographic account of Dutch praxis—in and out of genetic medicine—as we imagine the many ways it teaches us to think about normality. This is an important book. It provides a classic anthropological argument for the importance of thinking comparatively, as we approach 21st century genomic medicine.”—Rayna Rapp, author of Testing Women, Testing the Fetus: The Social Impact of Amniocentesis in America"An interesting case study of the interplay between science, culture and society. The book will be of particular relevance to scholars in medical anthropology, science and technology studies and health studies. This book will be of use to anyone seeking to explore the dynamics of history, religion, culture and their impact on the making of knowledge in natural science.” -- Masae Kato * Genomics, Society and Policy *“Taussig’s monograph provides a counter-weight not only to the bold universal truths declared in the field of science, but also to representations of ‘the west’ as a monolith, because the forces that shape genetic science and biomedicine are, in all their complexity, distinctly Dutch. . . . I encourage a reading of Ordinary Genomes because of its analysis, and also as an exercise in analytical departure, and unstructured flight.” -- Abigail Baim-Lance * Somatosphere *“This well-written book provides an interesting and insightful analysis of genetic knowledge and biosocial practices. The cultural and social connection she uncovers between genetics and the nation is particularly useful.” -- Casmir Macgregor * Society and Culture *Table of ContentsAcknowledgments ix Introduction. Science, Subjectivity, and Citizenship 1 1. "God Made the World and the Dutch Made Holland" 17 2. Genetics and the Organization of Genetic Practice in the Netherlands 57 3. The Social and Clinical Production of Ordinariness 85 4. Backward and Beautiful: Calvinism, Chromosomes, and the Production of Genetic Knowledge 135 5. Bovine Abominations: Contesting Genetic Technologies 159 Epilogue. Ordinary Genomes in a Globalizing World 189 Notes 201 Bibliography 217 Index 235

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Book SynopsisBased on ethnographic research in Brazil, Colombia, and Mexico, this title explores how the concepts of race, ethnicity, nation, and gender enter into and are affected by genomic research. It involves relations between European men and indigenous or African women, gender is a key factor in Latin American genomics and the analyses in this book.Trade Review“[T]he virtues of the book are many: it opens the geographical scope of studies of genomic research and productively engages with contemporary reconfigurations of race and nation. Last, but not least, it demonstrates the enormous value of collaborative transnational research for science and technology studies.” -- Edna Suárez-Díaz * Journal of Latin American Geography *"Mestizo Genomics makes an important contribution to the study of biology and the human sciences in Latin America.... This book will be useful to any scholar interested in science, race, and nation in Latin America as well as those considering how to formulate large-scale interdisciplinary projects." -- Sarah Walsh * The Latin Americanist *"...this collection is vibrant and exciting, throwing up (without closing down) a finessed repertoire of compelling debates that tantalize with irresistible conceptual nuggets primed for future inquiry.... This kind of heuristic analysis looks set to enhance and extend discussions of mestizaje in the twenty-first century, in the academy and beyond." -- Victoria Carroll * History *"All in all, the clarity of the project, the skill of the researchers, and the fine editing of the book as a whole allow for a study of great breadth and significance.... Mestizo Genomics will be of great interest to science studies scholars interested in racial science, biology, and genomics. Latin Americanists will find a compelling description of the historic and recent developments in scientific theories of diversity, unity, and homogenous identity in the area, and Latin America’s variety and specific taxonomies should be instructive to scholars of U.S. and European genomics." -- Julia Rodriguez * ISIS *"This book... clearly contributes to current international debates on race, genomics and biomedicine. This work is not only of interest to biological anthropologists and historians of science, but also to a wider audience that should include evolutionary biologists and social scientists.” -- Ana Barahona * Metascience *Table of ContentsPreface Acknowledgments Introduction: Genomics, Race Mixture, and Nation in Latin America / Peter Wade, Carlos López Beltrán, Eduardo Restrepo, and Ricardo Ventura Santos Part I. History and Context 1. From Degeneration to Meeting Point: Historical Views on Race, Mixture, and the Biological Diversity of the Brazilian Population / Ricardo Ventura Santos, Michael Kent, and Verlan Valle Gaspar Neto 2. Nation and Difference in the Genetic Imagination of Colombia / Eduardo Restrepo, Ernesto Schwartz-Marín, and Roosbelinda Cádenas 3. Negotiating the Mexican Mestizo: On the Possibility of a National Genomics / Carlos López Beltrán, Vivette García Deister, and Mariana Rios Sandoval Part II. Laboratory Case Studies 4. "The Charrua Are Alive": The Genetic Resurrection of an Extinct Indigenous Population in Southern Brazil / Michael Kent and Ricardo Ventura Santos 5. The Travels of Humans, Categories, and Other Genetic Products: A Case Study of the Practice of Population Genetics in Colombia / María Fernanda Olarte Sierra and Adriana Díaz del Castillo H. 6. Laboratory Life of the Mexican Mestizo / Vivette García Deister 7. Social Categories and Laboratory Practices in Brazil, Colombia, and Mexico: A Comparative Overview / Peter Wade, Vivette García Deister, Michael Kent, and María Fernanda Olarte Sierra Conclusion: Race, Multiculturalism, and Genomics in Latin America / Peter Wade Appendix; Methods and Contexts References Contributors Index

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Book SynopsisBased on ethnographic research in Brazil, Colombia, and Mexico, this title helps you explore how the concepts of race, ethnicity, nation, and gender enter into and are affected by genomic research.Trade Review“[T]he virtues of the book are many: it opens the geographical scope of studies of genomic research and productively engages with contemporary reconfigurations of race and nation. Last, but not least, it demonstrates the enormous value of collaborative transnational research for science and technology studies.” -- Edna Suárez-Díaz * Journal of Latin American Geography *"Mestizo Genomics makes an important contribution to the study of biology and the human sciences in Latin America.... This book will be useful to any scholar interested in science, race, and nation in Latin America as well as those considering how to formulate large-scale interdisciplinary projects." -- Sarah Walsh * The Latin Americanist *"...this collection is vibrant and exciting, throwing up (without closing down) a finessed repertoire of compelling debates that tantalize with irresistible conceptual nuggets primed for future inquiry.... This kind of heuristic analysis looks set to enhance and extend discussions of mestizaje in the twenty-first century, in the academy and beyond." -- Victoria Carroll * History *"All in all, the clarity of the project, the skill of the researchers, and the fine editing of the book as a whole allow for a study of great breadth and significance.... Mestizo Genomics will be of great interest to science studies scholars interested in racial science, biology, and genomics. Latin Americanists will find a compelling description of the historic and recent developments in scientific theories of diversity, unity, and homogenous identity in the area, and Latin America’s variety and specific taxonomies should be instructive to scholars of U.S. and European genomics." -- Julia Rodriguez * ISIS *"This book... clearly contributes to current international debates on race, genomics and biomedicine. This work is not only of interest to biological anthropologists and historians of science, but also to a wider audience that should include evolutionary biologists and social scientists.” -- Ana Barahona * Metascience *Table of ContentsPreface Acknowledgments Introduction: Genomics, Race Mixture, and Nation in Latin America / Peter Wade, Carlos López Beltrán, Eduardo Restrepo, and Ricardo Ventura Santos Part I. History and Context 1. From Degeneration to Meeting Point: Historical Views on Race, Mixture, and the Biological Diversity of the Brazilian Population / Ricardo Ventura Santos, Michael Kent, and Verlan Valle Gaspar Neto 2. Nation and Difference in the Genetic Imagination of Colombia / Eduardo Restrepo, Ernesto Schwartz-Marín, and Roosbelinda Cádenas 3. Negotiating the Mexican Mestizo: On the Possibility of a National Genomics / Carlos López Beltrán, Vivette García Deister, and Mariana Rios Sandoval Part II. Laboratory Case Studies 4. "The Charrua Are Alive": The Genetic Resurrection of an Extinct Indigenous Population in Southern Brazil / Michael Kent and Ricardo Ventura Santos 5. The Travels of Humans, Categories, and Other Genetic Products: A Case Study of the Practice of Population Genetics in Colombia / María Fernanda Olarte Sierra and Adriana Díaz del Castillo H. 6. Laboratory Life of the Mexican Mestizo / Vivette García Deister 7. Social Categories and Laboratory Practices in Brazil, Colombia, and Mexico: A Comparative Overview / Peter Wade, Vivette García Deister, Michael Kent, and María Fernanda Olarte Sierra Conclusion: Race, Multiculturalism, and Genomics in Latin America / Peter Wade Appendix; Methods and Contexts References Contributors Index

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Book SynopsisThe contributors to Postgenomics assess the changes to the life sciences the Human Genome Project's completion brought, develop new frameworks for studying the human genome in the postgenomic era, and show how the environment, technology, race, and gender influence the genome and how we think about it.Trade Review"The volume is an accessible and insightful collection of critical and informed perspectives on how technological and theoretical developments influence science and society, and how they shape the ways we think about biological systems like ourselves." -- Sara Green * Metascience *"Postgenomics suggests just how many questions we may productively ask, and marks some highly fruitful lines of inquiry, as we seek to understand this new chapter in the ongoing interaction among genes, society, and ourselves." -- Robin Wolfe Scheffler * Bulletin of the History of Medicine *"The authors convey exceptionally well the character of postgenomic science and how genomics has changed since the 1990s. . . . essential and very interesting reading for anyone interested in genomics and its recent trajectory." -- Peter Wade * Technology and Culture *"This book not only analyzes the impact of numerous [genome-wide association studies] but also examines emerging research areas such as epigenetics in political, social, and philosophical contexts, in so doing redefining the information ecology of the genome. Highly recommended." -- S. H. Jeong * Choice *"I recommend this book to all biologists and philosophers interested in an accessible overview of the effect of the genomic revolution on the biosciences. It capably discusses both the new discoveries and the technical improvements that have been made since the advent of genomics, as well as the attendant philosophical and sociological implications." -- P. William Hughes * Science *"This book . . . should be widely read by all who are interested in the current state and future of the genomic revolution." -- Michael Yudell * Social History of Medicine *"[Postgenomics] offers readers an imaginative and frequently playful way to approach the increasingly complicated question about how scientific innovation impacts society and vice versa." -- Adrianna Link * Journal of the History of Biology *Table of ContentsForeward. Biology's Love Affair with the Genome / Russ Altman vii 1. Beyond the Genome / Hallam Stevens and Sarah S. Richardson 1 2. The Postgenomic Genome / Evelyn Fox Keller 9 3. What Toll Pursuit: Affective Assemblages in Genomics and Postgenomics / Mike Fortun 32 4. The Polygenomic Organism / John Dupré 56 5. Machine Learning and Genomic Dimensionality: From Features to Landscapes / Adrian Mackenzie 73 6. Networks: Representations and Tools in Postgenomics / Hallam Stevens 103 7. Valuing Data in Postgenomic Biology: How Data Donation and Curation Practices Challenge the Scientific Publication System / Rachel A. Ankeny and Sabina Leonelli 126 8. From Behavior Genetics to Postgenomics / Aaron Panofsky 150 9. Defining Health Justice in the Postgenomic Era / Catherine Bliss 174 10. The Missing Piece of the Puzzle? Measuring the Environment in the Postgenomic Moment / Sara Shostak and Margot Moinester 192 11. Maternal Bodies in the Postgenomic Order: Gender and the Explanatory Landscape of Epigenetics / Sarah S. Richardson 210 12. Approaching Postgenomics / Hallam Stevens and Sarah S. Richardson 232 Bibliography 243 Contributors 281 Index 287

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Book SynopsisThe contributors to Postgenomics assess the changes to the life sciences the Human Genome Project's completion brought, develop new frameworks for studying the human genome in the postgenomic era, and show how the environment, technology, race, and gender influence the genome and how we think about it.Trade Review"The volume is an accessible and insightful collection of critical and informed perspectives on how technological and theoretical developments influence science and society, and how they shape the ways we think about biological systems like ourselves." -- Sara Green * Metascience *"Postgenomics suggests just how many questions we may productively ask, and marks some highly fruitful lines of inquiry, as we seek to understand this new chapter in the ongoing interaction among genes, society, and ourselves." -- Robin Wolfe Scheffler * Bulletin of the History of Medicine *"The authors convey exceptionally well the character of postgenomic science and how genomics has changed since the 1990s. . . . essential and very interesting reading for anyone interested in genomics and its recent trajectory." -- Peter Wade * Technology and Culture *"This book not only analyzes the impact of numerous [genome-wide association studies] but also examines emerging research areas such as epigenetics in political, social, and philosophical contexts, in so doing redefining the information ecology of the genome. Highly recommended." -- S. H. Jeong * Choice *"I recommend this book to all biologists and philosophers interested in an accessible overview of the effect of the genomic revolution on the biosciences. It capably discusses both the new discoveries and the technical improvements that have been made since the advent of genomics, as well as the attendant philosophical and sociological implications." -- P. William Hughes * Science *"This book . . . should be widely read by all who are interested in the current state and future of the genomic revolution." -- Michael Yudell * Social History of Medicine *"[Postgenomics] offers readers an imaginative and frequently playful way to approach the increasingly complicated question about how scientific innovation impacts society and vice versa." -- Adrianna Link * Journal of the History of Biology *Table of ContentsForeward. Biology's Love Affair with the Genome / Russ Altman vii 1. Beyond the Genome / Hallam Stevens and Sarah S. Richardson 1 2. The Postgenomic Genome / Evelyn Fox Keller 9 3. What Toll Pursuit: Affective Assemblages in Genomics and Postgenomics / Mike Fortun 32 4. The Polygenomic Organism / John Dupré 56 5. Machine Learning and Genomic Dimensionality: From Features to Landscapes / Adrian Mackenzie 73 6. Networks: Representations and Tools in Postgenomics / Hallam Stevens 103 7. Valuing Data in Postgenomic Biology: How Data Donation and Curation Practices Challenge the Scientific Publication System / Rachel A. Ankeny and Sabina Leonelli 126 8. From Behavior Genetics to Postgenomics / Aaron Panofsky 150 9. Defining Health Justice in the Postgenomic Era / Catherine Bliss 174 10. The Missing Piece of the Puzzle? Measuring the Environment in the Postgenomic Moment / Sara Shostak and Margot Moinester 192 11. Maternal Bodies in the Postgenomic Order: Gender and the Explanatory Landscape of Epigenetics / Sarah S. Richardson 210 12. Approaching Postgenomics / Hallam Stevens and Sarah S. Richardson 232 Bibliography 243 Contributors 281 Index 287

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Book SynopsisGenetics has transformed plant pathology on two occasions: first when Mendelian genetics enabled the discovery that disease resistance was a heritable trait in plants, and secondly when Flor proposed the gene-for-gene hypothesis to explain his observations of plant-parasite interactions, based on his work on flax rust in North Dakota starting in the 1930s. Our knowledge of the genetics of disease resistance and host-pathogen coevolution is now entering a new phase as a result of the cloning of the first resistance genes. This book provides a broad review of recent developments in this important and expanding subject. Both agricultural and natural host-pathogen situations are addressed. While most of the book focuses on plant pathology, in the usual sense of the term embracing fungal, bacterial and viral pathogens, there is also consideration of parasitic plants and a chapter demonstrating lessons to be learnt from the mammalian immune system. Three overall themes are addressed: geneticTable of Contents1: Contributors 2: Preface Part One: Genetic Analyses and Utilization of Resistance 3: Organization of Resistance Genes in Arabidopsis, 4: Genetic Fine Structure of Resistance Loci, 5: Mutation Analysis for the Dissection of Resistance, 6: Cultivar Mixtures in Intensive Agriculture, 7: Crop Resistance to Parasitic Plants, Part Two: Population Genetics 8: The UK Cereal Pathogen Virulence Survey, 9: Adaptation of Powdery Mildew Populations to Cereal Varieties in Relation to Durable and Non-durable Resistance 10: Virulence Dynamics and Genetics of Cereal Rust Populations in North America, 11: Interpreting Population Genetic Data with the Help of Genetic Linkage Maps U E Brändle, 12: Modelling Virulence Dynamics of Airborne Plant Pathogens in Relation to Selection by Host Resistance in Agricultural Crops, 13: An Epidemiological Approach to Modelling the Dynamics of Gene-for-gene Interactions, 14: Modelling Gene Frequency Dynamics, 15: The Genetic Structure of Natural Pathosystems, 16: The Evolution of Gene-for-Gene Interactions in Natural Pathosystems, Part Three: Cell Biology and Molecular Genetics 17: Structural and Biochemical Characterization of Gene-for-Gene Interactions, 18: The Molecular Genetics of Specificity Determinants in Plant Pathogenic Bacteria, 19: Molecular Characterization of Fungal Avirulence, 20: The Molecular Genetics of Plant-Virus Interactions, 21: Molecular Genetics of Disease Resistance: An End to the “Gene-for-Gene” Concept?, 22: Elicitor Generation and Receipt - The Mail Gets Through, But How?, 23: Learning from the Mammalian Immune System in the Wake of The R-Gene Flood, 24: Genetic Disease Control in Plants - Where Now?, 25: Index

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Book SynopsisThis book describes the methodology for predicting the genetic merit of animals in the context of genetic improvement in an animal breeding programme. Information on an animal and its relatives, on either the characteristic to be improved or from other traits, can be used to predict the animal's genetic merit, taking account of the relationships between measurements and the economic values of traits. The methodology is developed from first principles, without unnecessary detail or complexity, and all the required statistical and mathematical concepts are fully described in the book. The text discusses the methods for combining different sources of information and illustrates their use with examples of breeding programmes in cattle, sheep, pigs and poultry. A series of questions with detailed answers is included in the book, to help reinforce the ideas and provide some practical experience in the prediction of genetic merit. The text is aimed at final year undergraduate and first year pTable of Contents1: Introduction to variance 2: ANOVA in a quantitative genetics framework 3: Regression and correlation 4: Identification of animals of high genetic merit 5: Information from relatives 6: Selection index methodology 7: Examples of selection objectives and criteria 8: Factors affecting the rate of genetic improvement 9: Performance testing, progeny testing and MOET 10: Simultaneous prediction of breeding values for several animals 11: Prediction of breeding values and environmental effects 12: Multivariate breeding value prediction 13: Breeding values with a gene of large effect 14: Breeding values for binary traits I: :Appendix: Matrix algebra II: Questions III: Answers IV: References V: Index

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Book SynopsisDuring the last two decades major advances have been made in mammalian genetics. New methods in molecular and cytogenetics, and in biotechnology have been developed. Many of these have been applied to investigating the genetics of sheep and to improving the production of wool, meat and milk. This book is a comprehensive reference work on sheep genetics. All relevant topics have been included, from fundamental genetic structure to the genetics of various production and other traits, to transgenic sheep and genetic conservation. Chapters have been specially commissioned for the volume and written by internationally recognized experts from Europe, USA, Australia and New Zealand. The book will be invaluable to advanced students and research workers in animal genetics, breeding and biotechnology.Table of Contents1: Systematics and Phylogeny of the Sheep I R Franklin, CSIRO, Blacktown, Australia 2: Genetic Aspects of Domestication, Common Breeds and their Origin K Maijala, Helsinki, Finland 3: Genetics of Colour and Hair Texture D P Sponenberg, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, USA 4: Genetics of Morphological Traits and Inherited Disorders F W Nicholas, University of Sydney, Australia 5: Biochemical Genetics L Di Stasio, Department of Animal Science, Torino, Italy 6: Molecular Genetics of Sheep B C Powell, University of Adelaide, Glen Osmond, South Australia 7: Molecular Genetics of Immune Molecules W R Hein, Basle Institute for Immunology, Basle, Switzerland 8: Genetics of Disease Resistance and Vaccine Response H W Raadsma, University of Sydney, Australia, G D Gray, University of New England, Armidale, Australia and R R Woolaston, CSIRO Division of Animal Production, Armidale, Australia 9: Molecular Biology and Genetics of Scrapie in Sheep N Hunter, Institute for Animal Health, Edinburgh, UK 10: Cytogenetics: Physical Chromosome Maps T E Broad, AgResearch Invermay Agricultural Centre, New Zealand, H Hayes, Laboratoire de Genetique Biochimique et de Cytogenetique, France and S E Long, University of Bristol, Langford, Bristol, UK 11: The Sheep Linkage Map G W Montgomery and A M Crawford, University of Otago, Dunedin, New Zealand 12: Genetics of Behaviour G N Hinch, University of New England, Armidale, Australia 13: Biology and Genetics of Reproduction I W Purvis and M Hillard, CSIRO Division of Animal Production, Armidale, Australia 14: Modern Reproduction Technologies and Transgenics I Wilmut, K H S Campbell and L Young, Roslin Institute (Edinburgh), Midlothian, UK 15: Development Genetics N E Cockett, Utah State University, Logan, USA 16: Genetic Resources and Conservation R W Ponzoni, South Australian Research and Development Institute, Adelaide, Australia 17: Genetic Improvement of Wool Production K D Atkins, Agricultural Research and Research Centre, Orange, Australia 18: Genetics of Lamb and Meat Production R G Banks, University of New England, Armidale, Australia 19: Genetics of Meat Quality J M Thompson and A J Ball, University of New England, Armidale, Australia 20: Genetics of Milk Production F Barillet, INRA, Castanet-Tolosan Cedex, France 21: Genetic Improvement of Sheep B P Kinghorn, University of New England, Armidale, Australia 22: Standardized Genetic Nomenclature for Sheep C H S Dolling, President of COGNOSAG, South Australia

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Book SynopsisGenetics has transformed plant pathology on two occasions: first when Mendelian genetics enabled the discovery that disease resistance was a heritable trait in plants, and secondly when Flor proposed the gene-for-gene hypothesis to explain his observations of plant-parasite interactions, based on his work on flax rust in North Dakota starting in the 1930s. Our knowledge of the genetics of disease resistance and host-pathogen coevolution is now entering a new phase as a result of the cloning of the first resistance genes. This book provides a broad review of recent developments in this important and expanding subject. Both agricultural and natural host-pathogen situations are addressed. While most of the book focuses on plant pathology, in the usual sense of the term embracing fungal, bacterial and viral pathogens, there is also consideration of parasitic plants and a chapter demonstrating lessons to be learnt from the mammalian immune system. Three overall themes are addressed: geneticTable of Contents1: Genetic Approaches to Manipulation of Fruit Development and Quality in Tomato, J J Giovannoni et al., Texas A & M University, USA 2: Improving Tomato Fruit Quality by Cultivation, L C Ho, Horticulture Research International, UK 3: Applications of Molecular Biology and Genetic Manipulation to Understand and Improve Quality of Fruits and Vegetables, D Grierson, University of Nottingham, UK 4: Gene Expression in Ripening Bananas, R Drury, Horticulture Research International, UK, C R Bird, Zeneca Plant Science, UK and G B Seymour, Horticulture Research International, UK 5: Genes for Fruit Quality in Strawberry, K Manning, Horticulture Research International, UK 6: The Tomato Ethylene Receptor Gene Family: It’s Not Easy Being a Plant, D Tieman and H Klee, University of Florida, USA 7: Environmental Requirements as Determined by Rooting Potential in Leafy Cuttings, 8: R S Harrison-Murray and B H Howard, Horticulture Research International, UK 9: The Use of Mutants and Molecular Biology to Understand Competence for Root Formation, W P Hackett et al., University of Minnesota, USA 10: Physiological Analysis of the Floral Transition, G Bernier et al., Universite de Liege, Belgium 11: Genetic and Environmental Control of Flowering in Strawberry, N H Battey et al., University of Reading, UK 12: Manipulating the Photoperiodic Control of Plant Reproduction, S D Jackson and B Thomas, Horticulture Research International, UK 13: Regulation of Abscisic Acid and Water Stress Response Genes, P K Busk et al., CID, Barcelona, Spain 14: Manipulation of Growth of Horticultural Crops under Environmental Stress, W J Davies and D S Thompson, Lancaster University, UK and J E Taylor, University of Reading, UK 15: Engineering Phytochrome Genes to Improve Crop Performance, H Smith, University of Leicester, UK 16: Regulation of Stem Extension by Temperature, F Allen Langton, Horticulture Research International, UK 17: Modification of Plant Morphology by Genetic Manipulation of Gibberellin Biosynthesis, P Hedden et al., University of Bristol, UK

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Book SynopsisInternational concern over the threat to species and ecosystems caused by human activities is at an all time high, which may result in high costs to present and future generations. The economic costs and benefits associated with the conservation and sustainable use of genetic resources of actual or potential value for food and agriculture is largely unknown. Economic instruments that can encourage implementation of socially optimal genetic resource conservation strategies as well as the sharing of the real benefits and costs are a useful measurement tool. This book is an edited compilation of papers from the Symposium on the Economics of Valuation and Conservation of Genetic Resources for Agriculture held in Rome in May 1996. It addresses some of the key issues involved in the estimation of the economic value of conserving genetic resources for agriculture. It covers the modelling of the value of Plant Genetic Resources (PGRs), empirical studies of PGRs (including field diversity and yTable of ContentsPart I: Modelling the Role of Genetic Resources in Plant Breeding 1.1: Plant Breeding: A Case of Induced Innovation, R E Evenson 1.2: Search Modelling for Traits, D Gollin and M Smale 1.3: The Value of Genetic Resources for Use in Agricultural Improvement, R D Simpson and R A Sedjo 1.4: Development, Agriculture and Diversity: Externalities in the Diffusion of Agriculture, T Swanson Part II: Empirical Studies: Plant Breeding and Field Diversity 2.1: Indicators to Genetic Diversity in Bread Wheats: Selected Evidence on Cultivars Grown in Developing Countries, M Smale 2.2: Farmers’ Valuation and Conservation of Crop Genetic Resources, S B Brush and E Meng Part III: Empirical Studies: Breeding Values 3.1: Maize Breeding and Genetic Resources, W Salhuana and S Smith 3.2: Role of International Germplasm Collections in Italian Durum Wheat Breeding Programs, D Bagnara and V Santiello 3.3: An Application of Hedonic Pricing Methods to Value Rice Genetic Resources in India, D Gollin and R E Evenson 3.4: Varietal Trait Values for Rice in India, K P C Rao and R E Evenson 3.5: Modern Varieties, Traits, Commodity Supply and Factor Demand in Indian Agriculture, R E Evenson 3.6: Crop-Loss Data and Trait Value Estimates for Rice in Indonesia, R E Evenson 3.7: Breeding Values of Rice Genetic Resources, D Gollin and R E Evenson Part IV: Property Rights 4.1: Incentives for Genetic Resource Preservation, A Artuso 4.2: Farmers’ Rights, J Esquinas-Alcázar 4.3: Intellectual Property and Farmers’ Rights, B D Wright 4.4: Valuing Farmers’ Rights, D Gollin Part V: The Implication of Development in Biotechnology 5.1: Impact of Biotechnology on the Demand for Rice Biodiversity, C E Pray 5.2: Biotechnology and Genetic Resources, R E Evenson

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Book SynopsisWinner of a 2009 Outstanding Academic Title (OAT) award!Trees continue to maintain a unique significance in the social, ecological and economic systems of the world - as large, long-lived perennials covering 30% of land on Earth; their very nature dictates their importance. An understanding of forest genetics is essential for providing insight into the evolution, conservation, management and sustainability of both natural and managed forests. Providing a comprehensive introduction to the principles of genetics as important to forest trees, this text integrates the varied sub-disciplines of genetics and their applications in gene conservation, tree improvement and biotechnology. Topics discussed include genetic variation in natural forest trees, the application of genetics in tree improvement and breeding programs, and genomic sciences and molecular technologies.Table of Contents1: Forest Genetics - Concepts, Scope, History and Importance SECTION I: BASIC PRINCIPLES 2: Molecular Basis of Inheritance - Genome Organization, Gene Structure and Regulation 3: Transmission Genetics - Chromosomes, Recombination and Linkage Mendelian Genetics 4: Genetic Markers - Morphological, Biochemical and Molecular Markers 5: Population Genetics - Gene Frequencies, Inbreeding and Forces of Evolution 6: Quantitative Genetics - Polygenic Traits, Heritabilities and Genetic Correlations SECTION II: GENETIC VARIATION IN NATURAL POPULATIONS 7: Within-population Variation - Genetic Diversity, Mating Systems and Stand Structure 8: Geographic Variation - Races, Clines and Ecotypes 9: Evolutionary Genetics - Divergence, Speciation and Hybridization 10: Gene Conservation - In Situ, Ex Situ and Sampling Strategies SECTION III: TREE IMPROVEMENT 11: Tree Improvement Programs - Structure, Concepts and Importance 12: Base Populations - Species, Hybrids, Seed Sources and Breeding Zones 13: Phenotypic Mass Selection - Genetic Gain, Choice of Traits and Indirect Response 14: Genetic Testing - Mating Designs, Field Tests and Test Implementation 15: Data Analysis - Mixed Models, Variance Components and Breeding Values 16: Deployment - Open-pollinated Varieties, Full-sib Families and Clones 17: Advanced-generation Breeding Strategies - Breeding Population Size, Structure and Management SECTION IV: BIOTECHNOLOGY 18: Genomics - Discovery and Functional Analysis of Genes 19: Marker-assisted Selection and Breeding - Indirect Selection, Direct Selection and Breeding Applications 20: Genetic Engineering - Target Traits, Transformation and Regeneration 1: Forest Genetics - Concepts, Scope, History and Importance SECTION I: BASIC PRINCIPLES 2: Molecular Basis of Inheritance - Genome Organization, Gene Structure and Regulation 3: Transmission Genetics - Chromosomes, Recombination and Linkage Mendelian Genetics 4: Genetic Markers - Morphological, Biochemical and Molecular Markers 5: Population Genetics - Gene Frequencies, Inbreeding and Forces of Evolution 6: Quantitative Genetics - Polygenic Traits, Heritabilities and Genetic Correlations SECTION II: GENETIC VARIATION IN NATURAL POPULATIONS 7: Within-population Variation - Genetic Diversity, Mating Systems and Stand Structure 8: Geographic Variation - Races, Clines and Ecotypes 9: Evolutionary Genetics - Divergence, Speciation and Hybridization 10: Gene Conservation - In Situ, Ex Situ and Sampling Strategies SECTION III: TREE IMPROVEMENT 11: Tree Improvement Programs - Structure, Concepts and Importance 12: Base Populations - Species, Hybrids, Seed Sources and Breeding Zones 13: Phenotypic Mass Selection - Genetic Gain, Choice of Traits and Indirect Response 14: Genetic Testing - Mating Designs, Field Tests and Test Implementation 15: Data Analysis - Mixed Models, Variance Components and Breeding Values 16: Deployment - Open-pollinated Varieties, Full-sib Families and Clones 17: Advanced-generation Breeding Strategies - Breeding Population Size, Structure and Management SECTION IV: BIOTECHNOLOGY 18: Genomics - Discovery and Functional Analysis of Genes 19: Marker-assisted Selection and Breeding - Indirect Selection, Direct Selection and Breeding Applications 20: Genetic Engineering - Target Traits, Transformation and Regeneration

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Book SynopsisThis book focuses on the previously neglected interface between the conservation of plant genetic resources and their utilization. Only through utilization can the potential value of conserved genetic resources be realised. However, as this book shows, much conserved germplasm has to be subjected to long-term pre-breeding and genetic enhancement before it can be used in plant breeding programmes.The authors explore the rationale and approaches for such pre-breeding efforts as the basis for broadening the genetic bases of crop production. Examples from a range of major food crops are presented and issues analysed by leading authorities from around the world.Table of Contentsa: Foreword, M Duwayri and G Hawtin b: Preface, D Cooper, C Spillane and T Hodgkin PART ONE: GENERAL PRINCIPLES 1: Broadening the genetic base of crops: an overview, D Cooper, T Hodgkin and C Spillane 2: Evolutionary and genetic perspectives on the dynamics of crop genepools, C Spillane and P Gepts 3: Base broadening: introgression and incorporation, B Spoor and N Simmonds 4: The role of local level gene flow in enhancing and maintained genetic diversity, J Berthaud et al. 5: Regulatory aspects of breeding for diversity, N Louwaars 6: Decentralized and participatory plant breeding for marginal environments, S Ceccarelli et al. 7: Empowering farmers and broadening the genetic base: agricultural research and resource management, R Salazar PART TWO: CROP CASE STUDIES 8: The state of millet diversity and its use in West Africa, O Niangado 9: State of the use of maize genetic diversity in the USA and sub-Saharan Africa, S P Tallury and M M Goodman 10: The state of use of potato genetic diversity, R Ortiz 11: The state of use of cassava genetic diversity and a proposal to enhance it, G Second and C Iglesias 12: State of use of Musa diversity, S Sharrock and E Frison PART THREE: POPULATION MANAGEMENT 13: Dynamic management of genetic resources: a 13 year experiment on wheat, I Goldringer et al. 14: Genetic base broadening of barley (Hordeum vulgare L.) in the Nordic countries, M Vetelainen and E A J Nissila 15: Evolutionary changes in Cambridge Composite Cross Five of barley, K M Ibrahim and J A Barrett 16: Genetic base broadening in the West Indies Sugar Cane Breeding Program by the incorporation of wild species, A J Kennedy 17: Potential of genetic resources and breeding strategies for base broadening in Beta, L Frese, B Desprez, and D Ziegler 18: HOPE, a hierarchical, open-ended system for broadening the breeding base of maize, L Kannenberg 19: The germplasm enhancement of maize (GEM) project: Private and public sector collaboration, L Pollak and W Salhuana 20: A French cooperative program for management and utilization of maize genetic resources, A Gallais, J P Monod, and others PART FOUR: OTHER APPROACHES TO BROADENING THE GENETIC BASE OF CROPS 21: Broadening the genetic base of lentil in South Asia, W Erskine et al. 22: Genetic diversity of barley: use of locally adapted germplasm to enhance yield and yield stability of barley in dry areas, S Grando, R Von Bothmer, S Ceccarelli 23: Breeding Phaseolus for intercrop combinations in the Andean highlands, J P Baudoin, F Camarena and M Lobo 24: Improving potato resistance to disease under the Global Initiative on Late Blight, T Bodo, R Trognitz, M Bonierbale, J A Landeo, G Forbes, J E Bradshaw, G R Mackay, R Waugh, M A Huarte, and L Colon 25: A Mexican bean breeding program for comprehensive horizontal resistance to all locally important pests and diseases, R G Espinosa, R A Robinson, P R Vallejo, F C Gonzalez and F R Rosales 26: The impact of decentralized and participatory plant breeding on the genetic base of crops, J Witcombe 27: Base broadening for client-oriented impact, L Sperling et al.

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Book SynopsisPlant genotyping, or DNA fingerprinting of plants, is a technology that has matured and is poised for widespread practical application in the fields of breeding, commerce and research. This book examines the technologies available and their application in the analysis of:Wild plant populationsGermplasm collections Plant breedingContributors include leading research workers in this field from North America, Europe and Australasia.Table of Contents1: Molecular markers available for use in plant genotyping 2: Plant genotyping by analysis of single nucleotide polymorphisms, K J Edwards and R Mogg, University of Bristol, UK 3: Plant genotyping by analysis of microsatellites T A Holton, Southern Cross University, Australia 4: Plant genotyping using arbitrarily amplified DNA, G Caetano-Anollés, University of Oslo, Norway 5: Plant genotyping based upon analysis of single nucleotide polymorphisms using microarrays, B Lemieux, University ofDelaware, USAGenotyping plant genetic resource collections 6: Genotyping in plant genetic resources, B V Ford-Lloyd, University of Birmingham, UK 7: Applications of molecular marker techniques to the use of international germplasm collections, M Warburton and D Hoisington, Applied Biotechnology Center, CIMMYT, México Genotyping cultivated and wild germplasm 8: Molecular analysis of wild plant germplasm: the case of tea tree (Melaleuca alternifolia), L S Lee, M Rossetto, L Homer, R J Henry, Southern Cross University, Australia 9: Genotyping Pacific Island Taro (Colocasia esculenta (L.) Schott) germplasm, I D Godwin, E S Mace and Nurzuhairawaty,The University of Queensland, Australia 10: Molecular marker systems for sugarcane germplasm analysis, G M Cordeiro, Southern Cross University, Australia 11: Microsatellite analysis in cultivated hexaploid wheat and wild wheat relatives, A McLauchlan, R J Henry, Southern Cross University, Australia, P G Isaac, Agrogene, France and K J Edwards, University of Bristol, UK 12: Comparison of RFLP & AFLP marker systems for assessing genetic diversity in Australian barley varieties & breeding, K Chalmers, University of Adelaide, South Australia Development of molecular markers for use in plant genotyping 13: Discovery and application of single nucleotide polymorphism markers in plants, D Bhattramakki and A Rafalski, DuPont Agricultural Products, USA 14: Producing and exploiting enriched microsatellite libraries, T L Maguire, University of Queensland, Australia 15: Sourcing of SSR markers from related plant species, M Rossetto, Southern Cross University, Australia 16: Microsatellites derived from ESTs, and their comparison with those derived by other methods, K D Scott, Southern Cross University, AustraliaTechnical developments and issues in plant genotyping 17: Plant DNA Extraction, R J Henry, Southern Cross University, Australia 18: Collection, reporting and storage of microsatellite genotype data, N Harker, Southern Cross University, Australia 19: Commercial applications of plant genotyping, L S Lee and R J Henry, Southern Cross University, Australia 20: Non-gel based techniques for plant genotyping, R Kota, Southern Cross University, Australia 21: Using molecular information for decision support in wheat breeding, H Eagles, CRC for Molecular Plant Breeding, M Cooper, The University of Queensland, R Shorter, CSIRO Tropical Agriculture, P Fox, CIMMYT, 22: Application of DNA profiling to an outbreeding forage species, J Forster, E Jones, R Kölliker, M Drayton, M Dupal, K Guthridge, La Trobe University, Australia & K Smith, Pastoral & Veterinary Institute, Australia

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Book SynopsisThis book has been developed from the keynote addresses delivered at the third IOBC International Symposium (co-organized with CILBA) that was held in Montpellier in October 2002, to address recent developments in genetics and evolutionary biology as applied to biological control. Chapters are organized around the following themes: Genetic structure of pest and natural enemy populations Molecular diagnostic tools in biological control Tracing the origin of pests and natural enemies Predicting evolutionary change in pests and natural enemies Compatibility of transgenic crops and natural enemies Genetic manipulation of natural enemies. The authors identify new issues for each of the major approaches in applied biological control. These include the (1) use of molecular genetics to trace the origin of target pests in classical biological control, (2) potential of mass-reared, transgenic agents in augmentative biological control, and (3) compatibility of transgenic crops and natural eneTable of Contents1: Genetic structure of natural plant and pathogen populations, J J Burdon and P H Thrall, CSIRO, Canberra, Australia 2: Measuring genetic variation in natural enemies used for biological control: why and how? E Wajnberg, INRA, France 3: Molecular systematics, Chalcidoidea and biological control, J Heraty, University of California, USA 4: Genetic markers in rust fungi and their application to weed biocontrol, K J Evans, Tasmanian Institute of Agricultural Research, Australia and D R Gomez, University of Adelaide, Australia 5: Tracing the origin of pests and natural enemies: genetic and statistical approaches, G K Roderick, University of California, USA 6: Tracing the origin of cryptic insect pests and vectors, and their natural enemies, J K Brown, University of Arizona, USA 7: Predicting evolutionary change in invasive, exotic plants and its consequences for plant-herbivore interactions, H Müller-Schärer and T Steinger, Université de Fribourg, Swizterland 8: Experimental evolution in host-parasitoid interactions, A R Kraaijeveld, Imperial College at Silwood Park, Ascot, UK 9: Interactions between natural enemies and transgenic insecticidal crops, J J Obrycki, Iowa State University, USA, J R Ruberson, University of Georgia, USA and J E Losey, Cornell University, USA 10: The GMO guidelines project: development of international scientific environmental biosafety testing guidelines for transgenic plants, A Hilbeck, Swiss Federal Institute of Technology, (ETH), Switzerland and Steering Comittee of the GMO Guildlines Project 11: Genetic manipulation of natural enemies: can we improve biological control by manipulating the parasitoid and/or the plant? G M Poppy, University of Southampton, UK and W Powell, Rothamsted Research, Harpenden, UK 12: Sex-ratio distorters and other selfish genetic elements: implications for biological control, R Stouthamer, University of California, USA

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Book SynopsisThis volume explores the latest methods used by researchers to study the detection, characterization, and various aspects of viroids. The chapters in this book are organized into seven parts and cover topics such as detection methods based on the biology of viroids; detection techniques based on electrophoresis and hybridization techniques; PCR-based techniques that provide high degrees of sensitivity; emerging area of nucleic acid sequence-based technology; and emerging techniques in viroid research such as RNA silencing, splicing, and viroid structure. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Viroids: Methods and Protocols is a valuable resource for researchers and graduaTable of ContentsPreface…Table of Contents…Contributing Authors…Part I Biological Techniques1. Study and Detection of Citrus Viroids in Woody HostsRobert R. Krueger and Georgios Vidalakis2. Detection and Characterization of Viroids via Biological Assays on Herbaceous HostsRosemarie W. Hammond3. Analysis on RNA Motif-Based RNA Trafficking in PlantsHeather N. Smith, Junfei Ma, and Ying Wang4. Isolation and Transfection of Citrus Protoplasts with Citrus Exocortis ViroidSubhas Hajeri, James Ng, Jude Grosser, and Georgios VidalakisPart II Electrophoresis and Hybridization Techniques5. High-Throughput RNA Extraction from Citrus Tissues for the Detection of ViroidsTyler Dang, Fatima Osman, Jinbo Wang, Tavia Rucker, Sohrab Bodaghi, Shih-hua Tan, Deborah Pagliaccia, Irene Lavagi-Craddock, and Georgios Vidalakis6. Extraction and Purification of Viroids from Herbaceous HostsRosemarie W. Hammond7. Detection of Viroids by sPAGE Gel ElectrophoresisNúria Duran-Vila8. Two-Dimensional Polyacrylamide-Gel Electrophoresis Analysis of Viroid RNAsJosé-Antonio Daròs9. A Simplified Dot-Blot Hybridization Protocol for Potato spindle tuber viroid Detection in SolanaceaeOxana Kekstidou, Christina Varveri, and Nikon Vassilakos10. Gel Blot Hybridization for ViroidsPedro Serra11. Tissue Print Hybridization for Detection and Characterization of ViroidsMaria S. Kaponi, Teruo Sano, and Panayota E. Kyriakopoulou12. Fluorescein-Based Electrophoretic Mobility Shift AssayShachinthaka D. Dissanayaka Mudiyanselage and Ying WangPart III PCR Techniques13. Detection of Viroids by RT-PCRNerida J. Donovan, Grant A. Chambers, and Mengji Cao 14. Detection of Viroids using RT-qPCRSubhas Hajeri, Georgios Vidalakis, and Raymond Yokomi15. Multiplex RT-PCR Francesco Faggioli and Marta Luigi16. Real-Time Detection of Viroids using Singleplex and Multiplex Quantitative Polymerase Chain ReactionFatima Osman and Georgios Vidalakis17. Reverse Transcription-Loop Mediated Isothermal AMPlification (RT-LAMP) at the Service of Viroid DetectionIraklis N. Boubourakas and Panayota E. Kyriakopoulou18. SYBR ® Green RT-qPCR for the Universal Detection of Citrus ViroidsGeorgios Vidalakis, Jinbo Wang, Tyler Dang, Tavia Rucker, Sohrab Bodaghi, Shi-hua Tan, Irene Lavagi-Craddock, Alexandra Syed, Gerardo Uribe, Yi Hsieh, and Joana Carbajal-Moreno19. Detection of Avocado sunblotch and Other Viroids using RNA Filter Paper Capture and RT-PCRDeborah M. Mathews, Sohrab Bodaghi, James A. Heick, and J. Allan DoddsPart IV Cloning and Sequencing Techniques20. Cloning and Sequencing of ViroidsRosemarie W. Hammond21. QuantiGene Plex Assay: A Method for High-Throughput Multiplex Citrus Viroid Detection and IdentificationTyler Dang, Jinbo Wang, Tavia Rucker, Sohrab Bodaghi, Irene Lavagi-Craddock, and Georgios Vidalakis22. Culture-Independent Discovery of Viroids by Deep Sequencing and Computational AlgorithmsAli Raza, Shou-Wei Ding, and Qingfa Wu 23. An In Silico Detection of a Citrus Viroid from Raw High Throughput Sequencing DataTyler Dang, Andres Espindola, Georgios Vidalakis, and Kitty CardwellPart V RNA Silencing Techniques24. Detection of Viroid RNA and vd-siRNA in N. benthamiana Plants: Northern Blot Analyses for Viroid and vd-siRNAsKonstantina Katsarou, Nikoleta Kryovrysanaki, and Kriton KalantidisPart VI Splicing Techniques25. Production of Recombinant RNA in Escherichia coli Using Eggplant Latent Viroid as a ScaffoldBeltrán Ortolá and José-Antonio DaròsPart VII Structural Analysis26. Predicting the Structure of a ViroidGerhard StegerSubject Index List…

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Book SynopsisThis volume details generation of gene-edited cell lines and organisms as models for human diseases, pest control, and large animal welfare and production outcomes. Chapters guide readers through gene regulation, editing, screening of cell lines, genome editing, and an overview of the tools for efficient genome editing including; ZFNs, TALENs, and CRISPR. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step- by-step, readily reproducible protocols. Authoritative and cutting-edge, Applications of Genome Modulation and Editing aims to be a useful and practical guide for researchers to commence or advance their study in this field. Table of ContentsPart I: Gene Editing Approaches 1. Historical DNA manipulation Overview LLuis Montoliu 2. Tools for efficient genome editing; ZFN, TALEN, and CRISPR Yasaman Shamshirgaran,,Jun Liu, Huseyin Sumer, Paul J. Verma and Amir Taheri-Ghahfarokhi Part II: Genetic Manipulation Methods 3. Efficient generation of stable cell lines with inducible neuronal transgene expression using the piggyBac transposon system Jinchao Gu, Huseyin Sumer and Brett Cromer 4. Modifying Bacterial Artificial Chromosomes for Extended Genome Modification Hannah Auch, Nikolai Klymiuk and Petra Runa-Vochozkova 5. Site specific editing of the genome in Pluripotent cells Luis Ortega and Joseph Rosenbluh 6. Targeting the AAVS1 site with transgene cassette by CRISPR/Cas9 with an inducible transgene cassette for the to neuronal differentiation of human pluripotent stem cells Jinchao Gu, Ben Rollo, Huseyin Sumer and Brett Cromer 7. Microinjection of zygotes for CRISPR/Cas9 mediated insertion of transgenes into the murine Rosa26 safe harbour Fabien Delerue and Lars M. Ittner 8. CRISPR-on for endogenous activation of SMARCA4 expression in bovine embryos Virgilia Alberio, Virginia Savy and Daniel F. Salamone Part III: Applications of Genome Manipulation 9. CRISPR/Cas mutagenesis to generate novel traits in Bactrocera tryoni for Sterile Insect Technique Amanda Choo, Elisabeth Fung, Thu N.M. Nguyen, Anzu Okada and Peter Crisp 10. CRISPR/Cas9 Genome Editing in the New World Screwworm and Australian Sheep Blowfly Daniel F. Paulo, Megan E. Williamson and Maxwell J. Scott 11. Generation of gene drive mice for invasive pest population suppression Mark Bunting, Chandran Pfitzner, Luke Gierus, Melissa White, Sandra Piltz and Paul Thomas Part IV: Large animal models of human disease 12. Generation of a human deafness sheep model using the CRISPR/Cas system Martina Crispo, Vanessa Chenouard, Pedro dos Santos-Neto, Laurent Tesson, Marcela Souza, JeanMarie Heslan, Federico Cuadro, Ignacio Anegón and Alejo Menchaca 13. Targeted Gene Editing in Porcine Germ Cells Taylor Goldsmith, Alla Bondareva, Dennis Webster, Anna Laura Voigt, Lin Su, Daniel F. Carlson and Ina Dobrinski 14. Generating a Heat Tolerance Mouse Model Jun Liu and Paul J. Verma Part V: Large Animal Welfare and Production Outcomes 15. Generation of pigs that produce single sex progeny Björn Petersen and Stefanie Kurtz 16. Generation of Double-muscled Sheep and Goats by CRISPR/Cas9-mediated Knockout of the Myostatin Gene Peter Kalds, Martina Crispo, Chao Li, Laurent Tesson, Ignacio Anegon, Yulin Chen, Xiaolong Wang and Alejo Menchaca Part VI: Concluding Remarks 17. Regulatory and policy considerations around applications of genome editing in agriculture Steffi Friedrichs, Karinne Ludlowand Peter Kearns

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Book SynopsisThis second edition provides new and updated protocols that can be used for generation of knockout animals. Chapters guide the reader through basic protocols for three genome editing technologies, target design tools, and specific protocols for each animal. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Genome Editing in Animals: Methods and Protocols, Second Edition aims to be a useful practical guide to researches to help further their study in this field. Table of Contents1. Construction and Evaluation of Zinc Finger Nucleases Hiroshi Ochiai and Takashi Yamamoto 2. Updated overview of TALEN construction systems Tetsushi Sakuma and Takashi Yamamoto 3. CRISPR/Cas9 Izuho Hatada, Sumiyo Morita, and Takuro Horii 4 SNPD-CRISPR: Single Nucleotide Polymorphism-Distinguishable Repression or Enhancement of a Target Gene Expression by CRISPR System Shohei Maruyama, Takashi Kusakabe, Xinyi Zou, Yoshiaki Kobayashi, Yoshimasa Asano, Qingbo S. Wang, and Kumiko Ui-Tei 5. Utilizing large functional and population genomics resources for CRISPR/Cas perturbation experiment design Qingbo S. Wang, Kumiko Ui-Tei 6. Generation of genome-edited mice by cytoplasmic injection of CRISPR-Cas9 RNA Takuro Horii and Izuho Hatada 7. Gene targeting in mouse embryonic stem cells via CRISPR/Cas9 ribonucleoprotein (RNP) mediated genome editing. Manabu Ozawa, Chihiro Emori, and Masahito Ikawa 8. Generation of Knock-in Mouse by Genome Editing Wataru Fujii 9. Introduction of genetic mutations into mice by Base Editor and Target-AID Hiroki Sasaguri 10. Genome editing in mouse and rat by electroporation Takehito Kaneko 11. Generation of floxed mice by sequential electroporation Takuro Horii, Ryosuke Kobayashi, and Izuho Hatada 12. Efficient detection of flox mice using in vitro Cre recombination Ryosuke Kobayashi, Takuro Horii, and Izuho Hatada 13. VCre/VloxP and SCre/SloxP as reliable site-specific recombination systems for genome engineering Manabu Nakayama 14. Efficient CRISPR/Cas9-Assisted Knockin of Large DNA Donors by Pronuclear Microinjection During S-phase in Mouse Zygotes Takaya Abe, Ken-ichi Inoue, and Hiroshi Kiyonari 15. Genome editing of murine liver hepatocytes by AAV vector-mediated expression of Cas9 in vivo Yuji Kashiwakura and Tsukasa Ohmori 16. Non-Viral Ex Vivo Genome-Editing in Mouse Bona Fide Hematopoietic Stem Cells with CRISPR/Cas9 Hiromasa Hara1, Natsagdorj Munkh-Erdene, Suvd Byambaa, and Yutaka Hanazono 17. Genome editing of rat Takehito Kaneko 18. A simple and efficient method for generating KO rats using in vitro fertilized oocytes Kohtaro Morita, Arata Honda, and Masahide Asano 19. Editing the Genome of the Golden Hamster (Mesocricetus auratus) Michiko Hirose, Toshiko Tomishima, and Atsuo Ogura 20. Gene targeting in rabbits: single-step generation of knockout rabbits by microinjection of CRISPR/Cas9 plasmids Arata Honda 21. Genome Editing of Pig Masahito Watanabe and Hiroshi Nagashima 22. GEEP method: an optimized electroporation-mediated gene-editing approach for establishment of knockout pig lines Fuminori Tanihara, Maki Hirata, and Takeshige Otoi 23. Genome editing mediated by primordial germ cell in chicken Jae Yong Han and Hong Jo Lee 24. CRISPR–Cas9-mediated genome modifications in zebrafish Yusuke Kamachi and Atsuo Kawahara 25. Genome Editing of Medaka Rie Hara, Satoshi Ansai, and Masato Kinoshita 26. CRISPR-Cas9 based functional analysis in amphibians; Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl Miyuki Suzuki, Midori Iida, Toshinori Hayashi, and Ken-ichi T Suzuki 27. Genome Editing of Silkworms Takuya Tsubota, Hiroki Sakai, and Hideki Sezutsu 28. Improved genome editing in the ascidian Ciona with CRISPR/Cas9 and TALEN Yasunori Sasakura and Takeo Horie 29. Genome editing of C. elegans Takuma Sugi

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Book SynopsisRNA Isolation from Human Stem Cell Derived Retinal Organoids.- Next generation Sequencing Application a Systematic Approach for High quality RNA Isolation from Skeletal Muscles.- Ultrasound induced Enrichment of Ultra trace miRNA Biosensing in Nanoliter Samples.- Direct Detection of SARS CoV 2 RNA in Saliva with Colorimetric RT LAMP.- NASBA Coupled to Paper Microfluidics for RNA Detection.- Single cell Imaging of mRNA by Target RNA initiated RCA.- Detection of Foodborne RNA Viruses by Reverse Transcriptase Droplet Digital PCR.- Single molecule RNA Imaging in Live Cells with an Avidity based Fluorescent Light up Aptamer biRhoBAST.- Assessing MicroRNA Profiles from Low Concentration Extracellular Vesicle RNA Utilizing NanoString nCounter Technology.- Liquid and Solid Hybridization Methods to Detect RNAs.- Visualization of Individual RNA Molecules by Proximity Ligation based Chromogenic In Situ Hybridization Assay.- Quantum Dots Based Protocols for the Detection of RNAs.- RNA Analysis Using Immunoassay Detection Format.- Fluorescent Techniques for RNA Detection in Nanoparticles.- Sequencing 10X Genomics 3' HT assay for Gene Expression.- Single Cell Sequencing of 3' RNA Transcripts.- Short Read RNA Seq.- RNA Seq Data Analysis.- Bi clustering for Epi transcriptomic Co functional Analysis.- RNA Folding, Mutation and Detection.- Epitranscriptomic Mass Spectrometry.- Polyvinylamine and Its Derivative as Effective Carrier for Targeted Delivery of Small RNAs.- Delivery of mRNA with histidine-lysine peptides.- Plant Virus Like Particles for RNA Delivery.- Lipid-based Nanoparticles for RNA Delivery.- In vitro Amplification and Selection of Engineered RNase P ribozyme for Gene Targeting Applications.- Rapid Ribonuclease P Kinetics Measured by Stopped-Flow Fluorescence and Fluorescence Anisotropy.- Computational Design of Allosteric Ribozymes via Genetic Algorithms.

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Book SynopsisModified Alkaline Comet Assay to Detect Oxidative DNA Damage.- Radiation-Induced DNA Strand Break Detection by Gel Electrophoresis.- Quantitative Measurement of 8-Hydroxy-2′-Deoxyguanosine in Serum/Plasma and Urine Using an Enzyme-Linked Immunosorbent Assay.- Radiation-Induced Gamma-H2AX Foci Staining and Analysis.- Non-Radiolabeled Radioresistant DNA Synthesis and S-Phase Checkpoint Analysis.- Constant Field Gel Electrophoresis Analysis for DNA Double-Strand Break and Its Repair.- Detection of Chromatid Break and Micronucleus Formation Induced by Low- and High-LET Irradiation.- Measurement of DNA Polymerase and Microhomology-Mediated End-Joining Activities by Gel Electrophoresis and smFRET Techniques.- UV-Induced DNA Damage Detection by ELISA Analysis.- G2 Premature Chromosome Condensation (G2-PCC) by Calyculin A to Analyze DNA Double-Strand Breaks and Their Repair.- Mitotic Shake-Off and Cell Cycle Synchronization.- DCFDA Assay for Oxidative Stress Measurement in Fluorometer.- HPRT Mutation Assay for Chinese Hamster Ovary Cells.- Detection of De Novo Mutations by Sequencing Reduced Representation Libraries.- Chemical-Induced DNA Damage Identification by High-Throughput Detection of DNA Double-Strand Break.- Assessing DNA Damage Through the Cell Cycle Using Flow Cytometry.- A Mass Spectrometry-Based Proteomics Workflow for Concurrent Profiling of Protein Thiol Oxidation and Phosphorylation.- Analyzing Homologous Recombination Using Antibiotic Marker Substrates in Mammalian Cells.

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Book SynopsisMicroRNAs in Medicine provides an access point into the current literature on microRNA for both scientists and clinicians, with an up-to-date look at what is happening in the emerging field of microRNAs and their relevance to medicine.Table of ContentsForeword ix Sir David Baulcombe Preface xi Contributors xiii 1 MICRORNAS: A BRIEF INTRODUCTION 1 Charles H. Lawrie PART I: MICRORNAS AS PHYSIOLOGICAL REGULATORS 25 2 MICRORNA REGULATION OF STEM CELL FATE AND REPROGRAMMING 27 Erika Lorenzo Vivas, Gustavo Tiscornia, and Juan Carlos Izpisua Belmonte 3 MICRORNAS AS REGULATORS OF IMMUNITY 41 Donald T. Gracias and Peter D. Katsikis 4 REGULATION OF SENESCENCE BY MICRORNAS 59 Ioannis Grammatikakis and Myriam Gorospe 5 THE EMERGENCE OF GEROMIRS: A GROUP OF MICRORNAS IMPLICATED IN AGING 77 Alejandro P. Ugalde, Agnieszka Kwarciak, Xurde M. Caravia, Carlos López-Otín, and Andrew J. Ramsay 6 MICRORNAS AND HEMATOPOIESIS 91 Sukhinder K. Sandhu and Ramiro Garzon 7 MICRORNAS IN PLATELET PRODUCTION AND ACTIVATION 101 Leonard C. Edelstein, Srikanth Nagalla, and Paul F. Bray PART II: MICRORNAS IN INFECTIOUS DISEASE: HOST–PATHOGEN INTERACTIONS 117 8 MICRORNAS AS KEY PLAYERS IN HOST-VIRUS INTERACTIONS 119 Aurélie Fender and Sébastien Pfeffer 9 MICRORNA EXPRESSION IN AVIAN HERPESVIRUSES 137 Yongxiu Yao and Venugopal Nair 10 FUNCTION OF HUMAN CYTOMEGALOVIRUS MICRORNAS AND POTENTIAL ROLES IN LATENCY 153 Natalie L. Reynolds, Jon A. Pavelin, and Finn E. Grey 11 INVOLVEMENT OF SMALL NON-CODING RNA IN HIV-1 INFECTION 165 Guihua Sun, John J. Rossi, and Daniela Castanotto 12 MICRORNA IN MALARIA 183 Panote Prapansilp and Gareth D.H. Turner PART III: CANCER 199 13 THE MICRORNA DECALOGUE OF CANCER INVOLVEMENT 201 Tanja Kunej, Irena Godnic, Minja Zorc, Simon Horvat, and George A. Calin 14 MICRORNAS AS ONCOGENES AND TUMOR SUPPRESSORS 223 Eva E. Rufi no-Palomares, Fernando J. Reyes-Zurita, Jose Antonio Lupiáñez, and Pedro P. Medina 15 LONG NON-CODING RNAS AND THEIR ROLES IN CANCER 245 Yolanda Sánchez and Maite Huarte 16 REGULATION OF HYPOXIA RESPONSES BY MICRORNA EXPRESSION 267 Carme Camps, Adrian L. Harris, and Jiannis Ragoussis 17 CONTROL OF RECEPTOR FUNCTION BY MICRORNAS IN BREAST CANCER 287 Claudia Piovan and Marilena V. Iorio 18 MICRORNAS IN HUMAN PROSTATE CANCER: FROM PATHOGENESIS TO THERAPEUTIC IMPLICATIONS 311 Mustafa Ozen and Omer Faruk Karatas 19 MICRORNA SIGNATURES AS BIOMARKERS OF COLORECTAL CANCER 329 Katrin Pfütze, Xiaoya Luo, and Barbara Burwinkel 20 GENETIC VARIATIONS IN MICRORNA-ENCODING SEQUENCES AND MICRORNA TARGET SITES ALTER LUNG CANCER SUSCEPTIBILITY AND SURVIVAL 343 Ming Yang and Dongxin Lin 21 MICRORNA IN MYELOPOIESIS AND MYELOID DISORDERS 353 Sara E. Meyer and H. Leighton Grimes 22 MICRORNA DEREGULATION BY ABERRANT DNA METHYLATION IN ACUTE LYMPHOBLASTIC LEUKEMIA 371 Xabier Agirre and Felipe Prósper 23 ROLE OF MIRNAS IN THE PATHOGENESIS OF CHRONIC LYMPHOCYTIC LEUKEMIA 383 Veronica Balatti, Yuri Pekarsky, Lara Rizzotto, and Carlo M. Croce 24 MICRORNA IN B-CELL NON-HODGKIN’S LYMPHOMA: DIAGNOSTIC MARKERS AND THERAPEUTIC TARGETS 403 Nerea Martínez, Lorena Di Lisio, and Miguel Angel Piris 25 MICRORNAS IN DIFFUSE LARGE B-CELL LYMPHOMA 419 Izidore S. Lossos and Alvaro J. Alencar 26 THE ROLE OF MICRORNAS IN HODGKIN’S LYMPHOMA 435 Wouter Plattel, Joost Kluiver, Arjan Diepstra, Lydia Visser, and Anke van den Berg 27 MICRORNA EXPRESSION IN CUTANEOUS T-CELL LYMPHOMAS 449 Cornelis P. Tensen PART IV: HEREDITARY AND OTHER NON-INFECTIOUS DISEASES 463 28 MICRORNAS AND HEREDITARY DISORDERS 465 Matías Morín and Miguel A. Moreno-Pelayo 29 MICRORNAS AND CARDIOVASCULAR DISEASES 477 Koh Ono 30 MICRORNAS AND DIABETES 495 Romano Regazzi 31 MICRORNAS IN LIVER DISEASES 509 Patricia Munoz-Garrido, Marco Marzioni, Elizabeth Hijona, Luis Bujanda, and Jesus M. Banales 32 MICRORNA REGULATION IN MULTIPLE SCLEROSIS 523 Andreas Junker 33 THE ROLE OF MICRORNAS IN ALZHEIMER’S DISEASE 539 Shahar Barbash and Hermona Soreq 34 CURRENT VIEWS ON THE ROLE OF MICRORNAS IN PSYCHOSIS 553 Aoife Kearney, Javier A. Bravo, and Timothy G. Dinan PART V: CIRCULATING MICRORNAS AS CELLULAR MESSENGERS AND NOVEL BIOMARKERS 567 35 CIRCULATING MICRORNAS AS NON-INVASIVE BIOMARKERS 569 Heidi Schwarzenbach and Klaus Pantel 36 CIRCULATING MICRORNAS AS CELLULAR MESSENGERS 589 Kasey C. Vickers 37 RELEASE OF MICRORNA-CONTAINING VESICLES CAN STIMULATE ANGIOGENESIS AND METASTASIS IN RENAL CARCINOMA 607 Federica Collino, Cristina Grange, and Giovanni Camussi PART VI: THERAPEUTIC USES OF MICRORNAS: CURRENT PERSPECTIVES AND FUTURE DIRECTIONS 623 38 MICRORNA REGULATION OF CANCER STEM CELLS AND MICRORNAS AS POTENTIAL CANCER STEM CELL THERAPEUTICS 625 Can Liu and Dean G. Tang 39 THERAPEUTIC MODULATION OF MICRORNAS 639 Achim Aigner and Hannelore Dassow 40 LOCKED NUCLEIC ACIDS AS MICRORNA THERAPEUTICS 663 Henrik Ørum Index 673

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Book SynopsisLANDSCAPE GENETICS: CONCEPTS, METHODS, APPLICATIONS LANDSCAPE GENETICS: CONCEPTS, METHODS, APPLICATIONS Edited by Niko Balkenhol, Samuel A. Cushman, Andrew T. Storfer, Lisette P. Waits Landscape genetics is an exciting and rapidly growing field, melding methods and theory from landscape ecology and population genetics to address some of the most challenging and urgent ecological and evolutionary topics of our time. Landscape genetic approaches now enable researchers to study in detail how environmental complexity in space and time affect gene flow, genetic drift, and local adaptation. However, learning about the concepts and methods underlying the field remains challenging due to the highly interdisciplinary nature of the field, which relies on topics that have traditionally been treated separately in classes and textbooks. In this edited volume, some of the leading experts in landscape genetics provide the first comprehensive introduction to underlyinTable of ContentsList of Contributors ix Website xi Acknowledgments xiii Glossary xv 1 Introduction to Landscape Genetics – Concepts Methods Applications 1 Niko Balkenhol Samuel A. Cushman Andrew Storfer and Lisette P. Waits 1.1 Introduction 1 1.2 Defining landscape genetics 2 1.3 The three analytical steps of landscape genetics 3 1.4 The interdisciplinary challenge of landscape genetics 3 1.5 Structure of this book – concepts methods applications 5 References 6 Part 1: Concepts 2 Basics of Landscape Ecology: An Introduction to Landscapes and Population Processes for Landscape Geneticists 11 Samuel A. Cushman Brad H. McRae and Kevin McGarigal 2.1 Introduction 11 2.2 How landscapes affect population genetic processes 12 2.3 Defining the landscape for landscape genetic research 16 2.4 Defining populations and characterizing dispersal processes 21 2.5 Putting it together: combinations of landscape and population models 24 2.6 Frameworks for delineating landscapes and populations for landscape genetics 26 2.7 Current challenges and future opportunities 30 References 30 3 Basics of Population Genetics: Quantifying Neutral and Adaptive Genetic Variation for Landscape Genetic Studies 35 Lisette P. Waits and Andrew Storfer 3.1 Introduction 35 3.2 Overview of landscape influences on genetic variation 36 3.3 Overview of DNA types and molecular methods 38 3.4 Important population genetic models 41 3.5 Measuring genetic diversity 45 3.6 Evaluating genetic structure and detecting barriers 46 3.7 Estimating gene flow using indirect and direct methods 50 3.8 Conclusion and future directions 52 References 53 4 Basics of Study Design: Sampling Landscape Heterogeneity and Genetic Variation for Landscape Genetic Studies 58 Niko Balkenhol and Marie-Josée Fortin 4.1 Introduction 58 4.2 Study design terminology used in this Chapter 59 4.3 General study design considerations 60 4.4 Considerations for landscape genetic study design 61 4.5 Current knowledge about study design effects in landscape genetics 66 4.6 Recommendations for optimal sampling strategies in landscape genetics 71 4.7 Conclusions and future directions 73 References 74 5 Basics of Spatial Data Analysis: Linking Landscape and Genetic Data for Landscape Genetic Studies 77 Helene H. Wagner and Marie-Josée Fortin 5.1 Introduction 77 5.2 How to model landscape effects on genetic variation 84 5.3 How to model isolation-by-distance 93 5.4 Future directions 95 Acknowledgments 96 References 96 Part 2: Methods 6 Simulation Modeling in Landscape Genetics 101 Erin Landguth Samuel A. Cushman and Niko Balkenhol 6.1 Introduction 101 6.2 A brief overview of models and simulations 101 6.3 General benefits of simulation modeling 102 6.4 Landscape genetic simulation modeling 103 6.5 Examples of simulation modeling in landscape genetics 104 6.6 Designing and choosing landscape genetic simulation models 108 6.7 The future of landscape genetic simulation modeling 111 References 111 7 Clustering and Assignment Methods In Landscape Genetics 114 Olivier François and Lisette P. Waits 7.1 Introduction 114 7.2 Exploratory data analysis and model-based clustering for population structure analysis 115 7.3 Spatially explicit methods in landscape genetics 119 7.4 Spatial EDA methods: spatial PCA and spatial factor analysis 119 7.5 Spatial MBC methods 120 7.6 Habitat and environmental heterogeneity models 121 7.7 Discussion 123 References 125 8 Resistance Surface Modeling in Landscape Genetics 129 Stephen F. Spear Samuel A. Cushman and Brad H. McRae 8.1 Introduction 129 8.2 Techniques for parameterizing resistance surfaces 133 8.3 Estimating connectivity from resistance surfaces 137 8.4 Statistical validation of resistance surfaces 139 8.5 The future of the resistance surface in landscape genetics 142 8.6 Conclusions 144 References 144 9 Genomic Approaches in Landscape Genetics 149 Andrew Storfer Michael F. Antolin Stéphanie Manel Bryan K. Epperson and Kim T. Scribner 9.1 Introduction 149 9.2 Current landscape genomics methods 150 9.3 General challenges in landscape genomics 157 9.4 Spatial autocorrelation 157 9.5 Applications of landscape genomics to climate change 159 References 160 10 Graph Theory and Network Models In Landscape Genetics 165 Melanie Murphy Rodney Dyer and Samuel A. Cushman 10.1 Introduction 165 10.2 Background on graph theory 167 10.3 Landscape genetic applications 170 10.4 Recommendations for using graph approaches in landscape genetics 175 10.5 Current research needs 176 10.6 Conclusion – potential for application of graphs for conservation 176 References 177 Part 3: Applications 11 Landscapes and Plant Population Genetics 183 Rodney J. Dyer 11.1 Introduction 183 11.2 Contemporary population genetic processes 186 11.3 Historical population genetic processes 190 11.4 Future research 192 References 194 12 Applications of Landscape Genetics to Connectivity Research In Terrestrial Animals 199 Lisette P. Waits Samuel A. Cushman and Steve F. Spear 12.1 Introduction 199 12.2 General overview of terrestrial animal study systems and research challenges 199 12.3 Detecting barriers and defining corridors 202 12.4 Evaluating population dynamics 205 12.5 Detecting and predicting the response to landscape change 206 12.6 Common limitations of landscape genetic studies involving terrestrial animals 208 12.7 Testing ecological hypotheses about gene flow in heterogeneous landscapes 208 12.8 Knowledge gaps and future directions 213 References 214 13 Waterscape Genetics – Applications of Landscape Genetics To Rivers Lakes and Seas 220 Kimberly A. Selkoe Kim T. Scribner and Heather M. Galindo 13.1 Introduction 220 13.2 Understanding marine and freshwater environments 223 13.3 Typical research questions and approaches 229 13.4 Applications of landscape genetic approaches 234 13.5 Future directions: knowledge gaps research challenges and limitations 237 Acknowledgments 238 References 238 14 Current Status Future Opportunities and Remaining Challenges in Landscape Genetics 247 Niko Balkenhol Samuel A. Cushman Lisette P. Waits and Andrew Storfer 14.1 Introduction 247 14.2 Conclusion 1: issues of scale need to be considered 248 14.3 Conclusion 2: sampling needs to specifically target landscape genetic questions 248 14.4 Conclusion 3: choice of appropriate statistical methods remains challenging 249 14.5 Conclusion 4: simulations play a key role in landscape genetics 249 14.6 Conclusion 5: measures of genetic variation are rarely developed specifically for landscape genetics 249 14.7 Conclusion 6: landscape resistance is just one of the possible landscape–genetic relationships 250 14.8 Conclusion 7: genomics provides novel opportunities but also creates new challenges 250 14.9 Conclusion 8: the scope of landscape genetics needs to expand 251 14.10 Conclusion 9: specific hypotheses are rarely stated in current landscape genetic studies 251 14.11 Conclusion 10: a comprehensive theory for landscape genetics is currently missing 252 14.12 The future of landscape genetics 252 References 253 Index 257

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

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

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

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Book SynopsisPerform genome analysis and sequencing of data with Amazon Web Services Genomics in the AWS Cloud: Analyzing Genetic Code Using Amazon Web Services enables a person who has moderate familiarity with AWS Cloud to perform full genome analysis and research. Using the information in this book, you''ll be able to take a FASTQ file containing raw data from a lab or a BAM file from a service provider and perform genome analysis on it. You''ll also be able to identify potentially pathogenic gene sequences. Get an introduction to Whole Genome Sequencing (WGS) Make sense of WGS on AWS Master AWS services for genome analysis Some key advantages of using AWS for genomic analysis is to help researchers utilize a wide choice of compute services that can process diverse datasets in analysis pipelines. Genomic sequencers that generate raw data files are located in labs on premises and AWS provides solutions to make it easy for customTable of ContentsIntroduction xix Chapter 1 Why Do Genome Analysis Yourself When Commercial Offerings Exist? 1 Chapter 2 A Crash Course in Molecular Biology 9 Chapter 3 Obtaining Your Genome 25 Chapter 4 The Bioinformatics Workflow 39 Chapter 5 AWS Services for Genome Analysis 59 Chapter 6 Building Your Environment in the AWS Cloud 77 Chapter 7 Linux and AWS Command-Line Basics for Genomics 115 Chapter 8 Processing the Sequencing Data 143 Chapter 9 Visualizing the Genome 211 Chapter 10 Containerizing Your Workflow on the Desktop 235 Chapter 11 Variants and Applications 249 Chapter 12 Cancer Genomics 267 Index 291

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Book SynopsisEdited and written by leading researchers from around the world, The Ecological Genomics of Fungi covers a broad diversity of fungal systems and provides unique insight into the functions of those fungi in various ecosystems, from soil, to plant, to human.Trade Review“I think the volume may succeed in its ambition to serve as a catalyst for further studies by showing researchers venturing into ecological genomics and those already in genomics the width of the field. This may, in turn, further more integrative studies that will benefit our understanding of fungi.” (The Quarterly Review of Biology, 1 October 2015) Table of ContentsContributors vii Preface xiii Section 1 Sequencing Fungal Genomes 1 1 A Changing Landscape of Fungal Genomics 3 Igor V. Grigoriev 2 Repeated Elements in Filamentous Fungi with a Focus on Wood-Decay Fungi 21 Claude Murat, Thibaut Payen, Denis Petitpierre, and Jessy Labbé Section 2 Saprotrophic Fungi 41 3 Wood Decay 43 Dan Cullen 4 Aspergilli and Biomass-Degrading Fungi 63 Isabelle Benoit, Ronald P. de Vries, Scott E. Baker, and Sue A. Karagiosis 5 Ecological Genomics of Trichoderma 89 Irina S. Druzhinina and Christian P. Kubicek Section 3 Plant-Interacting Fungi 117 6 Dothideomycetes: Plant Pathogens, Saprobes, and Extremophiles 119 Stephen B. Goodwin 7 Biotrophic Fungi (Powdery Mildews, Rusts, and Smuts) 149 Sébastien Duplessis, Pietro D. Spanu, and Jan Schirawski 8 The Mycorrhizal Symbiosis Genomics 169 Francis Martin and Annegret Kohler 9 Lichen Genomics: Prospects and Progress 191 Martin Grube, Gabriele Berg, ólafur S. Andrésson, Oddur Vilhelmsson, Paul S. Dyer, and Vivian P.W. Miao Section 4 Animal-Interacting Fungi 213 10 Ecogenomics of Human and Animal Basidiomycetous Yeast Pathogens 215 Sheng Sun, Ferry Hagen, Jun Xu, Tom Dawson, Joseph Heitman, James Kronstad, Charles Saunders, and Teun Boekhout 11 Genomics of Entomopathogenic Fungi 243 Chengshu Wang and Raymond J. St. Leger 12 Ecological Genomics of the Microsporidia 261 Nicolas Corradi and Patrick J. Keeling Section 5 Metagenomics and Biogeography of Fungi 279 13 Metagenomics for Study of Fungal Ecology 281 Björn D. Lindahl and Cheryl R. Kuske 14 Metatranscriptomics of Soil Eukaryotic Communities 305 Laurence Fraissinet-Tachet, Roland Marmeisse, Lucie Zinger, and Patricia Luis 15 Fungi in Deep-Sea Environments and Metagenomics 325 Stéphane Mahé, Vanessa Rédou, Thomas Le Calvez, Philippe Vandenkoornhuyse, and Gaëtan Burgaud 16 The Biodiversity, Ecology, and Biogeography of Ascomycetous Yeasts 355 Marc-André Lachance Index 371

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Book SynopsisPlant Genes, Genomes and Genetics provides a comprehensive treatment of all aspects of plant gene expression. Unique in explaining the subject from a plant perspective, it highlights the importance of key processes, many first discovered in plants, that impact how plants develop and interact with the environment.Table of ContentsAcknowledgements xi Introduction xiii About the Companion Website xix PART I: PLANT GENOMES AND GENES Chapter 1 Plant genetic material 3 1.1 DNA is the genetic material of all living organisms, including plants 3 1.2 The plant cell contains three independent genomes 8 1.3 A gene is a complete set of instructions for building an RNA molecule 10 1.4 Genes include coding sequences and regulatory sequences 11 1.5 Nuclear genome size in plants is variable but the numbers of protein-coding, non-transposable element genes are roughly the same 12 1.6 Genomic DNA is packaged in chromosomes 15 1.7 Summary 15 1.8 Problems 15 References 16 Chapter 2 The shifting genomic landscape 17 2.1 The genomes of individual plants can differ in many ways 17 2.2 Differences in sequences between plants provide clues about gene function 20 2.3 SNPs and lengthmutations in simple sequence repeats are useful tools for genome mapping and marker assisted selection 22 2.4 Genome size and chromosome number are variable 28 2.5 Segments of DNA are often duplicated and can recombine 30 2.6 Some genes are copied nearby in the genome 31 2.7 Whole genome duplications are common in plants 34 2.8 Whole genome duplication has many effects on the genome and on gene function 37 2.9 Summary 41 2.10 Problems 42 Further reading 42 References 42 Chapter 3 Transposable elements 45 3.1 Transposable elements are common in genomes of all organisms 45 3.2 Retrotransposons are mainly responsible for increases in genome size 46 3.3 DNA transposons create small mutations when they insert and excise 52 3.4 Transposable elements move genes and change their regulation 57 3.5 How are transposable elements controlled? 60 3.6 Summary 60 3.7 Problems 61 References 61 Chapter 4 Chromatin, centromeres and telomeres 63 4.1 Chromosomes are made up of chromatin, a complex of DNA and protein 63 4.2 Telomeres make up the ends of chromosomes 66 4.3 The chromosome middles–centromeres 71 4.4 Summary 77 4.5 Problems 77 Further reading 77 References 77 Chapter 5 Genomes of organelles 79 5.1 Plastids and mitochondria are descendants of free-living bacteria 79 5.2 Organellar genes have been transferred to the nuclear genome 80 5.3 Organellar genes sometimes include introns 82 5.4 Organellar mRNA is often edited 82 5.5 Mitochondrial genomes contain fewer genes than chloroplasts 84 5.6 Plant mitochondrial genomes are large and undergo frequent recombination 87 5.7 All plastid genomes in a cell are identical 91 5.8 Plastid genomes are similar among land plants but contain some structural rearrangements 93 5.9 Summary 95 5.10 Problems 95 Further reading 95 References 95 PART II: TRANSCRIBING PLANT GENES Chapter 6 RNA 99 6.1 RNA links components of the Central Dogma 99 6.2 Structure provides RNA with unique properties 102 6.3 RNA has multiple regulatory activities 105 6.4 Summary 108 6.5 Problems 108 References 109 Chapter 7 The plant RNA polymerases 111 7.1 Transcription makes RNA from DNA 111 7.2 Varying numbers of RNA polymerases in the different kingdoms 112 7.3 RNA polymerase I transcribes rRNAs 114 7.4 RNA polymerase III recruitment to upstream and internal promoters 116 7.5 Plant-specific RNP-IV and RNP-V participate in transcriptional gene silencing 117 7.6 Organelles have their own set of RNA polymerases 117 7.7 Summary 118 7.8 Problems 118 References 118 Chapter 8 Making mRNAs – Control of transcription by RNA polymerase II 121 8.1 RNA polymerase II transcribes protein-coding genes 121 8.2 The structure of RNA polymerase II reveals how it functions 121 8.3 The core promoter 123 8.4 Initiation of transcription 125 8.5 The mediator complex 127 8.6 Transcription elongation: the role of RNP-II phosphorylation 128 8.7 RNP-II pausing and termination 129 8.8 Transcription re-initiation 130 8.9 Summary 130 8.10 Problems 130 References 130 Chapter 9 Transcription factors interpret cis-regulatory information 133 9.1 Information on when, where and how much a gene is expressed is codified by the gene’s regulatory regions 133 9.2 Identifying regulatory regions requires the use of reporter genes 134 9.3 Gene regulatory regions have a modular structure 135 9.4 Enhancers: Cis-regulatory elements or modules that function at a distance 137 9.5 Transcription factors interpret the gene regulatory code 138 9.6 Transcription factors can be classified in families 138 9.7 How transcription factors bind DNA 139 9.8 Modular structure of transcription factors 143 9.9 Organization of transcription factors into gene regulatory grids and networks 146 9.10 Summary 146 9.11 Problems 146 More challenging problems 147 References 147 Chapter 10 Control of transcription factor activity 149 10.1 Transcription factor phosphorylation 149 10.2 Protein–protein interactions 151 10.3 Preventing transcription factors from access to the nucleus 155 10.4 Movement of transcription factors between cells 156 10.5 Summary 158 10.6 Problems 158 References 158 Chapter 11 Small RNAs 161 11.1 The phenomenon of cosuppression or gene silencing 161 11.2 Discovery of small RNAs 162 11.3 Pathways for miRNA formation and function 163 11.4 Plant siRNAs originate from different types of double-stranded RNAs 166 11.5 Intercellular and systemic movement of small RNAs 168 11.6 Role of miRNAs in plant physiology and development 170 11.7 Summary 171 11.8 Problems 171 References 172 Chapter 12 Chromatin and gene expression 173 12.1 Packing long DNA molecules in a small space: the function of chromatin 173 12.2 Heterochromatin and euchromatin 173 12.3 Histone modifications 174 12.4 Histone modifications affect gene expression 175 12.5 Introducing and removing histone marks: writers and erasers 175 12.6 ‘Readers’ recognize histone modifications 177 12.7 Nucleosome positioning 177 12.8 DNA methylation 178 12.9 RNA-directed DNA methylation 179 12.10 Control of flowering by histone modifications 180 12.11 Summary 181 12.12 Problems 181 References 181 PART III: FROM RNA TO PROTEINS Chapter 13 RNA processing and transport 185 13.1 RNA processing can be thought of as steps 185 13.2 RNA capping provides a distinctive 5’ end to mRNAs 185 13.3 Transcription termination consists of mRNA 3’-end formation and polyadenylation 189 13.4 RNA splicing is another major source of genetic variation 192 13.5 Export of mRNA from the nucleus is a gateway for regulating which mRNAs actually get translated 194 13.6 Summary 196 13.7 Problems 196 References 196 Chapter 14 Fate of RNA 199 14.1 Regulation of RNA continues upon export from nucleus 199 14.2 Mechanisms for RNA turnover 199 14.3 RNA surveillance mechanisms 201 14.4 RNA sorting 202 14.5 RNA movement 203 14.6 Summary 204 14.7 Problems 204 Further reading 205 References 205 Chapter 15 Translation of RNA 207 15.1 Translation: a key aspect of gene expression 207 15.2 Initiation 209 15.3 Elongation 209 15.4 Termination 210 15.5 Tools for studying the regulation of translation 211 15.6 Specific translational control mechanisms 211 15.7 Summary 213 15.8 Problems 214 Further reading 214 References 214 Chapter 16 Protein folding and transport 215 16.1 The pathway to a protein’s function is a complicated matter 215 16.2 Protein folding and assembly 215 16.3 Protein targeting 218 16.4 Co-translational targeting 218 16.5 Post-translational targeting 219 16.6 Post-translational modifications regulating function 220 16.7 Summary 222 16.8 Problems 223 Further reading 223 References 224 Chapter 17 Protein degradation 225 17.1 Two sides of gene expression–synthesis and degradation 225 17.2 Autophagy, senescence and programmed cell death 225 17.3 Protein-tagging mechanisms 226 17.4 The ubiquitin proteasome system rivals gene transcription 228 17.5 Summary 231 17.6 Problems 231 Further reading 231 Reference 231 Index 233

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Book SynopsisEcological Genetics addresses the fundamental problems of which of the many molecular markers should be used and how the resulting data should be analysed in clear, accessible language, suitable for upper--level undergraduates through to research--level professionals.Trade ReviewMolecular ecologists finally have a text-book that deals with their discipline. Ecological Genetics fills the market-gap between general accounts of evolutionary biology and specialist texts focusing on individual research topics. The authors have brought together a useful mix of theory, practical approaches, conceptual issues, and individual case studies to provide a balanced and accessible overview of the field. Peter Hollingsworth, Royal Botanic Garden "This book is a pleasure to read: it is clearly written, well organized and leaves no ambiguity." Andre A Dhondt, Cornell University, Trends in Ecology and Evolution, August 2004 "This book is a well-written, comprehensive overview of the essential techniques underlying ecological genetics. I would certainly recommend it to any new student undertaking postgraduate study in the field of molecular ecology." Dr. Jim Provan, Queen's University BelfastTable of ContentsPreface vii Abbreviations x 1 Ecological genetics 1 Summary 1 1.1 What is ecological genetics? 1 1.2 Why study ecological genetics? 3 References 4 2 Markers and sampling in ecological genetics 6 Summary 6 2.1 Introduction 6 2.2 Methods of data generation 7 2.3 Principles of sampling 15 2.4Practice 20 2.5 Within-population sampling 22 2.6 Among-population sampling 34 2.7 Power analysis 34 2.8 Further reading 35 Essential methods information 36 References 45 3 Genetic diversity and differentiation 52 Summary 52 3.1 Introduction 52 3.2 Factors influencing diversity and differentiation 53 3.3 The Hardy–Weinberg equilibrium 58 3.4Genetic diversity 62 3.5 Genetic differentiation 69 3.6 Genetic distance 81 3.7 Statistical approaches 86 3.8 Use of genetic diversity statistics 89 3.9 Concluding remarks 100 3.10 Further reading 100 References 100 4 Gene flow and mating system 106 Summary 106 4.1 Introduction 106 4.2 Factors governing gene flow 107 4.3 Considerations for measuring gene flow 115 4.4 Measuring gene flow – indirect estimates 122 4.5 Measuring gene flow – direct estimates 134 4.6 The importance of biological and environmental factors on gene flow 143 References 145 5 Intraspecific phylogenies and phylogeography 150 Summary 150 5.1 Introduction 150 5.2 Homology, gene trees, and species trees 157 5.3 Tree form and building 159 5.4Tree interpretation 170 5.5 Organelle versus nuclear intraspecific phylogenies 179 5.6 Further reading 180 Essential methods information 181 References 185 6 Speciation and hybridization 189 Summary 189 6.1 Introduction 189 6.2 Species 190 6.3 Speciation 194 6.4 Hybridization 204 6.5 Analysis of speciation and hybridization 206 6.6 Future developments 233 6.7 Further reading 233 References 233 7 Case studies in ecological genetics: Lycaenid butterflies, ragworts, bears, and oaks 243 Summary 243 7.1 Introduction 244 7.2 Lycaenid butterflies 244 7.3 European ragworts 257 7.4Brown bears 265 7.5 European oaks 274 References 292 Appendix A: Data analysis software 300 Appendix B: Which distance algorithm should be used and when? 306 Glossary 313 Index 320

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Book SynopsisWith the first draft of the human genome project in the public domain and full analyses of model genomes now available, the subject matter of ''Principles of Genome Analysis and Genomics'' is even ''hotter'' now than when the first two editions were published in 1995 and 1998. In the new edition of this very practical guide to the different techniques and theory behind genomes and genome analysis, Sandy Primrose and new author Richard Twyman provide a fresh look at this topic. In the light of recent exciting advancements in the field, the authors have completely revised and rewritten many parts of the new edition with the addition of five new chapters. Aimed at upper level students, it is essential that in this extremely fast moving topic area the text is up to date and relevant. Completely revised new edition of an established textbook. Features new chapters and examples from exciting new research in genomics, including the human genome project. ExcelTrade Review"...an excellent distillation of current knowledge...The book is clearly written, well presented, and feels good. Recommended." Neil Stoker, Royal Veterninary College, London, Microbiology Today, Vol 30, November 2003 "There is no doubt that this book is a very useful source of information, for students and teachers alike. In spite of its dense text, it makes good reading and will help to reduce the general bewilderment induced by the rapid pace of technological and conceptual innovation in biology." Leon Otten, Plant Molecular Biology Institute, Plant Science, 2003. Principles of Genome Analysis and Genomics, 3rd edition, is "very good indeed and deserves to be a widely popular resource for newcomers to genome analysis." J.Armour, University of Nottingham, Heredity, June 2004 Table of ContentsPreface. Abbreviations. 1. Setting The Scene: The New Science Of Genomics. 2. The Organization And Structure Of Genomes. 3. Subdividing The Genome. 4. Assembling A Physical Map Of The Genome. 5. Sequencing Methods And Strategies. 6. Genome Annotation And Bioinformatics. 7. Comparative Genomics. 8. Protein Structural Genomics. 9. Global Expression Profiling. 10. Comprehensive Mutant Libraries. 11. Mapping Protein Interactions. 12. Applications Of Genome Analysis And Genomics. References. Index

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Book SynopsisMechanisms in Transcriptional Regulation provides a concise discussion of the fundamental concepts in transcription and its regulation.Table of ContentsList of boxes. Preface. Acknowledgments. 1 The vocabulary of transcription. 1.1 Introduction 1. 1.2 The vocabulary of transcription. 1.2.1 RNA biogenesis. 1.2.2 The transcriptional machinery. 1.2.3 Cis-elements. 1.3 Evolutionarily conserved mechanisms of transcription. 1.3.1 Conservation across the three domains of life. 1.3.2 Model eukaryotic organisms (and a plug for genetics). 1.4 What’s coming up. Problems. Further reading. 2 RNA polymerases and the transcription cycle. 2.1 Introduction. 2.2 Core RNA polymerases. 2.2.1 Bacterial core polymerases. 2.2.2 Eukaryotic and archaeal core polymerases. 2.3 Transcriptional elongation. 2.3.1 Phosphoester linkage formation. 2.3.2 Features of the ternary elongation complex. 2.3.3 RNA polymerase as a motor. 2.3.4 Elongation factors and backtracking. 2.4 Transcriptional initiation. 2.4.1 Distinct mechanisms for promoter recognition in bacteria and eukaryotes. 2.4.2 Bacterial σ factors and promoter specificity. 2.5 Transcriptional termination. 2.5.1 Why terminate?. 2.5.2 Termination in bacteria. 2.5.3 Termination in eukaryotes. 2.6 Summary. Problems. Further reading. 3 The eukaryotic basal machinery. 3.1 Introduction. 3.2 The class II core promoter. 3.3 The catalog of factors. 3.4 Pathway to the preinitiation complex. 3.5 Promoter recognition and nucleation of the PIC by TFIID. 3.5.1 TATA box recognition by TBP. 3.5.2 TBP-associated factors and their function in TFIID. 3.6 TFIIB: a functional analog of bacterial σ factors. 3.6.1 TFIIB as a bridge between the promoter and polymerase. 3.6.2 BRF, a TFIIB paralog in the class III machinery,and promoter melting. 3.6.3 Functional similarity between TFIIB family proteins and σ. 3.7 TFIIH in promoter opening and promoter clearance. 3.7.1 A unique DNA helicase requirement for class II promoter opening. 3.7.2 A connection between DNA repair and transcription. 3.7.3 TFIIH and RNA polymerase II phosphorylation. 3.8 Summary. Problems. Further reading. 4 Mechanisms of transcriptional activation. 4.1 Introduction. 4.2 Paradigms from E. coli. 4.2.1 CRP: a sensor of the nutritional environment. 4.2.2 λcI: regulator of the lysis/lysogeny switch. 4.2.3 Sequence-specific DNA recognition: the helix-turn-helix motif. 4.2.4 Dimerization. 4.2.5 Multiple targets for activators in the transcriptional machinery. 4.2.6 How do activator–RNA polymerase contacts activate promoters?. 4.3 Eukaryotic activators and their targets. 4.3.1 The modular nature of eukaryotic activators. 4.3.2 The Mediator: a special activator target in the eukaryotic transcriptional machinery. 4.3.3 Release of Pol II from a paused state as a mechanism of activation. 4.4 Summary. Problems. Further reading. 5 Transcriptional control through the modification of chromatin structure. 5.1 Introduction. 5.2 Chromatin structure. 5.2.1 The nucleosome. 5.2.2 Higher order chromatin structure. 5.2.3 Euchromatin and heterochromatin. 5.3 Histone modification. 5.3.1 Lysine acetylation: diverse roles in gene activation. 5.3.2 Lysine methylation: a chemically stable histone mark. 5.3.3 Cross talk between histone marks. 5.4 ATP-dependent chromatin remodeling enzymes. 5.4.1 A diverse family of chromatin remodeling complexes. 5.4.2 ATP-fueled motors for increasing DNA accessibility. 5.4.3 Targeting of chromatin remodeling complexes. 5.5 Protein motifs that recognize modified histones. 5.5.1 Chromodomains. 5.5.2 Bromodomains. 5.6 Coordination of activator–coactivator interactions. 5.7 Summary. Problems. Further reading. 6 Epigenetic control of transcription. 6.1 Introduction. 6.1.1 Common themes in epigenetics: a central role for histone methylation. 6.2 Heterochromatic silencing. 6.2.1 Chromosomal inheritance of the silent state. 6.2.2 Histone methylation and maintenance of the silent state. 6.2.3 Initiation of heterochromatic silencing. 6.2.4 Evolutionary conservation of mechanisms for heterochromatic silencing. 6.2.5 DNA methylation and heterochromatin. 6.2.6 A distinct mechanism for heterochromatic silencing in budding yeast. 6.3 Epigenetic control by Polycomb and Trithorax group proteins. 6.3.1 Combinatorial control of segment identity. 6.3.2 Establishment and maintenance phases of homeotic gene expression. 6.3.3 Parallels between heterochromatic and PcG silencing. 6.3.4 Maintenance of the active state by TrxG. 6.3.5 A model for the epigenetic regulation of homeoticgene activity. 6.4 X chromosome inactivation: parallels to heterochromatic and Polycomb group silencing. 6.4.1 Random inactivation of the X chromosome. 6.4.2 Cis-acting RNA in X inactivation. 6.4.3 Histone modifications characteristic of both heterochromatic and PcG silencing on Xi. 6.5 Summary. Problems. Further reading. 7 Combinatorial control in development and signal transduction. 7.1 Introduction. 7.2 Synergy and antagonism. 7.2.1 Integration of regulatory inputs by cis-regulatory modules. 7.2.2 The “AND” and “NOT” operators. 7.3 Synergy and the enhanceosome. 7.3.1 Enhanceosome assembly and architectural factors. 7.3.2 Cooperative recruitment of coactivators by enhanceosomes. 7.3.3 Sequential coactivator recruitment. 7.4 Antagonism and stripe formation. 7.4.1 Developmental regulatory networks. 7.4.2 Short-range repression and stripe formation. 7.5 Antagonism and the signal-mediated switch. 7.5.1 Nuclear receptors: antagonism between coregulators. 7.5.2 Receptor tyrosine kinase pathways: competition for a common DNA element. 7.6 Summary. Problems. Further reading. Answers to problems. Glossary. Index. Color plate section

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Book SynopsisThis guide covers aspects of designing microarray experiments and analysing the data generated, including information on some of the tools that are available from non-commercial sources. Concepts and principles underpinning gene expression analysis are emphasised and wherever possible, the mathematics has been simplified. The guide is intended for use by graduates and researchers in bioinformatics and the life sciences and is also suitable for statisticians who are interested in the approaches currently used to study gene expression. Microarrays are an automated way of carrying out thousands of experiments at once, and allows scientists to obtain huge amounts of information very quickly Short, concise text on this difficult topic area Clear illustrations throughout Written by well-known teachers in the subject Provides insight into how to analyse the data produced from microarrays Trade Review"Quite a few recently published books discuss analysis of microarray gene expression data for beginners. Microarray Gene Expression Data Analysis ... is arguably the best of its kind in this regard." Terry Speed, The Walter & Eliza Hall Institute of Medical Research, Nature Cell Biology, December 2003 "Overall this is an excellent book, it is well referenced and, to my mind, covers the vast majority of issues an experimenter needs to consider when venturing into the world of microarray data analysis. The book fills a clear gap in the field, providing a rigorous overview of the often confusing .... data analysis issues that most books on microarrays avoid or treat in a cursory way. I would say it is essential reading for any laboratory or researcher active in this rapidly evolving field and is recommended for the mathematician or statisitican who is interested in the field or who has been persuaded by their biologist colleague to help them with their analysis." Steven Russell, University of Cambridge, Genetical Research, February 2003 "Anyone wishing to gain a basic understanding of microarray gene expression studies will come away enriched ... A good and accessible entry point for any biologist who is interested in getting an overview about how to perform microarray gene expression studies." D.C.Jamison, George Mason University, Heredity, June 2004Table of ContentsPreface. Acknowledgements. Part I: Introduction:. 1. What Are Microarrays?. 2. Use Of Icroarrays To Monitor Gene Expression. 3. Other Uses For Microarrays. 4. Challenges Associated With The Generation Of Large Amounts Of Complex Data. 5. Future Directions. Part II: Aspects Of Experimental Design:. 6. Features Of Microarray Data. 7. Designing The Best Experiment. 8. Preparation of Target. 9. Design of Spotted Arrays. 10. Hybridisation. 11. Long Term Considerations. 12. Verification of Results. Part III: Data Analysis:. 13. Preliminary Processing of Data. 14. Methods for Data Analysis. 15. Graph Models. 16. Software In The Public Domain. 17. Visualisation of Data. Part IV: Glossary:. Index. Colour plates fall between pp. 84 and 85.

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Book SynopsisA study of the multifaceted dimensions of the genetic revolution and its philosophical, ethical, social and political significance. It includes 33 essays, written by prominent figures in the field.Trade Review“The editors are to be congratulated on compiling such a stimulating and provocative volume. This is for those who wish to examine the basis of human bioethics thoroughly, whether they be novice or expert. Those who think they have clear attitudes to many of the ethical and social issues raised by developments in human genetics are likely to be forced to rethink at least some of their positions by the challenging and well-presented arguments that have been gathered together here." Angus Clarke, University of Wales "This timely book makes clear that genetic research will transform healthcare, choices about children, and standards of property. The contributors here stake out key questions facing health professionals and social policy makers, and they have insightful things to say about how we should go about answering those questions." Timothy F. Murphy, University of IllinoisCollege of Medicine at Chicago " ... Genethics makes some important contributions, offering a primer on key aspects of contemporary genetics before focusing on some of the most important ethical, legal, economic, political issues facing researchers, politicians, and, to some extent, the general population ... The book's strengths are its multidisciplinary approach, the overall quality of its contributions, and the refusal of most contributors to oversimplify and risk the microdeterminism of many popular essays." ChoiceTable of ContentsList of Contributors. Acknowledgements. Introduction : Justine Burley (University of Manchester and Exeter College, Oxford) and John Harris (University of Manchester). 1. Stem cells: C.N. Svendsen (University of Cambridge). 2. Gene therapy for neurological disorders: P.R. Lowenstein (Gene Therapeutics Institute). 3. Cloning in biology and medicine: Ian Wilmut (Roslin Institute)Genetics of old age: Thomas B.L. Kirkwood (University of Newcastle). 4. The ethical legacy of Nazi medical war crimes: Paul Weindling (Oxford Bookes University). 5. Biotechnology and animals: Bernard E. Rollin (Colorado State University). 6. The role of informed consent in genetic experimentation: SørenHolm (University of Oslo). 7. Testing children and adolescents: Dorothy Wertz (University of Massachusetts). 8. Genetic testing of children: Lainie Friedman Ross (University of Chicago). 9. Mapping the human genome and "Monster Mythology": George J. Annas (Boston University). 10. The moral status of the gene: Mary Anne Warren (San Francisco State University). 11. The ethical use of human embryonic stem cells in research and therapy: John Harris (University of Manchester). 12. Preimplantation genetic diagnosis and embryo selection: Bonnie Steinbock (State University of New York at Albany). 13. Individual autonomy and genetic choice: Matthew Clayton (Brunel University). 14. Cloning and public policy: Ruth Macklin (Albert Einstein College of Medicine). 15. Sex-selection: The feminist response: Diemut Bubeck (London School of Economics). 16. Creating perfect people: Philip Kitcher (Columbia University). 17. Genetics and personal identity: Carol Rovane (Columbia University). 18. Genetic determinism and gene selection: Richard Dawkins (University of Oxford and New College). 19. The "Darwin Wars" and the human self image: Janet Radcliffe Richards (University College London. 20. Religion and Gene Therapy: Gerald McKenny (Rice University). 21. ‘Race', genetics and human difference: Hussein Kassim (University of London). 22. Self-ownership, begetting and germ-line information: Hillel Steiner (University of Manchester). 23. Justice, genetics and lifestyles: Inez de Beaufort (Erasmus University). 24. Commercial exploitation of the human genome: Ruth Chadwick (Lancaster University) and Adam Hedgecoe (University College London). 25. Forensic DNA typing: David Wasserman (University of Maryland). 26. Privacy and genetics: Madison Powers (Georgetown University). 27. DNA banking: Bartha Maria Knoppers (University of Montreal). 28. Genetic difference in the workplace: Michael Yesley (Los Alamos National Laboratory). 29. The insurance market and discriminatory practices: Tom Sorell (University of Ethics). 30. Legal and ethical issues in biotechnology patenting: Pilar Ossorio (American Medical Association. 31. Patented genes: Mark Sagoff (University of Maryland, College Park). 32. Property, patents, and genetic material: Stephen Munzer (University of California, Los Angeles). 33. Genetic screening from a public health perspective: Scott Burris (Temple University) and Lawrence Gostin (Georgetown University). Afterword: Sir David Weatherall (University of Oxford). Index

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Book SynopsisThe Handbook of Developmental Science, Behavior, and Genetics brings together the cutting-edge theory, research and methodology that contribute to our current scientific understanding of the role of genetics in the developmental system.Table of ContentsFOREWORD. Gilbert Gottlieb and the Developmental Point of View (Evelyn Fox Keller, Massachusetts Institute of Technology). I. INTRODUCTION. 1. Developmental Systems, Nature-Nurture, and the Role of Genes in Behavior and Development: On the Legacy of Gilbert Gottlieb (Kathryn E. Hood, The Pennsylvania State University, Carolyn Tucker Halpern, University of North Carolina at Chapel Hill, Gary Greenberg, Wichita State University, Richard M. Lerner, Tufts University). 2. Normally Occurring Environmental and Behavioral Influences on Gene Activity: From Central Dogma to Probabilistic Epigenesis (Gilbert Gottlieb). II. THEORETICAL FOUNDATIONS FOR THE DEVELOPMENTAL STUDY OF BEHAVIOR AND GENETICS. 3. Historical and Philosophical Perspectives on Behavioral Genetics and Developmental Science (James Tabery, University of Utah, Paul E. Griffiths, University of Sydney). 4. Development and Evolution Revisited (Mae Wan Ho, Institute of Science in Society). 5. Probabilistic Epigenesis and Modern Behavioral and Neural Genetics (Douglas Wahlsten, University of North Carolina at Greensboro). 6. The Roles of Environment, Experience, and Learning in Behavioral Development (George F. Michel, University of North Carolina at Greensboro). 7. Contemporary Ideas in Physics and Biology in Gottlieb’s Psychology (Ty Partridge, Wayne State University, Gary Greenberg, Wichita State University). III. EMPIRICAL STUDIES OF BEHAVIORAL DEVELOPMENT AND GENETICS. 8. Behavioral Development during the Mother-Young Interaction in Placental Mammals: The Development of Behavior in the Relationship with the Mother (Jay S. Rosenblatt, Institute of Animal Behavior, Rutgers). 9. Amniotic Fluid as an Extended Milieu Interieur (Scott R. Robinson, University of Iowa, Valerie Méndez-Gallardo, University of Iowa). 10. Developmental Effects of Selective Breeding for an Infant Trait (Susan A. Brunelli, Columbia University Medical Center, Betty Zimmerberg, Williams College, Myron A. Hofer, Columbia University Medical Center). 11. Emergence and Constraint in Novel Behavioral Adaptations (Kathryn E. Hood, The Pennsylvania State University). 12. Nonhuman Primate Research Contributions to Understanding Genetic and Environmental Influences on Phenotypic Outcomes across Development (Allyson Bennett and Peter J. Pierre, Wake Forest University). 13. Interactive Contributions of Genes and Early Experience to Behavioural Development: Sensitive Periods and Lateralized Brain and Behaviour (Lesley J. Rogers, University of New England, Armidale). 14. Trans-Generational Epigenetic Inheritance (Lawrence V. Harper, University of California, Davis). 15. The Significance of Non-Replication of Gene-Phenotype Associations (Carolyn Tucker Halpern, University of North Carolina at Chapel Hill). 16. Canalization and Malleability Reconsidered: The Developmental Basis of Phenotypic Stability and Variability (Robert Lickliter and Christopher Harshaw, Florida International University). IV. APPLICATIONS TO DEVELOPMENT. 17. Gene-Parenting Interplay in the Development of Infant Emotionality (Cathi B. Propper, The University of North Carolina at Chapel Hill, Ginger A. Moore, The Pennsylvania State University, W. Roger Mills-Koonce, The University of North Carolina at Chapel Hill). 18. Genetic Research in Psychiatry and Psychology: A Critical Overview (Jay Joseph, Licensed Psychologist). 19. On the Limits of Standard Quantitative Genetic Modeling of Inter-Individual Variation: Extensions, Ergodic Conditions and a New Genetic Factor Model of Intra-Individual Variation (Peter C. M. Molenaar, The Pennsylvania State University). 20. Songs My Mother Taught Me: Gene-Environment Interactions, Brain Development and the Auditory System: Thoughts on Non-Kin Rejection, Part II (Elaine L. Bearer, University of New Mexico). 21. Applications of Developmental Systems Theory to Benefit Human Development: On the Contributions of Gilbert Gottlieb to Individuals, Families, and Communities (Richard M. Lerner, Michelle J. Boyd, Megan K. Kiely, Christopher M. Napolitano, and Kristina L. Schmid, Tufts University). Name Index. Subject Index.

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Book SynopsisPlant biotechnology applies to three major areas of plants and their uses: (1) control of plant growth and development;Table of ContentsPreface.- Section I Plant Biotechnology From Inception to the Present: Overview of Plant Biotechnology from its Early Roots to the Present. The Use of Plant Cell Biotechnology for the Production of Phytochemicals. Molecular Farming of Antibodies in Plants. Use of Cyanobacterial Proteins to Engineer New Crops. Molecular Biology of Secondary Metabolism: Case Study for Glycyrrhiza Plants.- Section II Applications of Plant Biotechnology in Agriculture and Industry: New Developments in Agricultural and Industrial Biotechnology. Phytoremediation: The Wave of the Future. Biotechnology of the Rhizosphere. Plants as Sources of Energy.- Section III Use of Plant Secondary Metabolites in Medicine and Nutrition: Interactions of Bioactive Plant Metabolites: Synergism, Antagonism, and Additivity. The Use of Selected Medicinal Herbs for Chemoprevention and Treatment of Cancer, Parkinson's Disease, Heart Disease, and Depression. Regulating Phytonutrient Levels in Plants -- Towards Modification of Plant Metabolism for Human Health.- Section IV Risks and Benefits Associated with Plant Biotechnology: Risks and Benefits Associated with Genetically Modified (GM) Plants. Risks Involved in the Use of Herbal Products. Risks Associated with Over-collecting Medicinal Plants in Natural Habitats. The Potential of Biofumigants as Alternatives to Methyl Bromide for the Control of Pest Infestation in Grain and Dry Food Products.- Index.

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Book SynopsisHow scientific advances in genetic modification will fundamentally change the natural worldThe process of manipulating the genetic material of one animal to include the DNA of another creates a new transgenic organism. Several animals, notably goats, mice, sheep, and cattle are now genetically modified in this way. In Our Transgenic Future, Lisa Jean Moore wonders what such scientific advances portend. Will the natural world become so modified that it ceases to exist? After turning species into hybrids, can we ever get back to the original, or are they forever lost? Does genetic manipulation make better lives possible, and if so, for whom?Moore centers the story on goats that have been engineered by the US military and civilian scientists using the DNA of spiders. The goat's milk contains a spider-silk protein fiber; it can be spun into ultra-strong fabric that can be used to manufacture lightweight military body armor. Researchers also hope the transgenically produced spider silk willTrade Review"Lisa Jean Moore contributes a very needed conversation regarding the ways technology is built, maintained, and destroyed, and the tensions that evolve in its creation between funding entities, scientific knowledge production, and the general public. Moore walks a narrow line between a fear of dystopian consequences and a realization of the sheer possibilities associated with their human-driven existence. Her voice is nicely interwoven with interspecies relationships, the commodification of nonhuman-nonanimal animals (at least in the natural sense), scientific facts, economic drivers, and the oft-unrealized presence of transgenic technologies in our daily lives." * Andrea Laurent-Simpson, author of Just Like Family: How Companion Animals Joined the Household *"A fascinating and fun read. Lisa Jean Moore deftly analyzes a biologically and ethically complex topic, using reflexive analyses to guide the reader along, and contributing to emergent knowledge about genetically modified animals. Moore’s reflexivity invites the reader to witness her thinking about difficult issues, and thus the book also provides a path for us as readers to think alongside her. She doesn’t tell readers what to think on the topic, or even how to think about it, but by modeling her thinking through the topic, we are able to fully grasp the issue at hand and come to our own (messy) conclusions." * Elizabeth Cherry, author of For the Birds: Protecting Wildlife through the Naturalist Gaze *"For a reader interested in the details and daily routine of this kind of scientific interaction with large animals, there is much in this book to enjoy. One may also learn something about spiders, which are undoubtedly fascinating creatures." -- John Dupré * Los Angeles Review of Books *"Moore's narration is delicate, respectful, and wonder-filled... genuinely fun and eminently accessible. Lisa Jean Moore’s Our Transgenic Future is an entertaining, thoughtful inquiry into genetic engineering in general and all of the many ethical questions that it raises." -- Rebecca Coffey * Forbes *

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