Computational biology / bioinformatics Books

Book SynopsisThe past few years have seen a revolution in our ability to map whole genome DNA from ancient humans. With the ancient DNA revolution, combined with rapid genome mapping of present human populations, has come remarkable insights into our past. This important new data has clarified and added to our knowledge from archaeology and anthropology, helped resolve long-existing controversies, challenged long-held views, and thrown up some remarkable surprises.The emerging picture is one of many waves of ancient human migrations, so that all populations existing today are mixes of ancient ones, as well as in many cases carrying a genetic component from Neanderthals, and, in some populations, Denisovans. David Reich, whose team has been at the forefront of these discoveries, explains what the genetics is telling us about ourselves and our complex and often surprising ancestry. Gone are old ideas of any kind of racial ''purity'', or even deep and ancient divides between peoples. Instead, we are finding a rich variety of mixtures. Reich describes the cutting-edge findings from the past few years, and also considers the sensitivities involved in tracing ancestry, with science sometimes jostling with politics and tradition. He brings an important wider message: that we should celebrate our rich diversity, and recognize that every one of us is the result of a long history of migration and intermixing of ancient peoples, which we carry as ghosts in our DNA.What will we discover next?Trade ReviewA wonderfully illuminating exposition of how advances in reading ancient DNA have upended our ideas about past population movements and human interaction. * Paul Collier, Books of the Year 2018, The Times Literary Supplement *Hugely impressive. * Robin McKie, Books of the Year 2018: Science, The Observer *Remarkable ... Spectacular ... In making constant new discoveries about humanity, Reich and his Harvard team are now plunging into uncharted academic waters ... Reich's influence in this field has been immense and the output of his department monumental ... Thrilling in its clarity and its scope. * Peter Forbes, The Guardian *This is a compendious book ... its importance cannot be overstated and neither can some of its best stories. * Bryan Appleyard, The Sunday Times *A thrilling account of mapping humans through time and place ... Reich gives us a window into what ancient DNA can tell us about human evolution, the peopling of the world, continent by continent, and the population mixing that makes us who we are today. * Turi King, Nature *Few subjects fascinate us as much as human origins ... If you want to understand our origins over the course of the last 100,000 years, this book will be the best up-to-date account for you. * Jared Diamond, New York Times Book Review *The conclusions of this book are reassuringly complex and nuanced. But they are no less approachable, no less captivating for that. Indeed, the result is to bring prehistory almost disarmingly close. He brings whole societies from that past vividly to life. * Harry de Quetteville, The Daily Telegraph *Gives the first comprehensive account of this newly revealed prehistory ... an astonishing book. * Juliet Sam, The Daily Telegraph *Reich has produced an invaluable resource that is likely to become an enduring intellectual touchstone. * Tom Booth, British Archaeology *Who We Are and How We Got Here provides a marvellous synthesis of the field. * Clive Cookson, The Financial Times *Geneticists such as Reich have shown [...] that the human world has been made by people who move. This is an important lesson in a time when migration and mobility, in both reality and perception, play such a significant role. * Robert Foley, The Times Literary Supplement *In this comprehensive and provocative book, David Reich exhumes and examines fundamental questions about our origin and future using powerful evidence from human genetics. What does "race" mean in 2018? How alike and how unlike are we? What does identity mean? Reich's book is sobering and clear-eyed, and, in equal part, thrilling and thought provoking. There were times that I had to stand up and clear my thoughts to continue reading this astonishing and important book. * Siddhartha Mukherjee, author of The Emperor of All Maladies *The breakthrough that all archaeologists have been waiting for; a truly exciting account of the way in which ancient DNA is making us rethink prehistory. Essential reading for everyone interested in the past. * Barry Cunliffe, author of The Ancient Celts^ *David Reich uses the power of modern genome analysis to show the fascinating complexity of human migration and history. By letting the data lead him, he treads a narrow path between racists and xenophobes on one side and left-wing ideologues on the other. Although many of his conclusions will be controversial, he starts a necessary conversation about what modern genome analysis can tell us about the variability of human populations. * Sir Venki Ramakrishnan, Nobel Laureate and President of the Royal Society, London *This riveting book will blow you away with its rich and astounding account of where we came from and why that matters. Reich tells the surprising story of how humans got to every corner of the planet, which was revealed only after he and other scientists unlocked the secrets of ancient DNA. The courageous, compassionate and highly personal climax will transform how you think about the meaning of ancestry and race. * Daniel E. Lieberman, Professor of Human Evolutionary Biology at Harvard University and author of The Story of the Human Body: Evolution, Health and Disease *Who We Are and How We Got Here dramatically revises our understanding of the deep history of our species in our African homeland and beyond. Reich's beautifully written book reads like a detective novel and demonstrates a hard truth that often makes many of us uncomfortable: not only are all human beings mixed, but our intuitive understanding of the evolution of the population structure of the world around us is not to be trusted. * Henry Louis Gates, Jr., Professor of Literature at Harvard University and Executive Producer of "Finding Your Roots" *In just five years the study of ancient DNA has transformed our understanding of world prehistory. The geneticist David Reich, one of the pioneers in this field, here gives the brilliantly lucid first account of the resulting new view of human origins and of the later dispersals which went on to shape the modern world. * Colin Renfrew, Emeritus Disney Professor of Archaeology at the University of Cambridge *This book will revolutionize our understanding of human prehistory. David Reich sheds new light on our past from the vantage of a sparkling new discipline-the analysis of ancient DNA. He places migration in the limelight, demonstrating that humans did not just evolve, they spread, often on dramatic scales. * Peter Bellwood, Professor of Archaeology at Australian National University *Reich's book isn't just a collection of stories about the histories of human populations. It is a fascinating case study of scientific revolution ... Reich also has interesting things to say about the way his discipline has over the years been caught up in politics. * Steven Mithen, The London Review of Books *Whole genome mapping hasn't just revolutionised our world, it has helped us rethink our past. * Simon Ings & Liz Else, New Scientist *A hugely important book and essential reading. * Edward Biddulph, Current Archaeology *The Harvard professor [Reich], who is 43, was recently highlighted by the journal Nature as one of 10 people who mattered in all of science for his role in transforming the field of ancient DNA from "niche pursuit to industrial process". * Paul Rincon, BBC News *The work in [Reich's] lab has reshaped our understanding of human prehistory ... He and his colleagues have shed light on the peopling of the planet and the spread of agriculture, among other momentous events. * Carl Zimmer, The New York Times *Reich's intellectual curiosity and passion for research shine through every page of his book ... This book is required reading for everyone interested in an up-to-date account of the spellbinding story of human prehistory. * Debbie Kennett, Who Do You Think You Are? *I learned a good deal from this book, and I encourage others to do the same. * Bernard Wood, Current Biology *It is an incredibly exciting overview of a revolution in the making. * Leon Vlieger, The Inquisitive Biologist *Who We Are and How We Got Here is both comprehensive and exceptionally well-written ... [a] vast global scope as well as its myriad of fascinating details. * Richard Milner, Minerva *Introduces us to the 21st-century Rosetta Stone: ancient DNA, which will do more for our understanding of prehistory than radiocarbon dating did ... Who We Are and How We Got Here is less than 300 pages of text, but it is packed with startling facts and novel revelations that overturn the conventional expectations of both science and common sense. * The National Review *Professor David Reich of Harvard Medical School [...] is not a disinterested observer of a fast-developing field; he is a participant and, in fact, a driver, of the ancient DNA revolution and it is his and his team's research that has accomplished much of the reshaping of human history. So this book has the feel of a first-hand account from the trenches that also carries with it a high-level perspective of what is going on where and why. * Tony Joseph, The Hindu *David Reich's magisterial book is a riveting account of human pre-history and history, through the new lens provided by ancient DNA data. The story of human populations, as he shows, is ever one of widespread, repeated mixing, debunking the fiction of a "pure" population. * Molly Przeworski, Professor of Biological Sciences at Columbia University *Powerful writing and extraordinary insights animate this endlessly fascinating account, by a world scientific leader, of who we modern humans are and how our ancestors arrived in the diverse corners of the world. I could not put the book down. * Robert Weinberg, Professor of Cancer Research, Massachusetts Institute of Technology *Reich's book reads like notes from the frontline of the 'Ancient DNA Revolution' with all the spellbinding drama and intrigue that comes with such a huge transformation in our understanding of human history. * Anne Wojcicki, Chief Executive Officer and Co-Founder of 23andMe *Table of ContentsIntroductionPart I - The Deep History of Our Species1: How the Genome Explains Who We Are2: Interbreeding with Neanderthals3: Ancient DNA Opens the FloodgatesPart II - How We Got to Where We Are Today4: Humanity's Ghosts5: The Making of Modern Europe6: The Collision that Formed India7: In Search of American Ancestors8: The Genomic Origins of East Asians9: Rejoining Africa to the Human StoryPart III -The Disruptive Genome10: The Genomics of Inequality11: The Genomics of Race and Identity12: The Future of Ancient DNA

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Book Synopsis'A book that would have had Darwin swooning - anyone seriously interested in who we are and how we function should read this.' Guardian At the beginning of this century enormous progress had been made in genetics. The Human Genome Project finished sequencing human DNA. It seemed it was only a matter of time until we had all the answers to the secrets of life on this planet.The cutting-edge of biology, however, is telling us that we still don't even know all of the questions.How is it that, despite each cell in your body carrying exactly the same DNA, you don't have teeth growing out of your eyeballs or toenails on your liver? How is it that identical twins share exactly the same DNA and yet can exhibit dramatic differences in the way that they live and grow?It turns out that cells read the genetic code in DNA more like a script to be interpreted than a mould that replicates the same result each time. This is epigenetics and it's the fastest-moving field in biology today.The Epigenetics Revolution traces the thrilling path this discipline has taken over the last twenty years. Biologist Nessa Carey deftly explains such diverse phenomena as how queen bees and ants control their colonies, why tortoiseshell cats are always female, why some plants need a period of cold before they can flower, why we age, develop disease and become addicted to drugs, and much more. Most excitingly, Carey reveals the amazing possibilities for humankind that epigenetics offers for us all - and in the surprisingly near future.Trade ReviewNessa Carey takes us on a lively and up-to-date tour of what's known about epigenetic mechanisms and their implications for ageing and cancer. -- BBC FocusA book that would have had Darwin swooning - anyone seriously interested in who we are and how we function should read this book. -- Guardian[A] splendidly clear explanation -- Colin Berry * The Oldie *Fascinating stuff. -- BooksellerA hugely compelling explanation of the very latest from the frontline of modern biology ... The Epigenetics Revolution traces the thrilling path this discipline has taken over the last twenty years. -- WaterstonesThis is a readable book that applies scientific theory to the everyday world. -- BooksellerHer book combines an easy style with a textbook's thoroughness. -- NatureSees DNA as a film script, with plenty of room for interpretation and retakes. Carey's experience of the biotechnology industry shows in her concluding remarks on the pros and cons of our growing understanding of epigenetics for drug discovery, and on understanding the impact of diet and environment on disease. -- NatureAn exhilarating exploration of an exciting new field, and a good gift for a bright biology student looking for a career choice. -- Kirkus Review

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Book SynopsisThe latest edition of this highly successful textbook introduces the key techniques and concepts involved in cloning genes and in studying their expression and variation. The new edition features: * Increased coverage of whole-genome sequencing technologies and enhanced treatment of bioinformatics.Trade Review“This third edition is absolutely necessary to incorporate the recent advances, such as genome sequencing, polymerase chain reaction, and microarray technology, in this field.” (Doody’s, 19 October 2012)Table of ContentsPreface xiii 1 From Genes to Genomes 1 1.1 Introduction 1 1.2 Basic molecular biology 4 1.2.1 The DNA backbone 4 1.2.2 The base pairs 6 1.2.3 RNA structure 10 1.2.4 Nucleic acid synthesis 11 1.2.5 Coiling and supercoilin 11 1.3 What is a gene? 13 1.4 Information flow: gene expression 15 1.4.1 Transcription 16 1.4.2 Translation 19 1.5 Gene structure and organisation 20 1.5.1 Operons 20 1.5.2 Exons and introns 21 1.6 Refinements of the model 22 2 How to Clone a Gene 25 2.1 What is cloning? 25 2.2 Overview of the procedures 26 2.3 Extraction and purification of nucleic acids 29 2.3.1 Breaking up cells and tissues 29 2.3.2 Alkaline denaturation 31 2.3.3 Column purification 31 2.4 Detection and quantitation of nucleic acids 32 2.5 Gel electrophoresis 33 2.5.1 Analytical gel electrophoresis 33 2.5.2 Preparative gel electrophoresis 36 2.6 Restriction endonucleases 36 2.6.1 Specificity 37 2.6.2 Sticky and blunt ends 40 2.7 Ligation 42 2.7.1 Optimising ligation conditions 44 2.7.2 Preventing unwanted ligation: alkaline phosphatase and double digests 46 2.7.3 Other ways of joining DNA fragments 48 2.8 Modification of restriction fragment ends 49 2.8.1 Linkers and adaptors 50 2.8.2 Homopolymer tailing 52 2.9 Plasmid vectors 53 2.9.1 Plasmid replication 54 2.9.2 Cloning sites 55 2.9.3 Selectable markers 57 2.9.4 Insertional inactivation 58 2.9.5 Transformation 59 2.10 Vectors based on the lambda bacteriophage 61 2.10.1 Lambda biology 61 2.10.2 In vitro packaging 65 2.10.3 Insertion vectors 66 2.10.4 Replacement vectors 68 2.11 Cosmids 71 2.12 Supervectors: YACs and BACs 72 2.13 Summary 73 3 Genomic and cDNA Libraries 75 3.1 Genomic libraries 77 3.1.1 Partial digests 77 3.1.2 Choice of vectors 80 3.1.3 Construction and evaluation of a genomic library 83 3.2 Growing and storing libraries 86 3.3 cDNA libraries 87 3.3.1 Isolation of mRNA 88 3.3.2 cDNA synthesis 89 3.3.3 Bacterial cDNA 93 3.4 Screening libraries with gene probes 94 3.4.1 Hybridization 94 3.4.2 Labelling probes 98 3.4.3 Steps in a hybridization experiment 99 3.4.4 Screening procedure 100 3.4.5 Probe selection and generation 101 3.5 Screening expression libraries with antibodies 103 3.6 Characterization of plasmid clones 106 3.6.1 Southern blots 107 3.6.2 PCR and sequence analysis 108 4 Polymerase Chain Reaction (PCR) 109 4.1 The PCR reaction 110 4.2 PCR in practice 114 4.2.1 Optimisation of the PCR reaction 114 4.2.2 Primer design 115 4.2.3 Analysis of PCR products 117 4.2.4 Contamination 118 4.3 Cloning PCR products 119 4.4 Long-range PCR 121 4.5 Reverse-transcription PCR 123 4.6 Quantitative and real-time PCR 123 4.6.1 SYBR Green 123 4.6.2 TaqMan 125 4.6.3 Molecular beacons 125 4.7 Applications of PCR 127 4.7.1 Probes and other modified products 127 4.7.2 PCR cloning strategies 128 4.7.3 Analysis of recombinant clones and rare events 129 4.7.4 Diagnostic applications 130 5 Sequencing a Cloned Gene 131 5.1 DNA sequencing 131 5.1.1 Principles of DNA sequencing 131 5.1.2 Automated sequencing 136 5.1.3 Extending the sequence 137 5.1.4 Shotgun sequencing; contig assembly 138 5.2 Databank entries and annotation 140 5.3 Sequence analysis 146 5.3.1 Identification of coding region 146 5.3.2 Expression signals 147 5.4 Sequence comparisons 148 5.4.1 DNA sequences 148 5.4.2 Protein sequence comparisons 151 5.4.3 Sequence alignments: Clustal 157 5.5 Protein structure 160 5.5.1 Structure predictions 160 5.5.2 Protein motifs and domains 162 5.6 Confirming gene function 165 5.6.1 Allelic replacement and gene knockouts 166 5.6.2 Complementation 168 6 Analysis of Gene Expression 169 6.1 Analysing transcription 169 6.1.1 Northern blots 170 6.1.2 Reverse transcription-PCR 171 6.1.3 In situ hybridization 174 6.2 Methods for studying the promoter 174 6.2.1 Locating the promoter 175 6.2.2 Reporter genes 177 6.3 Regulatory elements and DNA-binding proteins 179 6.3.1 Yeast one-hybrid assays 179 6.3.2 DNase I footprinting 181 6.3.3 Gel retardation assays 181 6.3.4 Chromatin immunoprecipitation (ChIP) 183 6.4 Translational analysis 185 6.4.1 Western blots 185 6.4.2 Immunocytochemistry and immunohistochemistry 187 7 Products from Native and Manipulated Cloned Genes 189 7.1 Factors affecting expression of cloned genes 190 7.1.1 Transcription 190 7.1.2 Translation initiation 192 7.1.3 Codon usage 193 7.1.4 Nature of the protein product 194 7.2 Expression of cloned genes in bacteria 195 7.2.1 Transcriptional fusions 195 7.2.2 Stability: conditional expression 198 7.2.3 Expression of lethal genes 201 7.2.4 Translational fusions 201 7.3 Yeast systems 204 7.3.1 Cloning vectors for yeasts 204 7.3.2 Yeast expression systems 206 7.4 Expression in insect cells: baculovirus systems 208 7.5 Mammalian cells 209 7.5.1 Cloning vectors for mammalian cells 210 7.5.2 Expression in mammalian cells 213 7.6 Adding tags and signals 215 7.6.1 Tagged proteins 215 7.6.2 Secretion signals 217 7.7 In vitro mutagenesis 218 7.7.1 Site-directed mutagenesis 218 7.7.2 Synthetic genes 223 7.7.3 Assembly PCR 223 7.7.4 Synthetic genomes 224 7.7.5 Protein engineering 224 7.8 Vaccines 225 7.8.1 Subunit vaccines 225 7.8.2 DNA vaccines 226 8 Genomic Analysis 229 8.1 Overview of genome sequencing 229 8.1.1 Strategies 230 8.2 Next generation sequencing (NGS) 231 8.2.1 Pyrosequencing (454) 232 8.2.2 SOLiD sequencing (Applied Biosystems) 235 8.2.3 Bridge amplification sequencing (Solexa/Ilumina) 237 8.2.4 Other technologies 239 8.3 De novo sequence assembly 239 8.3.1 Repetitive elements and gaps 240 8.4 Analysis and annotation 242 8.4.1 Identification of ORFs 243 8.4.2 Identification of the function of genes and their products 250 8.4.3 Other features of nucleic acid sequences 251 8.5 Comparing genomes 256 8.5.1 BLAST 256 8.5.2 Synteny 257 8.6 Genome browsers 258 8.7 Relating genes and functions: genetic and physical maps 260 8.7.1 Linkage analysis 261 8.7.2 Ordered libraries and chromosome walking 262 8.8 Transposon mutagenesis and other screening techniques 263 8.8.1 Transposition in bacteria 263 8.8.2 Transposition in Drosophila 266 8.8.3 Transposition in other organisms 268 8.8.4 Signature-tagged mutagenesis 269 8.9 Gene knockouts, gene knockdowns and gene silencing 271 8.10 Metagenomics 273 8.11 Conclusion 274 9 Analysis of Genetic Variation 275 9.1 Single nucleotide polymorphisms 276 9.1.1 Direct sequencing 278 9.1.2 SNP arrays 279 9.2 Larger scale variations 280 9.2.1 Microarrays and indels 281 9.3 Other methods for studying variation 282 9.3.1 Genomic Southern blot analysis: restriction fragment length polymorphisms (RFLPs) 282 9.3.2 VNTR and microsatellites 285 9.3.3 Pulsed-field gel electrophoresis 287 9.4 Human genetic variation: relating phenotype to genotype 289 9.4.1 Linkage analysis 289 9.4.2 Genome-wide association studies (GWAS) 292 9.4.3 Database resources 294 9.4.4 Genetic diagnosis 294 9.5 Molecular phylogeny 295 9.5.1 Methods for constructing trees 298 10 Post-Genomic Analysis 305 10.1 Analysing transcription: transcriptomes 305 10.1.1 Differential screening 306 10.1.2 Other methods: transposons and reporters 308 10.2 Array-based methods 308 10.2.1 Expressed sequence tag (EST) arrays 309 10.2.2 PCR product arrays 310 10.2.3 Synthetic oligonucleotide arrays 312 10.2.4 Important factors in array hybridization 313 10.3 Transcriptome sequencing 315 10.4 Translational analysis: proteomics 316 10.4.1 Two-dimensional electrophoresis 317 10.4.2 Mass spectrometry 318 10.5 Post-translational analysis: protein interactions 320 10.5.1 Two-hybrid screening 320 10.5.2 Phage display libraries 321 10.6 Epigenetics 323 10.7 Integrative studies: systems biology 324 10.7.1 Metabolomic analysis 324 10.7.2 Pathway analysis and systems biology 325 11 Modifying Organisms: Transgenics 327 11.1 Transgenesis and cloning 327 11.1.1 Common species used for transgenesis 328 11.1.2 Control of transgene expression 330 11.2 Animal transgenesis 333 11.2.1 Basic methods 333 11.2.2 Direct injection 333 11.2.3 Retroviral vectors 335 11.2.4 Embryonic stem cell technology 336 11.2.5 Gene knockouts 339 11.2.6 Gene knock-down technology: RNA interference 340 11.2.7 Gene knock-in technology 341 11.3 Applications of transgenic animals 342 11.4 Disease prevention and treatment 343 11.4.1 Live vaccine production: modification of bacteria and viruses 343 11.4.2 Gene therapy 346 11.4.3 Viral vectors for gene therapy 347 11.5 Transgenic plants and their applications 349 11.5.1 Introducing foreign genes 349 11.5.2 Gene subtraction 351 11.5.3 Applications 352 11.6 Transgenics: a coda 353 Glossary 355 Bibliography 375 Index 379

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Book SynopsisLonglisted for the National Book Award for Nonfiction and A New York Times Notable Book of 2018.Our understanding of the tree of life', with powerful implications for human genetics, human health and our own human nature, has recently completely changed.This book is about a new method of telling the story of life on earth through molecular phylogenetics. It involves a fairly simple method the reading of the deep history of life by looking at the variation in protein molecules found in living organisms. For instance, we now know that roughly eight per cent of the human genome arrived not through traditional inheritance from directly ancestral forms, but sideways by viral infection.In The Tangled Tree, acclaimed science writer David Quammen chronicles these discoveries through the lives of the researchers who made them such as Carl Woese, the most important little-known biologist of the twentieth century; Lynn Margulis, the notorious maverick whose wild ideas about mosaic' creatures pTrade ReviewPraise for Tangled Tree: ‘[Quammen] is our greatest living chronicler of the natural world … There are vivacious descriptions on almost every page.’ New York Times ‘In The Tangled Tree, celebrated science writer David Quammen tells perhaps the grandest tale in biology … He presents the science – and the scientists involved – with patience, candour and flair.’ Nature ‘Quammen adds some intriguing new discoveries’ New Scientist Praise for David Quammen: ‘One of that rare breed of science journalists who blends exploration with a talent for synthesis and storytelling’ Nature ‘Mr. Quammen is, by trade, neither professional environmentalist nor scientist. He is a writer. And the book he has worked on for 10 years is intelligent, playful and refreshingly free of cant … In Mr. Quammen’s hands, the bad news of species extinction unaccountably uplifts. For it reminds us of nature’s sheer, ornery diversity, and why it needs to be preserved. We share in the excitement of a new scientific discipline aborning. By book’s end, we glean hints of hope that the future may not be entirely bleak … Here is what a book can be’The New York Times Book Review ‘Quammen is no ordinary writer. He is simply astonishing, one of that rare class of writer gifted with verve, ingenuity, humour, guts, and great heart’ Elle

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Book SynopsisA Copernican revolution for the life sciences.—Medical TribuneUnlock the mysteries of biology, anthropology, and ancient civilizations in this thought-provoking read where science and spirituality intersect. Through Jeremy Narby′s travels and research in the Amazon, he discovered that shamans were able to use hallucinogens to tap into knowledge and insights that rival our discoveries using modern scientific methods, particularly with regards to DNA and molecular biology. Drawing on visionary experiences, indigenous knowledge, and pharmacology, Narby challenges conventional understanding, unraveling the connections between consciousness, serpent symbolism, and the origins of life itself. This enlightening book blends science, anthropology, and mysticism into a captivating narrative that will expand your mind.

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Book SynopsisThe DNA sequence that comprises the human genome--the genetic blueprint found in each of our cells--is undoubtedly the greatest code ever to be broken. Completed at the dawn of a new millennium, the feat electrified both the scientific community and the general public with its tantalizing promise of new and better treatments for countless diseases, including Alzheimer's, cancer, diabetes, and Parkinson's.Yet what is arguably the most important discovery of our time has also opened a Pandora's box of questions about who we are as humans and how the unique information stored in our genomes can and might be used, making it all the more important for everyone to understand the new science of genomics. In the CURIOSITY GUIDE TO THE HUMAN GENOME, Dr. John Quackenbush, a renowned scientist and professor, conducts a fascinating tour of the history and science behind the Human Genome Project and the technologies that are revolutionizing the practice of medicine today. With a clear and engaging narrative style, he demystifies the fundamental principles of genetics and molecular biology, including the astounding ways in which genes function, alone or together with other genes and the environment, to either sustain life or trigger disease.In addition, Dr. Quackenbush goes beyond medicine to examine how DNA-sequencing technology is changing how we think of ourselves as a species by providing new insights about our earliest ancestors and reconfirming our inextricable link to all life on earth.Finally, he explores the legal and ethical questions surrounding such controversial topics as stem cell research, prenatal testing, forensics, and cloning, making this volume of the Curiosity Guides series an indispensable resource for navigating our brave new genomic world.

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Book SynopsisEpigenetics is the most exciting field in biology today, developing our understanding of how and why we inherit certain traits, develop diseases and age, and evolve as a species. This non-fiction comic book introduces us to genetics, cell biology and the fascinating science of epigenetics, which is rapidly filling in the gaps in our knowledge, allowing us to make huge advances in medicine. We'll look at what identical twins can teach us about the epigenetic effects of our environment and experiences, why certain genes are 'switched on' or off at various stages of embryonic development, and how scientists have reversed the specialization of cells to clone frogs from a single gut cell. In Introducing Epigenetics, Cath Ennis and Oliver Pugh pull apart the double helix, examining how the epigenetic building blocks and messengers that interpret and edit our genes help to make us, well, us.

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Book SynopsisAbout our authors William S. Klug is an Emeritus Professor of Biology at The College of New Jersey (formerly Trenton State College) in Ewing, New Jersey, where he served as Chair of the Biology Department for 17 years. He received his B.A. degree in Biology from Wabash College in Crawfordsville, Indiana, and his Ph.D. from Northwestern University in Evanston, Illinois. Prior to coming to The College of New Jersey, he was on the faculty of Wabash College, where he first taught genetics, as well as general biology and electron microscopy. His research interests have involved ultrastructural and molecular genetic studies of development, utilizing oogenesis in Drosophila as a model system. He has taught the genetics course as well as the senior capstone seminar course in Human and Molecular Genetics to undergraduate biology majors for over four decades. He was the recipient in 2001 of the first annual teaching award given at The College of New Jersey, granted tTable of Contents1. Introduction to Genetics2. Mitosis and Meiosis3. Mendelian Genetics4. Modification of Mendelian Ratios5. Sex Determination and Sex Chromosomes6. Chromosome Mutations: Variation in Number and Arrangement7. Linkage and Chromosome Mapping in Eukaryotes8. Genetic Analysis and Mapping in Bacteria and Bacteriophages9. DNA Structure and Analysis10. DNA Replication11. Chromosome Structure and DNA Sequence Organization12. The Genetic Code and Transcription13. Translation and Proteins14. Gene Mutation, DNA Repair, and Transposition15. Regulation of Gene Expression in Bacteria16. Regulation of Gene Expression in Eukaryotes17. Recombinant DNA Technology18. Genomics, Bioinformatics, and Proteomics19. The Genetics of Cancer20. Quantitative Genetics and Multifactorial Traits21. Population and Evolutionary Genetics Special Topics in Modern Genetics1. Epigenetics2. Genetic Testing3. Gene Therapy4. Advances in Neurogenetics: The Study of Huntington Disease5. DNA Forensics6. Genetically Modified Foods7. Genomics and Precision Medicine

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Book SynopsisThis accessible and entertaining book explores the fundamental connections between life and information and how they emerged inextricably linked, taking the reader on a journey through all the major evolutionary transitions. It records the entire path of how life''s information has evolved, starting from the growing polymers of prelife leading to the first replicators, through RNA and DNA to neural networks and animal brains, continuing through the major transition of human language and writing, into computer clouds, and finally heading towards an unknown future.All currently known life is based on three classes of molecules: proteins - life''s main structural and functional building blocks; DNA - life''s information molecule; and RNA - a molecule that provides the link between these two. Despite the existence of language and the new means of information recording and processing it enabled, at the current stage of life''s evolution, the information stored in the natural repository of oTable of ContentsPreface 1: How to clone oneself? 2: Self-organising molecules 3: Informed self-organisation 4: The simplest life 5: Evolving replicators 6: Life on Earth 7: Evolution as a ratchet of information 8: From DNA to language 9: Epilogue - beyond language

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Book SynopsisAn Introduction to Molecular Evolution and Phylogenetics offers an engaging yet highly informative narrative to demonstrate how molecular data can be used to answer evolutionary questions.Trade ReviewEngaging and entertaining writing, with concepts clearly conveyed in a way accessible to less numerate students. It is by far one of the most enjoyable and interesting text books on evolutionary genetics I have read. * Simon Goodman, University of Leeds *Nothing else comes close in terms of completeness and accessibility to our students. Reading the text is almost like having a conversation. * Lawrence Mays, University of North Carolina at Charlotte *Table of Contents1. Introduction - The story in DNA ; 2. DNA - The immortal germline ; 3. Mutation - We are all mutants ; 4. Replication - Endless copies ; 5. Genome - Accident and design ; 6. Gene - Making an organism ; 7. Selection - Descent with modification ; 8. Drift - Chance and necessity ; 9. Species - Origin of species ; 10. Alignment - Same but different ; 11. Phylogeny - Tree of life ; 12. Hypotheses - Seeing the wood for the trees ; 13. Rates - Tempo and mode ; 14. Dates - Telling the time

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Book SynopsisThe most up-to-date and complete textbook for first time genomics students, Introduction to Genomics offers a fascinating insight into how organisms differ or match; how different organisms evolved; how the genome is constructed and how it operates; and what our understanding of genomics means in terms of our future health and wellbeing.Trade ReviewReview from previous edition This book is great for introducing the field of genomics, providing the basic concepts underpinning the field, including cutting edge techniques, along with examples of its application. * Dr Emma Laing, University of Surrey *The writing is eloquent and engages the curious reader with a wide range of background stories. The practical applications are always highlighted. Rather than a text book studied to pass an exam, this book is a pleasure to read. * Dr Richard Bingham, University of Huddersfield *It's the best textbook that I have reviewed for upper level undergraduates. It has good basic coverage of human aspects, databases, and comparative genomics. I like the questions and problems at the end of the chapters. * Professor Michael Shiaris, University of Massachusetts Boston *Table of Contents1: Introduction 2: The Human Genome Project 3: Mapping, Sequencing, Annotation, and Databases 4: Evolution and Genomic Change 5: Genomes of Prokaryotes and Viruses 6: Genomes of Eukaryotes 7: Comparative Genomics 8: The Impact of Genomics on Human Health and Disease 9: Genomics and Anthropology 10: Transcriptomics 11: Proteomics 12: Metabolomics 13: Systems Biology

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Book SynopsisEnvironmental DNA (eDNA) refers to DNA that can be extracted from environmental samples (such as soil, water, feces, or air) without the prior isolation of any target organism. The analysis of environmental DNA has the potential of providing high-throughput information on taxa and functional genes in a given environment, and is easily amenable to the study of both aquatic and terrestrial ecosystems. It can provide an understanding of past or present biological communities as well as their trophic relationships, and can thus offer useful insights into ecosystem functioning. There is now a rapidly-growing interest amongst biologists in applying analysis of environmental DNA to their own research. However, good practices and protocols dealing with environmental DNA are currently widely dispersed across numerous papers, with many of them presenting only preliminary results and using a diversity of methods. In this context, the principal objective of this practical handbook is to provide biTrade ReviewThis volume fills a much-needed gap, offering a gentle introduction into the field of environmental DNA, which will be especially useful for readers of minor to intermediate experience with environmental DNA. * Vasco Elbrecht, Centre for Biodiversity Genomics, University of Guelph, The Quarterly Review of Biology *An excellent instructional book or supplementary reading for any eDNA based classes...It is a timely and important addition to the field of molecular ecology, and will undoubtedly remain the go-to book on metabarcoding for several years. * Dr Anthony A. Charlton, Macquarie University, Sydney, Australia, Molecular Ecology *This book is a timely overview of eDNA as a complimentary and non-invasive approach for investigating and monitoring biodiversity. The book is an ideal introduction to all ecologists looking to eDNA, but also speaks to the more experienced researchers in molecular ecology. Lastly, it provides textbook material for university courses around the world. * Philip Francis Thomsen, Trends in Ecology & Evolution Journal *If you are contemplating moving into this topic, or just want to understand it better, do try and get your hands on a copy - something that might not be that easy just now as I understand the book has proved to be so popular that it is already having to be reprinted. * IMA FUNGUS *In a world faced with accelerating environmental change and loss of biodiversity, this book is a timely overview of eDNA as a complementary and noninvasive approach for investigating and monitoring biodiversity ... an ideal introduction to all ecologists looking to eDNA as a method of choice, but also speaks to the more experienced researchers in molecular ecology. Lastly, it provides textbook material for university courses around the world, where eDNA is continuously increasing in popularity. * Philip Francis Thomsen, Department of Bioscience, University of Aarhus, Trends in Ecology and Evolution *Table of Contents1: Introduction to environmental DNA (eDNA) 2: DNA metabarcode choice and design 3: Reference databases 4: Sampling 5: DNA extraction 6: DNA amplification and multiplexing 7: DNA sequencing 8: DNA metabarcoding data analysis 9: Single-species detection 10: Environmental DNA for functional diversity 11: Some early landmark studies 12: Freshwater ecosystems 13: Marine environments 14: Terrestrial ecosystems 15: Palaeoenvironments 16: Host-associated microbiota 17: Diet analysis 18: Analysis of bulk samples 19: The future of eDNA metabarcoding

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Book SynopsisThe objective of this practical handbook is to provide ecologists (both students and researchers) with the scientific background necessary to assist with the understanding and implementation of best practice studies and analyses based on environmental DNA.Trade ReviewThis volume fills a much-needed gap, offering a gentle introduction into the field of environmental DNA, which will be especially useful for readers of minor to intermediate experience with environmental DNA. * Vasco Elbrecht, Centre for Biodiversity Genomics, University of Guelph, The Quarterly Review of Biology *An excellent instructional book or supplementary reading for any eDNA based classes...It is a timely and important addition to the field of molecular ecology, and will undoubtedly remain the go-to book on metabarcoding for several years. * Dr Anthony A. Charlton, Macquarie University, Sydney, Australia, Molecular Ecology *This book is a timely overview of eDNA as a complimentary and non-invasive approach for investigating and monitoring biodiversity. The book is an ideal introduction to all ecologists looking to eDNA, but also speaks to the more experienced researchers in molecular ecology. Lastly, it provides textbook material for university courses around the world. * Philip Francis Thomsen, Trends in Ecology & Evolution Journal *If you are contemplating moving into this topic, or just want to understand it better, do try and get your hands on a copy - something that might not be that easy just now as I understand the book has proved to be so popular that it is already having to be reprinted. * IMA FUNGUS *In a world faced with accelerating environmental change and loss of biodiversity, this book is a timely overview of eDNA as a complementary and noninvasive approach for investigating and monitoring biodiversity ... an ideal introduction to all ecologists looking to eDNA as a method of choice, but also speaks to the more experienced researchers in molecular ecology. Lastly, it provides textbook material for university courses around the world, where eDNA is continuously increasing in popularity. * Philip Francis Thomsen, Department of Bioscience, University of Aarhus, Trends in Ecology and Evolution *Table of Contents1: Introduction to environmental DNA (eDNA) 2: DNA metabarcode choice and design 3: Reference databases 4: Sampling 5: DNA extraction 6: DNA amplification and multiplexing 7: DNA sequencing 8: DNA metabarcoding data analysis 9: Single-species detection 10: Environmental DNA for functional diversity 11: Some early landmark studies 12: Freshwater ecosystems 13: Marine environments 14: Terrestrial ecosystems 15: Palaeoenvironments 16: Host-associated microbiota 17: Diet analysis 18: Analysis of bulk samples 19: The future of eDNA metabarcoding

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Book SynopsisGenomics has transformed the biological sciences. From epidemiology and medicine to evolution and forensics, the ability to determine an organism''s complete genetic makeup has changed the way science is done and the questions that can be asked of it. Its most celebrated achievement was the Human Genome Project, a technologically challenging endeavor that took thousands of scientists around the world 13 years and over 3 billion US dollars to complete. In this Very Short Introduction John Archibald explores the science of genomics and its rapidly expanding toolbox. Sequencing a human genome now takes only a few days and costs as little as $1,000. The genomes of simple bacteria and viruses can be sequenced in a matter of hours on a device that fits in the palm of your hand. The resulting sequences can be used to better understand our biology in health and disease and to ''personalize'' medicine. Archibald shows how the field of genomics is on the cusp of another quantum leap; the implications for science and society are profound.ABOUT THE SERIES: The Very Short Introductions series from Oxford University Press contains hundreds of titles in almost every subject area. These pocket-sized books are the perfect way to get ahead in a new subject quickly. Our expert authors combine facts, analysis, perspective, new ideas, and enthusiasm to make interesting and challenging topics highly readable.Trade ReviewGenomics does an amazingly good job of covering the gist and gestalt of arguably the most wide-ranging and fastest developing of the biological sciences. * CHOICE Reviews *Table of Contents1: What is genomics? 2: How to read the book of life 3: Making sense of genes and genomes 4: The human genome in biology and medicine 5: Evolutionary genomics 6: Genomics and the microbial world 7: The future of genomics Further Reading Index

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Book SynopsisA Primer of Population Genetics and Genomics has been completely revised and updated to provide a concise but comprehensive introduction to the basic concepts of population genetics and genomics. Recent textbooks have tended to focus on such specialized topics as the coalescent, molecular evolution, human population genetics, or genomics. This primer bucks that trend by encouraging a broader familiarity with, and understanding of, population genetics and genomics as a whole. The overview ranges from mating systems through the causes of evolution, molecular population genetics, and the genomics of complex traits. Interwoven are discussions of ancient DNA, gene drive, landscape genetics, identifying risk factors for complex diseases, the genomics of adaptation and speciation, and other active areas of current research. The principles are illuminated by numerous examples from a wide variety of animals, plants, microbes, and human populations. The approach also emphasizes learning by doing, which in this case means solving numerical or conceptual problems. The rationale behind this is that the use of concepts in problem-solving lead to deeper understanding and longer knowledge retention. This accessible, introductory textbook is aimed principally at students of various levels and abilities (from senior undergraduate to postgraduate) as well as practising scientists in the fields of population genetics, ecology, evolutionary biology, computational biology, bioinformatics, biostatistics, physics, and mathematics.Table of ContentsPreface 1: Genetic Polymorphisms 2: Organization of Genetic Variation 3: Inbreeding and Population Structure 4: Mutation, Gene Conversion, and Migration 5: Natural Selection in Large Populations 6: Random Genetic Drift in Small Populations 7: Molecular Population Genetics 8: Population Genetics of Complex Traits 9: Complex Traits in Natural Populations

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Book SynopsisDNA profiling is often heralded as unassailable criminal evidence, a veritable "truth machine" that can overturn convictions based on eyewitness testimony, confessions, and other forms of forensic evidence. This book traces the controversial history of DNA fingerprinting by looking at court cases in the US and UK from the mid-1980s onwards.Trade Review"I could not put it down. This is a must-read for anyone interested in the history of science." (Times Higher Education) "An interesting read.... It illustrates that the controversy of DNA profiling is rooted not in the science, but mainly in the restrictions of the adversarial system." (Nature)"

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Book SynopsisDNA profiling is often heralded as unassailable criminal evidence, a veritable "truth machine" that can overturn convictions based on eyewitness testimony, confessions, and other forms of forensic evidence. This book traces the controversial history of DNA fingerprinting by looking at court cases in the US and UK from the mid-1980s onwards.Trade Review"I could not put it down. This is a must-read for anyone interested in the history of science." (Times Higher Education) "An interesting read.... It illustrates that the controversy of DNA profiling is rooted not in the science, but mainly in the restrictions of the adversarial system." (Nature)"

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Book SynopsisCovers various aspects of contemporary biology including gene therapy, the Human Genome Project, DNA testing, and genetic engineering, and fundamental concepts. This book discusses classical and molecular genetics, quantitative and population genetics including cloning and genetic diseases, and the many applications of genetics to the world.Trade ReviewThe book covers much of the material in a high school textbook...but Omoto and Lurquin write in a way that makes things relevan to any interested adult. I think this is an excellent book that will be of great value in any public library collection...also in university and college libraries. -- Margaret Henderson E-Stream Very useful introduction to genes and genetic applications...Recommended. General readers. -- P. M. Watt Choice As a society we are asked to make informed decisions on complex issues such as stem cell research and the labeling of our food based on its level of genetic modification. We have a lot of homework to do, and this book is a good start. -- Stephen Jones Washington State MagazineTable of ContentsPreface: Why Is Genetics Important? 1. What Are Genes? Try This at Home: Extract DNA from Vegetables in Your Kitchen 2. Inheritance of Single-Gene Traits 3. Mendelian Traits in Humans Try This at Home: Pedigree Game 4. From Genes to Phenotype Try This at Home: DNA Replication, Transcription, and Translation Game 5. Using Bacteria as Protein Factories 6. Genetically Modified Plants 7. When Things Go Wrong 8. Mutagens, Teratogens, and Human Reproduction 9. Linkage and Mapping: Gene Discovery Try This at Home: Independent Assortment of Chromosomes and the Making of a Unique Individual Try This at Home: Explore Genetics Databases 10. Genetics of Populations and Genetic Testing 11. Survival of the Fittest? Try This at Home: Demonstrations of the Effects of Small Population Size 12. Nature Versus Nurture 13. Genetically Modified Animals and the Applications of Gene Technology for Humans Appendix A. Internet Resources Appendix B. Glossary of Scientific Names of Organisms Appendix C. Glossary of Human Genetic Diseases Appendix D. Glossary of Terms

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Book SynopsisTrade ReviewThe book is novel, easy to read and combines excellent cartoons with good personal vignettes and history. I spent many years mastering genetics and yet learned new and valuable things from this book. Take a look, you will not be disappointed. -- Robert Trivers, Rutgers University A unique, richly detailed, and fun biography of DNA grounded in deep historical and philosophical knowledge--Rosenfield, Ziff and Van Loon give us everything we need to know about biology's most important molecule. -- Oliver Sacks Right now, you may not know the difference between a prokaryote and a eukaryote, but read this richly detailed work and that could be your next cocktail party opener. Toronto Globe & Mail A clear summary of the DNA story with a lighthearted approach. CHOICE

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Book SynopsisA compact guide to DNA: who we are, how we're wired, and how we repair ourselves. Table of ContentsMeet your genome • How do genes work? • Our genetic journey • Under attack! • Who do you think you are? • People are not peas • Genetic superheroes • Turn me on • Epigenetics • The RNA world • Building a baby • Wiring the brain • Compatibility genes • Why women are stripy • The viruses that made us human • When things go wrong • Human 2.0.

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Book SynopsisIn 1957 two young scientists produced an experiment confirming that DNA replicates as predicted by the double helix structure Watson and Cricks had proposed. This text reconstructs the complex route that led to the experiment and provides an inside view of day-to-day scientific research.Trade Review"Holmes has written a remarkable history of one of molecular biology's most significant experiments. His recreation of a seminal time in the development of the field is masterful and detailed, and it is exciting reading for anyone interested in how experimentation is actually done in a molecular biology laboratory." David Baltimore, president, California Institute of Technology

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Book SynopsisNeuropathology of Transmissible Spongiform Encephalopathies (Prion Diseases).- Central Pathogenesis of Prion Diseases.- Hereditary Prion Protein Amyloidoses.- Mouse Behavioural Studies and What They Can Teach Us about Prion Diseases.- Electrophysiological Approaches to the Study of Prion Diseases.- Prion Protein, Prion Protein-Like Protein, and Neurodegeneration.- Oxidative Stress and Mitochondrial Dysfunction in Neurodegeneration of Transmissible Spongiform Encephalopathies (TSEs).- Mechanisms of Prion Toxicity and Their Relationship to Prion Infectivity.- A Stone Guest on the Brain: Death as a Prion.- Molecular Mechanisms Mediating Neuronal Cell Death in Experimental Models of Prion Diseases, in vitro.- Processing and Mis-Processing of the Prion Protein: Insights into the Pathogenesis of Familial Prion Disorders.- Signaling Pathways Controling Prion Neurotoxicity: Role of Endoplasmic Reticulum Stress-Mediated Apoptosis.- Cell Culture Models to Unravel Prion Protein Function and AberrTable of ContentsNeuropathology of transmissible spongiform encephalopathies (prion diseases).- Central pathogenesis of prion diseases.- Hereditory prion protein Amyloidoses.- Mouse behavioural studies and what they can teach us about prion diseases.- Electrophysiological approaches to the study of prion diseases.- Prion protein, prion protein-like protein, and neurodegeneration.- Oxidative stress and mitochondrial dysfunction in neurodegeneration of transmissible spongiform encephalopathies (TSEs).- Mechanisms of prion toxicity and their relationship to prion infectivity.- A stone guest on the brain: Death as a prion.- Molecular mechanisms mediating neuronal cell death in experimental models of prion diseases, in vitro.- Processing and mis-processing of the prion protein: Insights into the pathogenesis of familial prion disorders.- Signaling pathways controling prion protein neurotoxicity: Role of endoplasmic reticulum stress-mediated apoptosis.- Cell culture models to unravel prion protein function and aberrancies in TSE.- Insights into the cellular trafficking of prion proteins.- The molecular basis of prion protein-mediated neuronal damage.

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Book SynopsisDevoted to local and global analysis of weakly connected systems with applications to neurosciences, this book uses bifurcation theory and canonical models as the major tools of analysis.Trade ReviewFrom the reviews: "...After the introduction, written according to the authors in ordinary language, and well readable even for laymen, follows a nicely written Chapter 2 on bifurcations in neuron dynamics which must be read. Here also spiking and bursting phenomena are clearly described. Chapter 3 contains a short sketch of nonhyperbolic (when the Jacobian matrix of (1) has at least one eigenvalue with zero real part) neural networks. The remaining part of the book is mainly devoted to canonical models (Chapter 4), their derivation (Chapters 6--9), and their analysis (Chapters 10--12). The term canonical model is not precisely defined here. The authors say that a model is canonical if there is a continuous change of variables that transforms any other model from a given class into this one. As the method of deriving the canonical models, the authors exploit the normal form theory. Canonical models treated in the book have only restricted value: They provide information about local behavior of (1) when there is an exponentially stable limit cycle but they say nothing about global behavior of (1), including the transients. The last Chapter 13 describes the relationship between synaptic organizations and dynamical properties of networks of neural oscillators. In other words, the problem of learning and memorization of phase information in the weakly connected network of oscillators corresponding to multiple Andronov-Hopf bifurcation is treated analytically. Surprisingly the book ends without any conclusions. Also there are no appendices to the book. The references are representative and sufficiently cover the problematics treated in the book." (Ladislav Andrey, Mathematical Reviews) Table of Contents1 Introduction.- 2 Bifurcations in Neuron Dynamics.- 3 Neural Networks.- 4 Introduction to Canonical Models.- 5 Local Analysis of WCNNs.- 6 Local Analysis of Singularly Perturbed WCNNs.- 7 Local Analysis of Weakly Connected Maps.- 8 Saddle-Node on a Limit Cycle.- 9 Weakly Connected Oscillators.- 10 Multiple Andronov-Hopf Bifurcation.- 11 Multiple Cusp Bifurcation.- 12 Quasi-Static Bifurcations.- 13 Synaptic Organizations of the Brain.- References.

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Book SynopsisProviding an in-depth look at the practical use of math modeling, it features exercises throughout that are drawn from a variety of bioscientific disciplines - population biology, developmental biology, physiology, epidemiology, and evolution, among others.Trade ReviewReviews of the original edition: "Murray has produced a magnificent compilation of mathematical models and their applications in biology." Nature "Murray's Mathematical Biology belongs on the shelf of any person with a serious interest in mathematical biology." Bulletin of Mathematical Biology SIAM, 2004: "Murray's Mathematical Biology is a classic that belongs on the shelf of any serious student or researcher in the field. Together the two volumes contain well over 1000 references, a rich source of material, together with an excellent index to help readers quickly find key words. ... I recommend the new and expanded third edition to any serious young student interested in mathematical biology who already has a solid basis in applied mathematics." From the reviews of the third edition: "Mathematical Biology would be eminently suitable as a text for a final year undergraduate or postgraduate course in mathematical biology … . It is also a good source of examples for courses in mathematical methods … . Mathematical Biology provides a good way in to the field and a useful reference for those of us already there. It may attract more mathematicians to work in biology by showing them that there is real work to be done." (Peter Saunders, The Mathematical Gazette, Vol. 90 (519), 2006)Table of ContentsContinuous Population Models for Single Species * Discrete Population Models for a Single Species * Models for Interacting Populations * Temperature-Dependent Sex Determination (TSD): Crocodilian Survivorship * Modelling the Dynamics of Marital Interaction: Divorce Prediction and Marriage Repair * Reaction Kinetics * Biological Oscillators and Switches * BZ Oscillating Reactions * Perturbed and Coupled Oscillators and Black Holes * Dynamics of Infectious Diseases: Epidemic Models and AIDS * Reaction Diffusion, Chemotaxis, and Non-local Mechanisms * Oscillator Generated Wave Phenomena and Central Pattern Generators * Biological Waves: Single Species Models * Use and Abuse of Fractals

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Book SynopsisOne of the world’s leading cultural psychologists debunks the hype surrounding DNA testing and puts to rest our mistaken anxieties about our genes.Trade Review"Steven Heine is one of the leading cultural psychologists in the world. In DNA Is Not Destiny, Heine serves as a trustworthy guide through the moral minefield of genetic differences and lays out a new way to think rationally about our genes." -- Jonathan Haidt, Thomas Cooley Professor of Ethical Leadership at New York University's Stern School of Business and author of The Righteous Mind "Steven Heine is one of the leading cultural psychologists in the world. In DNA Is Not Destiny, Heine serves as a trustworthy guide through the moral minefield of genetic differences and lays out a new way to think rationally about our genes." -- Jonathan Haidt, Thomas Cooley Professor of Ethical Leadership at New York University's Stern School of Business and author of The Righteous Mind "At some point everyone wonders: 'Who am I and where did I come from?' Is there any question more fascinating? In this important book, Steve Heine tells us what our DNA can and cannot reveal about our nature, our origins, and our futures. The material is fascinating, and Heine's vibrant writing makes it come alive with personal significance for every reader." -- Carol Dweck, Lewis and Virginia Eaton Professor of Psychology at Stanford University and author of Mindset "At some point everyone wonders: 'Who am I and where did I come from?' Is there any question more fascinating? In this important book, Steve Heine tells us what our DNA can and cannot reveal about our nature, our origins, and our futures. The material is fascinating, and Heine's vibrant writing makes it come alive with personal significance for every reader." -- Carol Dweck, Lewis and Virginia Eaton Professor of Psychology at Stanford University and author of Mindset "Your genes contribute to your beliefs, behaviors, and life outcomes. Only in rare cases are they determinative. This brilliant, invaluable book sets straight crucial matters of heredity and environment and their interaction-and does so in lively and lucid prose." -- Richard Nisbett, Theodore M. Newcomb Distinguished Professor of Social Psychology at the University of Michigan and author of Mindware "Your genes contribute to your beliefs, behaviors, and life outcomes. Only in rare cases are they determinative. This brilliant, invaluable book sets straight crucial matters of heredity and environment and their interaction-and does so in lively and lucid prose." -- Richard Nisbett, Theodore M. Newcomb Distinguished Professor of Social Psychology at the University of Michigan and author of Mindware "A highly accessible and entertaining guide to genes: what they are, how they work, and most important, what they can and cannot explain. For all the dinner table or classroom conversations on the genetic bases of gender, race, or intelligence; the morality of genetic engineering; or the hardest question of all, 'Who am I?,' DNA Is Not Destiny is the new must-read." -- Hazel Markus, Davis-Brack Professor in the Behavioral Sciences at Stanford University and author of Clash!: How to Thrive in a Multicultural World "A highly accessible and entertaining guide to genes: what they are, how they work, and most important, what they can and cannot explain. For all the dinner table or classroom conversations on the genetic bases of gender, race, or intelligence; the morality of genetic engineering; or the hardest question of all, "Who am I?," DNA Is Not Destiny is the new must-read." -- Hazel Markus, Davis-Brack Professor in the Behavioral Sciences at Stanford University and author of Clash!: How to Thrive in a Multicultural World "Heine ranges broadly, discussing both historical and ethical concerns, and draws heavily on social science research to investigate how people's beliefs about the power of genes influence their behavior. Heine also makes a strident critique of the direct-to-consumer genetic testing industry and a robust defense of most genetically modified organisms... Enjoyable and informative." -- Publishers Weekly "An accessible contribution to what the author calls 'genetic literacy' and a satisfyingly hard-edged work of popular science." -- Kirkus Reviews

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Book SynopsisThe national bestseller that reveals how we are descended from seven prehistoric women.Trade Review"A lovely, rollicking book, direct and clear.... [A] fascinating glimpse into anthropology in the era of the genome." -- Wall Street Journal"Sykes recounts his tale of discovery with the drama it warrants...gripping." -- New York Times Book Review"Scientifically accurate and understandable to the layperson.... [The Seven Daughters of Eve] will be recognized as an important work, bringing molecular anthropology to a mass audience." -- Nature"A natural storyteller, [Sykes] relates the history of developing genetics up to contemporary times as the DNA of genes is decoded.... A riveting account showing how archeological evidence and molecular biology findings complement one another in the challenge to unearth our past and our beginnings." -- Choice"Sykes has solved some of the hottest debates about human origins." -- Publishers Weekly

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Book SynopsisOne of the world’s leading cultural psychologists debunks the hype surrounding DNA testing and puts to rest our mistaken anxieties about our genes.

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

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Book SynopsisData Analysis and Visualization in Genomics and Proteomics is the first book addressing integrative data analysis and visualization in this field. It addresses important techniques for the interpretation of data originating from multiple sources, encoded in different formats or protocols, and processed by multiple systems.Table of ContentsPreface. List of Contributors. SECTION I: INTRODUCTION - DATA DIVERSITY AND INTEGRATION. 1. Integrative Data Analysis and Visualization: Introduction to Critical Problems, Goals and Challenges (Francisco Azuaje and Joaquín Dopazo). 1.1 Data Analysis and Visualization: An Integrative Approach. 1.2 Critical Design and Implementation Factors. 1.3 Overview of Contributions. References. 2. Biological Databases: Infrastructure, Content and Integration (Allyson L. Williams, Paul J. Kersey, Manuela Pruess and Rolf Apweiler). 2.1 Introduction. 2.2 Data Integration. 2.3 Review of Molecular Biology Databases. 2.4 Conclusion. References. 3. Data and Predictive Model Integration: an Overview of Key Concepts, Problems and Solutions (Francisco Azuaje, Joaquín Dopazo and Haiying Wang). 3.1 Integrative Data Analysis and Visualization: Motivation and Approaches. 3.2 Integrating Informational Views and Complexity for Understanding Function. 3.3 Integrating Data Analysis Techniques for Supporting Functional Analysis. 3.4 Final Remarks. References. SECTION II: INTEGRATIVE DATA MINING AND VISUALIZATION -EMPHASIS ON COMBINATION OF MULTIPLE DATA TYPES. 4. Applications of Text Mining in Molecular Biology, from Name Recognition to Protein Interaction Maps (Martin Krallinger and Alfonso Valencia). 4.1 Introduction. 4.2 Introduction to Text Mining and NLP. 4.3 Databases and Resources for Biomedical Text Mining. 4.4 Text Mining and Protein-Protein Interactions. 4.5 Other Text-Mining Applications in Genomics. 4.6 The Future of NLP in Biomedicine. Acknowledgements. References. 5. Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis (Long J. Lu, Yu Xia, Haiyuan Yu, Alexander Rives, Haoxin Lu, Falk Schubert and Mark Gerstein). 5.1 Introduction. 5.2 Genomic Features in Protein Interaction Predictions. 5.3 Machine Learning on Protein-Protein Interactions. 5.4 The Missing Value Problem. 5.5 Network Analysis of Protein Interactions. 5.6 Discussion. References. 6. Integration of Genomic and Phenotypic Data (Amanda Clare). 6.1 Phenotype. 6.2 Forward Genetics and QTL Analysis. 6.3 Reverse Genetics. 6.4 Prediction of Phenotype from Other Sources of Data. 6.5 Integrating Phenotype Data with Systems Biology. 6.6 Integration of Phenotype Data in Databases. 6.7 Conclusions. References. 7. Ontologies and Functional Genomics (Fátima Al-Shahrour and Joaquín Dopazo). 7.1 Information Mining in Genome-Wide Functional Analysis. 7.2 Sources of Information: Free Text Versus Curated Repositories. 7.3 Bio-Ontologies and the Gene Ontology in Functional Genomics. 7.4 Using GO to Translate the Results of Functional Genomic Experiments into Biological Knowledge. 7.5 Statistical Approaches to Test Significant Biological Differences. 7.6 Using FatiGO to Find Significant Functional Associations in Clusters of Genes. 7.7 Other Tools. 7.8 Examples of Functional Analysis of Clusters of Genes. 7.9 Future Prospects. References. 8. The C. elegans Interactome: its Generation and Visualization (Alban Chesnau and Claude Sardet). 8.1 Introduction. 8.2 The ORFeome: the first step toward the interactome of C. elegans. 8.3 Large-Scale High-Throughput Yeast Two-Hybrid Screens to Map the C. elegans Protein-Protein Interaction (Interactome) Network: Technical Aspects. 8.4 Visualization and Topology of Protein-Protein Interaction Networks. 8.5 Cross-Talk Between the C. elegans Interactome and other Large-Scale Genomics and Post-Genomics Data Sets. 8.6 Conclusion: From Interactions to Therapies. References. SECTION III: INTEGRATIVE DATA MINING AND VISUALIZATION - EMPHASIS ON COMBINATION OF MULTIPLE PREDICTION MODELS AND METHODS. 9. Integrated Approaches for Bioinformatic Data Analysis and Visualization - Challenges, Opportunities and New Solutions (Steve R. Pettifer, James R. Sinnott and Teresa K. Attwood). 9.1 Introduction. 9.2 Sequence Analysis Methods and Databases. 9.3 A View Through a Portal. 9.4 Problems with Monolithic Approaches: One Size Does Not Fit All. 9.5 A Toolkit View. 9.6 Challenges and Opportunities. 9.7 Extending the Desktop Metaphor. 9.8 Conclusions. Acknowledgements. References. 10. Advances in Cluster Analysis of Microarray Data (Qizheng Sheng, Yves Moreau, Frank De Smet, Kathleen Marchal and Bart De Moor). 10.1 Introduction. 10.2 Some Preliminaries. 10.3 Hierarchical Clustering. 10.4 k-Means Clustering. 10.5 Self-Organizing Maps. 10.6 A Wish List for Clustering Algorithms. 10.7 The Self-Organizing Tree Algorithm. 10.8 Quality-Based Clustering Algorithms. 10.9 Mixture Models. 10.10 Biclustering Algorithms. 10.11 Assessing Cluster Quality. 10.12 Open Horizons. References. 11. Unsupervised Machine Learning to Support Functional Characterization of Genes: Emphasis on Cluster Description and Class Discovery (Olga G. Troyanskaya). 11.1 Functional Genomics: Goals and Data Sources. 11.2 Functional Annotation by Unsupervised Analysis of Gene Expression Microarray Data. 11.3 Integration of Diverse Functional Data For Accurate Gene Function Prediction. 11.4 MAGIC - General Probabilistic Integration of Diverse Genomic Data. 11.5 Conclusion. References. 12. Supervised Methods with Genomic Data: a Review and Cautionary View (Ramón Díaz-Uriarte). 12.1 Chapter Objectives. 12.2 Class Prediction and Class Comparison. 12.3 Class Comparison: Finding/Ranking Differentially Expressed Genes. 12.4 Class Prediction and Prognostic Prediction. 12.5 ROC Curves for Evaluating Predictors and Differential Expression. 12.6 Caveats and Admonitions. 12.7 Final Note: Source Code Should be Available. Acknowledgements. References. 13. A Guide to the Literature on Inferring Genetic Networks by Probabilistic Graphical Models (Pedro Larrañaga, Iñaki Inza and Jose L. Flores). 13.1 Introduction. 13.2 Genetic Networks. 13.3 Probabilistic Graphical Models. 13.4 Inferring Genetic Networks by Means of Probabilistic Graphical Models. 13.5 Conclusions. Acknowledgements. References. 14. Integrative Models for the Prediction and Understanding of Protein Structure Patterns (Inge Jonassen). 14.1 Introduction. 14.2 Structure Prediction. 14.3 Classifications of Structures. 14.4 Comparing Protein Structures 14.5 Methods for the Discovery of Structure Motifs. 14.6 Discussion and Conclusions. References. Index.

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Book SynopsisThis book is the first to approach the fast developing field of wildlife forensics with a focus on the application of DNA profiling and analysis. Case studies throughout link theory and practice and highlight the use of DNA testing in species testing.Table of ContentsForeword ix Preface xi About the Authors xiii Acknowledgements xv 1 Introduction 1 1.1 Importance of wildlife forensic science investigations 1 1.2 Role of forensic science in wildlife crimes 3 1.3 Legislation covering wildlife crime 4 1.4 Role of non-human DNA in forensic science 8 1.5 Development of wildlife DNA testing 9 1.5.1 History and current state of wildlife DNA forensic science 10 1.5.2 Wildlife forensic science testing 11 1.5.3 Performing DNA typing in wildlife investigations 13 1.6 Accreditation and certification 14 1.7 Standardisation and validation 20 1.8 Collection of evidential material, continuity of evidence and transportation to the laboratory 24 1.9 Note taking and maintenance of a casefile 29 1.10 Case assessment and initial testing 30 1.11 Scope of book 32 Useful websites 32 References 33 2 DNA, Genomes and Genetic Variation 37 2.1 Introduction 37 2.2 The DNA molecule 37 2.3 Chromosomes and nuclear DNA 39 2.4 Genomes 41 2.4.1 Nuclear DNA 41 2.4.2 Mitochondrial and chloroplast DNA 44 2.5 DNA mutation and genetic variation 47 2.5.1 Genetic variation of repetitive DNA 48 2.5.2 Single base changes leading to genetic variation 48 2.5.3 Genetic loci used in species testing 50 2.6 DNA polymorphisms leading to speciation 53 2.6.1 Genetic isolation 54 2.6.2 Other processes leading to speciation 56 2.7 What is a species? 56 2.7.1 Subspecies 60 2.7.2 Genus to Kingdom 61 2.8 Summary 63 References 64 3 Methods in Wildlife Forensic DNA Analysis 69 3.1 Introduction 69 3.2 Protein polymorphisms 69 3.3 DNA isolation, purification and concentration 70 3.3.1 Generic aspects of DNA isolation 70 3.3.2 Lysis step 71 3.3.3 DNA purification: silica-based extraction 72 3.3.4 DNA purification: Chelex R 100 resin 73 3.3.5 DNA purification: organic extraction 74 3.3.6 Microconcentration 76 3.4 DNA quantification 76 3.5 Restriction fragment length polymorphisms (RFLP) 78 3.6 Methods based on the polymerase chain reaction 81 3.6.1 Factors affecting PCR efficiency and optimisation of PCR 84 3.6.2 PCR-based methods of DNA quantification 88 3.6.3 Random amplification of polymorphic DNA 91 3.6.4 Amplification of fragment length polymorphisms (AFLP) 93 3.7 PCR set-up 95 3.8 PCR clean-up 98 3.9 DNA sequencing 99 3.10 SNP typing 100 3.11 New generation of DNA sequence methods 102 Suggested reading 104 4 Species Testing 105 4.1 Introduction 105 4.2 Species 106 4.2.1 Genetic variation and correspondence with taxonomy 106 4.3 Attributes of a species testing locus 106 4.4 Application of a locus to a species 110 4.5 Tests available and how they are performed 110 4.5.1 Sequencing 111 4.5.2 Species-specific primers 124 4.6 Developing a species test 127 4.6.1 Use of data on GenBank and sequence alignment 128 4.6.2 Designing primers 135 4.6.3 Validation 156 4.7 Interpretation and reporting of results 159 4.7.1 Interpretation and reporting sequencing results 160 4.7.2 Interpretation and reporting species-specific testing results 169 4.8 Other limitations: hybrids and wild/captive bred 171 4.9 Future methodologies 173 References 173 5 Genetic Linkage 177 5.1 Introduction 177 5.2 Whole genome testing 177 5.3 Types of individualisation testing 178 5.3.1 Short Tandem Repeats 179 5.4 Identifying STR loci 182 5.4.1 DNA libraries 183 5.4.2 Locating novel microsatellite motifs using Next Generation Sequencing 184 5.5 Allele databases 190 5.5.1 Number of theoretical genotypes 192 5.5.2 Allelic ladders 192 5.6 Hardy–Weinberg equilibrium 193 5.7 Kinship factors and accounting for shared alleles 199 5.7.1 Rare or absent alleles on the database 202 5.8 Assessing the suitability of STR loci 203 5.8.1 The Genetic Data Analysis software (GDA) 205 5.8.2 The Excel Microsatellite Toolkit 214 5.8.3 Arlequin 220 5.8.4 API-Calc 228 5.8.5 Genepop 230 5.8.6 FSTAT 235 5.8.7 Structure 236 5.8.8 Summary 242 5.9 Genetic assignment: paternity testing 244 5.9.1 Genetic assignment: paternity testing if one parent is not available 249 5.9.2 Genetic assignment in paternity testing, incorporating kinship factor 251 5.10 Concluding comments 253 References 254 6 Interpretation, Evaluation and Reporting of Results 259 6.1 Introduction 259 6.2 Case assessment 260 6.3 Hierarchies of propositions 261 6.4 DNA evidence evaluation 262 6.4.1 The frequentist approach 263 6.4.2 Likelihood ratios 264 6.4.3 The Bayesian approach 266 6.4.4 Comparison of the three approaches 267 6.5 Evaluation of DNA evidence in wildlife cases 269 6.5.1 Case scenario 1 269 6.5.2 Case scenario 2 271 6.5.3 Case scenario 3 272 6.6 Role of the expert witness 273 6.7 Report writing 275 6.8 Summary and comments 277 Statement of witness 278 References 299 Measurements 303 Glossary 305 Appendix A Simulated Sample Populations 311 Appendix B Useful websites 323 Index 325

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Book SynopsisThe latest edition of this highly successful textbook introduces the key techniques and concepts involved in cloning genes and in studying their expression and variation. The new edition features: Increased coverage of whole-genome sequencing technologies and enhanced treatment of bioinformatics. Clear, two-colour diagrams throughout. A dedicated website including all figures. Noted for its outstanding balance between clarity of coverage and level of detail, this book provides an excellent introduction to the fast moving world of molecular genetics.Trade Review“This third edition is absolutely necessary to incorporate the recent advances, such as genome sequencing, polymerase chain reaction, and microarray technology, in this field.” (Doody’s, 19 October 2012)Table of ContentsPreface xiii 1 From Genes to Genomes 1 1.1 Introduction 1 1.2 Basic molecular biology 4 1.2.1 The DNA backbone 4 1.2.2 The base pairs 6 1.2.3 RNA structure 10 1.2.4 Nucleic acid synthesis 11 1.2.5 Coiling and supercoilin 11 1.3 What is a gene? 13 1.4 Information flow: gene expression 15 1.4.1 Transcription 16 1.4.2 Translation 19 1.5 Gene structure and organisation 20 1.5.1 Operons 20 1.5.2 Exons and introns 21 1.6 Refinements of the model 22 2 How to Clone a Gene 25 2.1 What is cloning? 25 2.2 Overview of the procedures 26 2.3 Extraction and purification of nucleic acids 29 2.3.1 Breaking up cells and tissues 29 2.3.2 Alkaline denaturation 31 2.3.3 Column purification 31 2.4 Detection and quantitation of nucleic acids 32 2.5 Gel electrophoresis 33 2.5.1 Analytical gel electrophoresis 33 2.5.2 Preparative gel electrophoresis 36 2.6 Restriction endonucleases 36 2.6.1 Specificity 37 2.6.2 Sticky and blunt ends 40 2.7 Ligation 42 2.7.1 Optimising ligation conditions 44 2.7.2 Preventing unwanted ligation: alkaline phosphatase and double digests 46 2.7.3 Other ways of joining DNA fragments 48 2.8 Modification of restriction fragment ends 49 2.8.1 Linkers and adaptors 50 2.8.2 Homopolymer tailing 52 2.9 Plasmid vectors 53 2.9.1 Plasmid replication 54 2.9.2 Cloning sites 55 2.9.3 Selectable markers 57 2.9.4 Insertional inactivation 58 2.9.5 Transformation 59 2.10 Vectors based on the lambda bacteriophage 61 2.10.1 Lambda biology 61 2.10.2 In vitro packaging 65 2.10.3 Insertion vectors 66 2.10.4 Replacement vectors 68 2.11 Cosmids 71 2.12 Supervectors: YACs and BACs 72 2.13 Summary 73 3 Genomic and cDNA Libraries 75 3.1 Genomic libraries 77 3.1.1 Partial digests 77 3.1.2 Choice of vectors 80 3.1.3 Construction and evaluation of a genomic library 83 3.2 Growing and storing libraries 86 3.3 cDNA libraries 87 3.3.1 Isolation of mRNA 88 3.3.2 cDNA synthesis 89 3.3.3 Bacterial cDNA 93 3.4 Screening libraries with gene probes 94 3.4.1 Hybridization 94 3.4.2 Labelling probes 98 3.4.3 Steps in a hybridization experiment 99 3.4.4 Screening procedure 100 3.4.5 Probe selection and generation 101 3.5 Screening expression libraries with antibodies 103 3.6 Characterization of plasmid clones 106 3.6.1 Southern blots 107 3.6.2 PCR and sequence analysis 108 4 Polymerase Chain Reaction (PCR) 109 4.1 The PCR reaction 110 4.2 PCR in practice 114 4.2.1 Optimisation of the PCR reaction 114 4.2.2 Primer design 115 4.2.3 Analysis of PCR products 117 4.2.4 Contamination 118 4.3 Cloning PCR products 119 4.4 Long-range PCR 121 4.5 Reverse-transcription PCR 123 4.6 Quantitative and real-time PCR 123 4.6.1 SYBR Green 123 4.6.2 TaqMan 125 4.6.3 Molecular beacons 125 4.7 Applications of PCR 127 4.7.1 Probes and other modified products 127 4.7.2 PCR cloning strategies 128 4.7.3 Analysis of recombinant clones and rare events 129 4.7.4 Diagnostic applications 130 5 Sequencing a Cloned Gene 131 5.1 DNA sequencing 131 5.1.1 Principles of DNA sequencing 131 5.1.2 Automated sequencing 136 5.1.3 Extending the sequence 137 5.1.4 Shotgun sequencing; contig assembly 138 5.2 Databank entries and annotation 140 5.3 Sequence analysis 146 5.3.1 Identification of coding region 146 5.3.2 Expression signals 147 5.4 Sequence comparisons 148 5.4.1 DNA sequences 148 5.4.2 Protein sequence comparisons 151 5.4.3 Sequence alignments: Clustal 157 5.5 Protein structure 160 5.5.1 Structure predictions 160 5.5.2 Protein motifs and domains 162 5.6 Confirming gene function 165 5.6.1 Allelic replacement and gene knockouts 166 5.6.2 Complementation 168 6 Analysis of Gene Expression 169 6.1 Analysing transcription 169 6.1.1 Northern blots 170 6.1.2 Reverse transcription-PCR 171 6.1.3 In situ hybridization 174 6.2 Methods for studying the promoter 174 6.2.1 Locating the promoter 175 6.2.2 Reporter genes 177 6.3 Regulatory elements and DNA-binding proteins 179 6.3.1 Yeast one-hybrid assays 179 6.3.2 DNase I footprinting 181 6.3.3 Gel retardation assays 181 6.3.4 Chromatin immunoprecipitation (ChIP) 183 6.4 Translational analysis 185 6.4.1 Western blots 185 6.4.2 Immunocytochemistry and immunohistochemistry 187 7 Products from Native and Manipulated Cloned Genes 189 7.1 Factors affecting expression of cloned genes 190 7.1.1 Transcription 190 7.1.2 Translation initiation 192 7.1.3 Codon usage 193 7.1.4 Nature of the protein product 194 7.2 Expression of cloned genes in bacteria 195 7.2.1 Transcriptional fusions 195 7.2.2 Stability: conditional expression 198 7.2.3 Expression of lethal genes 201 7.2.4 Translational fusions 201 7.3 Yeast systems 204 7.3.1 Cloning vectors for yeasts 204 7.3.2 Yeast expression systems 206 7.4 Expression in insect cells: baculovirus systems 208 7.5 Mammalian cells 209 7.5.1 Cloning vectors for mammalian cells 210 7.5.2 Expression in mammalian cells 213 7.6 Adding tags and signals 215 7.6.1 Tagged proteins 215 7.6.2 Secretion signals 217 7.7 In vitro mutagenesis 218 7.7.1 Site-directed mutagenesis 218 7.7.2 Synthetic genes 223 7.7.3 Assembly PCR 223 7.7.4 Synthetic genomes 224 7.7.5 Protein engineering 224 7.8 Vaccines 225 7.8.1 Subunit vaccines 225 7.8.2 DNA vaccines 226 8 Genomic Analysis 229 8.1 Overview of genome sequencing 229 8.1.1 Strategies 230 8.2 Next generation sequencing (NGS) 231 8.2.1 Pyrosequencing (454) 232 8.2.2 SOLiD sequencing (Applied Biosystems) 235 8.2.3 Bridge amplification sequencing (Solexa/Ilumina) 237 8.2.4 Other technologies 239 8.3 De novo sequence assembly 239 8.3.1 Repetitive elements and gaps 240 8.4 Analysis and annotation 242 8.4.1 Identification of ORFs 243 8.4.2 Identification of the function of genes and their products 250 8.4.3 Other features of nucleic acid sequences 251 8.5 Comparing genomes 256 8.5.1 BLAST 256 8.5.2 Synteny 257 8.6 Genome browsers 258 8.7 Relating genes and functions: genetic and physical maps 260 8.7.1 Linkage analysis 261 8.7.2 Ordered libraries and chromosome walking 262 8.8 Transposon mutagenesis and other screening techniques 263 8.8.1 Transposition in bacteria 263 8.8.2 Transposition in Drosophila 266 8.8.3 Transposition in other organisms 268 8.8.4 Signature-tagged mutagenesis 269 8.9 Gene knockouts, gene knockdowns and gene silencing 271 8.10 Metagenomics 273 8.11 Conclusion 274 9 Analysis of Genetic Variation 275 9.1 Single nucleotide polymorphisms 276 9.1.1 Direct sequencing 278 9.1.2 SNP arrays 279 9.2 Larger scale variations 280 9.2.1 Microarrays and indels 281 9.3 Other methods for studying variation 282 9.3.1 Genomic Southern blot analysis: restriction fragment length polymorphisms (RFLPs) 282 9.3.2 VNTR and microsatellites 285 9.3.3 Pulsed-field gel electrophoresis 287 9.4 Human genetic variation: relating phenotype to genotype 289 9.4.1 Linkage analysis 289 9.4.2 Genome-wide association studies (GWAS) 292 9.4.3 Database resources 294 9.4.4 Genetic diagnosis 294 9.5 Molecular phylogeny 295 9.5.1 Methods for constructing trees 298 10 Post-Genomic Analysis 305 10.1 Analysing transcription: transcriptomes 305 10.1.1 Differential screening 306 10.1.2 Other methods: transposons and reporters 308 10.2 Array-based methods 308 10.2.1 Expressed sequence tag (EST) arrays 309 10.2.2 PCR product arrays 310 10.2.3 Synthetic oligonucleotide arrays 312 10.2.4 Important factors in array hybridization 313 10.3 Transcriptome sequencing 315 10.4 Translational analysis: proteomics 316 10.4.1 Two-dimensional electrophoresis 317 10.4.2 Mass spectrometry 318 10.5 Post-translational analysis: protein interactions 320 10.5.1 Two-hybrid screening 320 10.5.2 Phage display libraries 321 10.6 Epigenetics 323 10.7 Integrative studies: systems biology 324 10.7.1 Metabolomic analysis 324 10.7.2 Pathway analysis and systems biology 325 11 Modifying Organisms: Transgenics 327 11.1 Transgenesis and cloning 327 11.1.1 Common species used for transgenesis 328 11.1.2 Control of transgene expression 330 11.2 Animal transgenesis 333 11.2.1 Basic methods 333 11.2.2 Direct injection 333 11.2.3 Retroviral vectors 335 11.2.4 Embryonic stem cell technology 336 11.2.5 Gene knockouts 339 11.2.6 Gene knock-down technology: RNA interference 340 11.2.7 Gene knock-in technology 341 11.3 Applications of transgenic animals 342 11.4 Disease prevention and treatment 343 11.4.1 Live vaccine production: modification of bacteria and viruses 343 11.4.2 Gene therapy 346 11.4.3 Viral vectors for gene therapy 347 11.5 Transgenic plants and their applications 349 11.5.1 Introducing foreign genes 349 11.5.2 Gene subtraction 351 11.5.3 Applications 352 11.6 Transgenics: a coda 353 Glossary 355 Bibliography 375 Index 379

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Book SynopsisThe increase in the use of microarray technology has led to the need for good standards of microarray experimental notation, data representation, and the introduction of standard experimental controls, as well as standard data normalization and analysis techniques. This book covers the subject.Trade Review"I liked this book and would recommend it to any statistician new to microarray data analysis…a unique combination of features that make it a contender among the standard textbooks…" (Journal of the American Statistical Association, June 2006) "...clear...up-to-date...lively advice...an excellent reference text for any researcher interested in the analysis of transcriptomic data." (Short Book Reviews, Vol.25, No.1, April 2005) "...this is a very good introduction to one of the most widely used methods for assessing differential expression..." (Journal of the Royal Statistical Society, Vol 168 (4) 2005) "...presents a coherent and systematic overview of statistical methods in all stages of the process of analysing microarray data..." (Zentralblatt Math, Vol.1049, 2004)Table of ContentsPreface. 1 Preliminaries. 1.1 Using the R Computing Environment. 1.1.1 Installing smida. 1.1.2 Loading smida. 1.2 Data Sets from Biological Experiments. 1.2.1 Arabidopsis experiment: Anna Amtmann. 1.2.2 Skin cancer experiment: Nighean Barr. 1.2.3 Breast cancer experiment: John Bartlett. 1.2.4 Mammary gland experiment: Gusterson group. 1.2.5 Tuberculosis experiment: BµG@S group. I Getting Good Data. 2 Set-up of a Microarray Experiment. 2.1 Nucleic Acids: DNA and RNA. 2.2 Simple cDNA Spotted Microarray Experiment. 2.2.1 Growing experimental material. 2.2.2 Obtaining RNA. 2.2.3 Adding spiking RNA and poly-T primer. 2.2.4 Preparing the enzyme environment. 2.2.5 Obtaining labelled cDNA. 2.2.6 Preparing cDNA mixture for hybridization. 2.2.7 Slide hybridization. 3 Statistical Design of Microarrays. 3.1 Sources of Variation. 3.2 Replication. 3.2.1 Biological and technical replication. 3.2.2 How many replicates? 3.2.3 Pooling samples. 3.3 Design Principles. 3.3.1 Blocking, crossing and randomization. 3.3.2 Design and normalization. 3.4 Single-channelMicroarray Design. 3.4.1 Design issues. 3.4.2 Design layout. 3.4.3 Dealing with technical replicates. 3.5 Two-channelMicroarray Designs. 3.5.1 Optimal design of dual-channel arrays. 3.5.2 Several practical two-channel designs. 4 Normalization. 4.1 Image Analysis. 4.1.1 Filtering. 4.1.2 Gridding. 4.1.3 Segmentation. 4.1.4 Quantification. 4.2 Introduction to Normalization. 4.2.1 Scale of gene expression data. 4.2.2 Using control spots for normalization. 4.2.3 Missing data. 4.3 Normalization for Dual-channel Arrays. 4.3.1 Order for the normalizations. 4.3.2 Spatial correction. 4.3.3 Background correction. 4.3.4 Dye effect normalization. 4.3.5 Normalization within and across conditions. 4.4 Normalization of Single-channel Arrays. 4.4.1 Affymetrix data structure. 4.4.2 Normalization of Affymetrix data. 5 Quality Assessment. 5.1 Using MIAME in Quality Assessment. 5.1.1 Components of MIAME. 5.2 Comparing Multivariate Data. 5.2.1 Measurement scale. 5.2.2 Dissimilarity and distance measures. 5.2.3 Representing multivariate data. 5.3 Detecting Data Problems. 5.3.1 Clerical errors. 5.3.2 Normalization problems. 5.3.3 Hybridization problems. 5.3.4 Array mishandling. 5.4 Consequences of Quality Assessment Checks. 6 Microarray Myths: Data. 6.1 Design. 6.1.1 Single-versus dual-channel designs? 6.1.2 Dye-swap experiments. 6.2 Normalization. 6.2.1 Myth: ‘microarray data is Gaussian’. 6.2.2 Myth: ‘microarray data is not Gaussian’. 6.2.3 Confounding spatial and dye effect. 6.2.4 Myth: ‘non-negative background subtraction’. II Getting Good Answers. 7 Microarray Discoveries. 7.1 Discovering Sample Classes. 7.1.1 Why cluster samples? 7.1.2 Sample dissimilarity measures. 7.1.3 Clustering methods for samples. 7.2 Exploratory Supervised Learning. 7.2.1 Labelled dendrograms. 7.2.2 Labelled PAM-type clusterings. 7.3 Discovering Gene Clusters. 7.3.1 Similarity measures for expression profiles. 7.3.2 Gene clustering methods. 8 Differential Expression. 8.1 Introduction. 8.1.1 Classical versus Bayesian hypothesis testing. 8.1.2 Multiple testing ‘problem’. 8.2 Classical Hypothesis Testing. 8.2.1 What is a hypothesis test? 8.2.2 Hypothesis tests for two conditions. 8.2.3 Decision rules. 8.2.4 Results from skin cancer experiment. 8.3 Bayesian Hypothesis Testing. 8.3.1 A general testing procedure. 8.3.2 Bayesian t-test. 9 Predicting Outcomes with Gene Expression Profiles. 9.1 Introduction. 9.1.1 Probabilistic classification theory. 9.1.2 Modelling and predicting continuous variables. 9.2 Curse of Dimensionality: Gene Filtering. 9.2.1 Use only significantly expressed genes. 9.2.2 PCA and gene clustering. 9.2.3 Penalized methods. 9.2.4 Biological selection. 9.3 Predicting ClassMemberships. 9.3.1 Variance-bias trade-off in prediction. 9.3.2 Linear discriminant analysis. 9.3.3 k-nearest neighbour classification. 9.4 Predicting Continuous Responses. 9.4.1 Penalized regression: LASSO. 9.4.2 k-nearest neighbour regression. 10 Microarray Myths: Inference. 10.1 Differential Expression. 10.1.1 Myth: ‘Bonferroni is too conservative’. 10.1.2 FPR and collective multiple testing. 10.1.3 Misinterpreting FDR. 10.2 Prediction and Learning. 10.2.1 Cross-validation. Bibliography. Index.

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Book SynopsisThe transposable genetic elements, or transposons, as they are now known, have had a tumultuous history. Discovered in the mid-20th century by Barbara McClintock, they were initially received with puzzlement. When their genomic abundance began to be apparent, they were categorized as junk DNA and acquired the label of parasites.Trade Review“I do love books where the text points toward the future as well as distilling the past and present. This volume does both.” (The Quarterly Review of Biology, 1 December 2014) Table of ContentsContributors ix Foreword xiDavid Botstein Introduction xiiiNina V. Fedoroff Chapter 1 The Discovery of Transposition 3Nina V. Fedoroff Introduction 3 Studies on Variegation 3 Mutable Genes 5 McClintock’s Studies on Chromosome Breakage 6 Recognition that Ds Transposes 8 Explaining Mutable Genes 9 Molecular Endnote 12 References 12 Chapter 2 A Field Guide to Transposable Elements 15Alan H. Schulman and Thomas Wicker The C-value Paradox 15 The Quantity of Transposable Elements Determines Genome Size 16 General Classification Scheme for Transposable Elements 17 Class II Elements 19 Class I: The Non-LTR and LTR Retrotransposons 20 Evolutionary Origins of Transposable Elements 25 Non-autonomous Transposable Elements 28 Transposable Element Demography and Genome Ecology 30 Conclusions: Rehabilitation of Transposable Elements 32 Acknowledgments 34 References 34 Chapter 3 The Mechanism of Ac/Ds Transposition 41Thomas Peterson and Jianbo Zhang Transposition of Ac/Ds Elements 41 The Enigmatic Ac Dosage Effect 42 cis and trans Effects on Ac/Ds Transposition 43 Molecular Characterization of Transposable Elements 44 The Excision and Insertion Reactions 45 Formation of Ds from Ac 48 Standard versus Alternative Transposition 48 Sister Chromatid Transposition 48 Reversed-ends Transposition 51 How Does Ds Break Chromosomes? 53 Alternative Transposition, DNA Methylation, and the Sequence of Transposition Reactions 54 Potential Applications of Alternative Transposition 55 Perspective 56 References 56 Chapter 4 McClintock and Epigenetics 61Nina V. Fedoroff Introduction 61 Spm-suppressible Alleles 61 Spm-dependent Alleles 64 Cryptic Spm 66 Presetting 66 Molecular Machinery of Epigenetic Regulation 67 Summary 68 References 69 Chapter 5 Molecular Mechanisms of Transposon Epigenetic Regulation 71Robert A. Martienssen and Vicki L. Chandler Introduction 71 Chromatin Remodeling, DNA and Histone Modification 73 RNA Interference (RNAi) and RNA-Directed DNA Methylation (RdDM) 75 Heterochromatin Reprogramming and Germ Cell Fate 79 Transgenerational Inheritance of Transposon Silencing 82 Paramutation 83 Conclusions 85 References 85 Chapter 6 Transposons in Plant Gene Regulation 93Damon R. Lisch Introduction 93 New Regulatory Functions 94 TE-Induced Down-Regulation 97 Deletions and Rearrangements 98 Suppressible Alleles 100 TEs and Plant Domestication 103 The Dynamic Genome 108 References 110 Chapter 7 Imprinted Gene Expression and the Contribution of Transposable Elements 117Mary A. Gehring Why are Genes Imprinted? 118 The Developmental Origin of Endosperm 118 Selection for Imprinted Expression 121 Principles Derived from the First Imprinted Gene 122 Gene Imprinting and Parent-of-Origin Effects on Seed Development 124 What Genes are Imprinted? 124 Epigenome Dynamics during Seed Development 127 Epigenetic Landscape in Vegetative Tissues 127 Cytological Observations of Chromatin in Seeds 129 Epigenomic Profiling in Seeds 130 Mechanisms of Gene Imprinting and the Relation to TEs 132 TEs and Allele-Specific Imprinting 136 Insights from Whole Genome Studies 137 Outstanding Questions 138 References 138 Chapter 8 Transposons and Gene Creation 143Hugo K. Dooner and Clifford F. Weil Introduction 143 Capture of Gene Fragments by TEs and Formation of Chimeric Genes 144 Co-Option of a TE Gene by the Host 148 Fusion of TE and Host Genes 150 Alterations of Host Gene Sequences by TE Excisions 151 Alterations of Host Coding Sequences by TE Insertions 152 Acquisition by Host Genes of New Regulatory Sequences from TEs 153 Interaction of TEs with Target Gene mRNA Splicing and Structure 155 Reshuffling of Host Sequences by Alternative Transpositions 156 Conclusion 158 References 158 Chapter 9 Transposons in Plant Speciation 165Avraham A. Levy Introduction 165 Genetic Models of Speciation 165 Speciation – a Gradual or a Rapid Process? 166 Speciation Through Accumulation of Mutations 166 DNA Cut-and-Paste TEs and Speciation 167 Copy-and-Paste TEs and Speciation 168 TE-Mediated Speciation – a Likely Scenario? 169 Plant Speciation Through Hybridization and Allopolyploidization 169 Induction of Transposition upon Hybridization and Polyploidization 170 Epigenetic Alteration of TEs upon Hybridization and Polyploidization 170 Transcriptional Activation of TEs upon Hybridization and Polyploidization 171 Alterations in Small RNAs upon Hybridization and Polyploidization 171 A Mechanistic Model for Responses to Genome Shock 172 Dysregulation of Gene Expression by Novel Interactions Between Regulatory Factors 173 Altered Protein Complexes 174 Why TEs Become Activated when Cellular Processes are Dysregulated 174 Conclusions 175 Acknowledgments 176 References 176 Chapter 10 Transposons, Genomic Shock, and Genome Evolution 181Nina V. Fedoroff and Jeffrey L. Bennetzen How Transposons Came to be Called “Selfish” DNA 181 The “Selfish DNA” Label Stuck to Transposons 182 Transposons Coevolved with Eukarotic Genomes 182 Sequence Duplication: The Real Innovation 183 The Facilitator: Epigenetic Control of Homologous Recombination 183 Epigenetic Mechanisms, Duplication and Genome Evolution 185 Plant Genome Organization: Gene Islands in a Sea of Repetitive DNA 186 Transposon Neighborhoods and Insertion Site Selection 187 Genome Evolution: Colinearity and Its Erosion 189 Genome Contraction and Divergence of Intergenic Sequences 191 Transposases Sculpt Genomes 192 Small Regulatory RNAs from Transposons 193 Genome Shocks 194 Genome Evolvability 195 References 196 Index 203

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Book SynopsisThe field of whole genome selection has quickly developed into the breeding methodology of the future. As efforts to map a wide variety of animal genomes have matured and full animal genomes are now available for many animal scientists and breeders are looking to apply these techniques to livestock production.Trade Review"Genomic Selection in Animals is a well-written book by a leading animal quantitative geneticist...This book will be particularly useful for graduate students in animal breeding and genetics, and more broadly for professionals with an interest in understanding how genomic information is being incorporated into breeding programs...Overall, this book is a readable summary of the concepts and current methods underlying genomic selection and a useful reference that I recommend for those with an interest in this rapidly evolving field." (Journal of the American Veterinary Medical Association 15/03/2017)Table of ContentsPreface: Welcome to the “Promised Land” xiii Chapter 1 Historical Overview 1 Introduction 1 The Mendelian Theory of Genetics 1 The Mendelian Basis of Quantitative Variation 2 Detection of QTL with Morphological and Biochemical Markers 2 DNA-Level Markers, 1974–1994 3 DNA-Level Markers Since 1995: SNPs and CNV 4 QTL Detection Prior to Genomic Selection 4 MAS Prior to Genomic Selection 5 Summary 6 Chapter 2 Types of Current Genetic Markers and Genotyping Methodologies 7 Introduction 7 From Biochemical Markers to DNA]Level Markers 7 DNA Microsatellites 8 Single Nucleotide Polymorphisms 8 Copy Number Variation 9 Complete Genome Sequencing 9 Summary 10 Chapter 3 Advanced Animal Breeding Programs Prior to Genomic Selection 11 Introduction 11 Within a Breed Selection: Basic Principles and Equations 11 Traditional Selection Schemes for Dairy Cattle 12 Crossbreeding Schemes: Advantages and Disadvantages 14 Summary 15 Chapter 4 Economic Evaluation of Genetic Breeding Programs 17 Introduction 17 National Economy versus Competition among Breeders 17 Criteria for Economic Evaluation: Profit Horizon, Interest Rate, and Return on Investment 18 Summary 20 Chapter 5 Least Squares, Maximum Likelihood, and Bayesian Parameter Estimation 21 Introduction 21 Least Squares Parameter Estimation 21 ML Estimation for a Single Parameter 22 ML Multiparameter Estimation 24 Methods to Maximize Likelihood Functions 26 Confidence Intervals and Hypothesis Testing for MLE 26 Bayesian Estimation 27 Parameter Estimation via the Gibbs Sampler 28 Summary 29 Chapter 6 Trait-Based Genetic Evaluation: The Mixed Model 31 Introduction 31 Principles of Selection Index 31 The Mixed Linear Model 34 The Mixed Model Equations 34 Solving the Mixed Model Equations 35 Important Properties of Mixed Model Solutions 36 Multivariate Mixed Model Analysis 37 The Individual Animal Model 38 Yield Deviations and Daughter Yield Deviations 39 Analysis of DYD as the Dependent Variable 40 Summary 41 Chapter 7 Maximum Likelihood and Bayesian Estimation of QTL Parameters with Random Effects Included in the Model 43 Introduction 43 Maximum Likelihood Estimation of QTL Effects with Random Effects Included in the Model, the Daughter Design 43 The Granddaughter Design 45 Determination of Prior Distributions of the QTL Parameters for the Granddaughter Design 46 Formula for Bayesian Estimation and Tests of Significance of a Segregating QTL in a Granddaughter Design 49 Summary 50 Chapter 8 Maximum Likelihood, Restricted Maximum Likelihood, and Bayesian Estimation for Mixed Models 51 Introduction 51 Derivation of Solutions to the Mixed Model Equations by Maximum Likelihood 51 Estimation of the Mixed Model Variance Components 52 Maximum Likelihood Estimation of Variance Components 52 Restricted Maximum Likelihood Estimation of Variance Components 54 Estimation of Variance Components via the Gibbs Sampler 55 Summary 58 Chapter 9 Distribution of Genetic Effects, Theory, and Results 59 Introduction 59 Modeling the Polygenic Variance 59 The Effective Number of QTL 61 The Case of the Missing Heritability 61 Methods for Determination of Causative Mutations for QTL in Animals and Humans 62 Determination of QTN in Dairy Cattle 63 Estimating the Number of Segregating QTL Based on Linkage Mapping Studies 64 Results of Genome Scans of Dairy Cattle by Granddaughter Designs 65 Results of Genome]Wide Association Studies in Dairy Cattle by SNP Chips 66 Summary 66 Chapter 10 The Multiple Comparison Problem 69 Introduction 69 Multiple Markers and Whole Genome Scans 69 QTL Detection by Permutation Tests 71 QTL Detection Based on the False Discovery Rate 71 A Priori Determination of the Proportion of False Positives 74 Biases with Estimation of Multiple QTL 75 Bayesian Estimation of QTL from Whole Genome Scans: Theory 76 Bayes A and Bayes B Models 77 Bayesian Estimation of QTL from Whole Genome Scans: Simulation Results 79 Summary 80 Chapter 11 Linkage Mapping of QTL 81 Introduction 81 Interval Mapping by Nonlinear Regression: The Backcross Design 81 Interval Mapping for Daughter and Granddaughter Designs 83 Computation of Confidence Intervals 84 Simulation Studies of CIs 85 Empirical Methods to Estimate CIs, Parametric and Nonparametric Bootstrap, and Jackknife Methods 86 Summary 87 Chapter 12 Linkage Disequilibrium Mapping of QTL 89 Introduction 89 Estimation of Linkage Disequilibrium in Animal Populations 89 Linkage Disequilibrium QTL Mapping: Basic Principles 90 Joint Linkage and Linkage Disequilibrium Mapping 92 Multitrait and Multiple QTL LD Mapping 93 Summary 93 Chapter 13 Marker-Assisted Selection: Basic Strategies 95 Introduction 95 Situations in Which Selection Index is Inefficient 95 Potential Contribution of MAS for Selection within a Breed: General Considerations 96 Phenotypic Selection versus MAS for Individual Selection 97 MAS for Sex-Limited Traits 98 MAS Including Marker and Phenotypic Information on Relatives 99 Maximum Selection Efficiency of MAS with All QTL Known, Relative to Trait-Based Selection, and the Reduction in RSE Due to Sampling Variance 99 Marker Information in Segregating Populations 100 Inclusion of Marker Information in “Animal Model” Genetic Evaluations 100 Predicted Genetic Gains with Genomic Estimated Breeding Values: Results of Simulation Studies 101 Summary 102 Chapter 14 Genetic Evaluation Based on Dense Marker Maps: Basic Strategies 103 Introduction 103 The Basic Steps in Genomic Evaluation 103 Evaluation of Genomic Estimated Breeding Values 104 Sources of Bias in Genomic Evaluation 104 Marker Effects Fixed or Random? 105 Individual Markers versus Haplotypes 106 Total Markers versus Usable Markers 106 Deviation of Genotype Frequencies from Their Expectations 107 Inclusion of All Markers versus Selection of Markers with Significant Effects 107 The Genomic Relationship Matrix 108 Summary 109 Chapter 15 Genetic Evaluation Based on Analysis of Genetic Evaluations or Daughter-Yield Evaluations 111 Introduction 111 Comparison of Single]Step and Multistep Models 111 Derivation and Properties of Daughter Yields and DYD 112 Computation of “Deregressed” Genetic Evaluations 113 Analysis of DYD as the Dependent Variable with All Markers Included as Random Effects 114 Computation of Reliabilities for Genomic Estimated Breeding Values 116 Bayesian Weighting of Marker Effects 116 Additional Bayesian Methods for Genomic Evaluation 117 Summary 117 Chapter 16 Genomic Evaluation Based on Analysis of Production Records 119 Introduction 119 Single-Step Methodologies: The Basic Strategy 119 Computation of the Modified Relationship Matrix when only a Fraction of the Animals are Genotyped: The Problem 120 Criteria for Valid Genetic Relationship Matrices 120 Computation of the Modified Relationship Matrix when only a Fraction of the Animals are Genotyped, the Solution 121 Solving the Mixed Model Equations without Inverting H 121 Inverting the Genomic Relationship Matrix 122 Estimation of Reliabilities for Genomic Breeding Values Derived by Single]Step Methodologies 122 Single-Step Computation of Genomic Evaluations with Unequally Weighted Marker Effects 123 Summary 124 Chapter 17 Validation of Methods for Genomic Estimated Breeding Values 125 Introduction 125 Criteria for Evaluation of Estimated Genetic Values 125 Methods Used to Validate Genomic Genetic Evaluations 126 Evaluation of Two-Step Methodology Based on Simulated Dairy Cattle Data 127 Evaluation of Multistep Methodology Based on Actual Dairy Cattle Data 127 Evaluation of Single-Step Methodologies Based on Actual Dairy Cattle Data 128 Evaluation of Single- and Multistep Methodologies Based on Actual Poultry Data 129 Evaluation of Single- and Multistep Methodologies Based on Actual Swine Data 130 Evaluation of GEBV for Plants Based on Actual Data 130 Summary 131 Chapter 18 By-Products of Genomic Analysis: Pedigree Validation and Determination 133 Introduction 133 The Effects of Incorrect Parentage Identification on Breeding Programs 133 Principles of Parentage Verification and Identification with Genetic Markers 134 Paternity Validation Prior to High]Density SNP Chips 135 Paternity Validation and Determination with SNP Chips 135 Validation of More Distant Relationships 136 Pedigree Reconstruction with High]Density Genetic Markers 137 Summary 137 Chapter 19 Imputation of Missing Genotypes: Methodologies, Accuracies, and Effects on Genomic Evaluations 139 Introduction 139 Determination of Haplotypes for Imputation 139 Imputation in Humans versus Imputation in Farm Animals 140 Algorithms Proposed for Imputation in Human and Animal Populations 141 Comparisons of Accuracy and Speed of Imputation Methods 142 Effect of Imputation on Genomic Genetic Evaluations 143 Summary 144 Chapter 20 Detection and Validation of Quantitative Trait Nucleotides 145 Introduction 145 GWAS for Economic Traits in Commercial Animals 146 Detection of QTN: Is It Worth the Effort? 146 QTN Determination in Farm Animals: What Constitutes Proof? 147 Concordance between DNA-Level Genotypes and QTL Status 148 Determination of Concordance by the “APGD” 148 Determination of Phase for Grandsires Heterozygous for the QTL 149 Determination of Recessive Lethal Genes by GWAS and Effects Associated with Heterozygotes 150 Verification of QTN by Statistical and Biological Methods 150 Summary 151 Chapter 21 Future Directions and Conclusions 153 Introduction 153 More Markers versus More Individuals with Genotypes 153 Computation of Genomic Evaluations for Cow and Female Calves 154 Improvement of Genomic Evaluation Methods 154 Long-Term Considerations 155 Weighting Evaluations of Old versus Young Bulls 156 Direct Genetic Manipulation in Farm Animals 156 Velogenetics: The Synergistic Use of MAS and Germ-Line Manipulation 157 Summary 157 References 159 Index 171

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Book SynopsisThis up-to-date review of seed genomics, from basic seed biology to practical applications in crop science, provides a thorough background understanding of seed biology from a basic science perspective.Table of ContentsContributors xi Introduction 1 Philip W. Becraft Chapter 1 Large-Scale Mutant Analysis of Seed Development in Arabidopsis 5 David W. Meinke Introduction 5 Historical Perspective 5 Arabidopsis Embryo Mutant System 7 Large-Scale Forward Genetic Screens for Seed Mutants 7 Approaches to Mutant Analysis 8 Strategies for Approaching Saturation 10 SeedGenes Database of Essential Genes in Arabidopsis 11 Embryo Mutants with Gametophyte Defects 13 General Features of EMB Genes in Arabidopsis 14 Value of Large Datasets of Essential Genes 15 Directions for Future Research 16 Acknowledgments 17 References 17 Chapter 2 Embryogenesis in Arabidopsis: Signaling, Genes, and the Control of Identity 21 D. L. C. Kumari Fonseka, Xiyan Yang, Anna Mudge, Jennifer F. Topping, and Keith Lindsey Introduction 21 Cellular Events 21 Genes and Signaling – the Global Picture 23 Coordination of Genes and Cellular Processes: a Role for Hormones 25 Genes and Pattern 30 Conclusion and Future Directions 36 References 36 Chapter 3 Endosperm Development 43 Odd-Arne Olsen and Philip W. Becraft Introduction 43 Overview of Endosperm Structure and Development 43 Endosperm Cell Fate Specification and Differentiation 48 Genomic Resources 53 Transcriptional Profiling of Endosperm Development 54 Gene Imprinting in Cereal Endosperm 56 Conclusion 57 Acknowledgments 58 References 58 Chapter 4 Epigenetic Control of Seed Gene Imprinting 63 Christian A. Ibarra, Jennifer M. Frost, Juhyun Shin, Tzung-Fu Hsieh, and Robert L. Fischer Introduction 63 Genomic Imprinting and Parental Conflict Theory 63 Epigenetic Regulators of Arabidopsis Imprinting 65 Mechanisms Establishing Arabidopsis Gene Imprinting 69 Imprinting in the Embryo 74 Imprinting in Monocots 75 Evolution of Plant Imprinting 77 Conclusion 78 Acknowledgments 78 References 78 Chapter 5 Apomixis 83 Anna M. G. Koltunow, Peggy Ozias-Akins, and Imran Siddiqi Introduction 83 Biology of Apomixis in Natural Systems 84 Phylogenetic and Geographical Distribution of Apomixis 89 Inheritance of Apomixis 90 Genetic Diversity in Natural Apomictic Populations 93 Molecular Relationships between Sexual and Apomictic Pathways 94 Features of Chromosomes Carrying Apomixis Loci and Implications for Regulation of Apomixis 95 Genes Associated with Apomixis 96 Transferring Apomixis to Sexual Plants: Clues from Apomicts 97 Synthetic Approach to Building Apomixis 98 Synthetic Clonal Seed Formation 102 Conclusion and Future Prospects 103 References 103 Chapter 6 High-Throughput Genetic Dissection of Seed Dormancy 111 Jose M. Barrero, Colin Cavanagh, and Frank Gubler Introduction 111 Profiling of Transcriptomic Changes 113 Use of New Sequencing Platforms and Associated Techniques to Study Seed Dormancy 114 Visualization Tools 116 Coexpression Studies and Systems Biology Approaches 116 Mapping Populations for Gene Discovery 117 Perspective 118 Acknowledgments 119 References 119 Chapter 7 Genomic Specification of Starch Biosynthesis in Maize Endosperm 123 Tracie A. Hennen-Bierwagen and Alan M. Myers Introduction 123 Overview of Starch Biosynthetic Pathway 124 Genomic Specification of Endosperm Starch Biosynthesis in Maize 126 Conclusion 134 References 134 Chapter 8 Evolution, Structure, and Function of Prolamin Storage Proteins 139 David Holding and Joachim Messing Introduction 139 Prolamin Multigene Families 139 Endosperm Texture and Storage of Prolamins 143 Conclusion 154 References 154 Chapter 9 Improving Grain Quality: Wheat 159 Peter R. Shewry Introduction 159 Grain Structure and Composition 159 End Use Quality 161 Redesigning the Grain 163 Manipulation of Grain Protein Content and Quality 163 Manipulation of Grain Texture 167 Development of Wheat with Resistant Starch 168 Improving Content and Composition of Dietary Fiber 169 Wheat Grain Cell Walls 169 Conclusion 173 Acknowledgments 173 References 173 Chapter 10 Legume Seed Genomics: How to Respond to the Challenges and Potential of a Key Plant Family? 179 Mélanie Noguero, Karine Gallardo, Jérôme Verdier, Christine Le Signor, Judith Burstin, and Richard Thompson Introduction 179 Development of Genomics Tools 180 Applications of Genomics Tools to Legume Seed Biology 185 Future Challenges 192 References 193 Chapter 11 Cotton Fiber Genomics 203 Xueying Guan and Z. Jeffrey Chen Introduction 203 Cotton Fiber Development 204 Roles for Transcription Factors in Development of Arabidopsis Leaf Trichomes, Seed Hairs, and Cotton Fibers 204 Fiber Cell Expansion through Cell Wall Biosynthesis 208 Regulation of Phytohormones during Cotton Fiber Development 209 Cotton Fiber Genes in Diploid and Tetraploid Cotton 210 Roles for Small RNAs in Cotton Fiber Development 211 Conclusion 212 References 213 Chapter 12 Genomic Changes in Response to 110 Cycles of Selection for Seed Protein and Oil Concentration in Maize 217 Christine J. Lucas, Han Zhao, Martha Schneerman, and Stephen P. Moose Introduction 217 Background on the Illinois Long-Term Selection Experiment 217 Phenotypic Responses to Selection 219 Additional Traits Affected by Selection 220 Unlimited Genetic Variation? 221 Genetic Response to Selection: QTL Mapping in the Crosses of IHP x ILP and IHO x ILO 222 New Mapping Population: Illinois Protein Strain Recombinant Inbreds 223 Characterization of Zein Genes and Their Expression in Illinois Protein Strains 225 Contribution of Zein Regulatory Factor Opaque2 to Observed Responses to Selection in Illinois Protein Strains 227 Major Effect QTL May Explain IRHP Phenotype 228 Zein Promoter-Reporter Lines to Investigate Regulation of 22-kDa α-Zein Gene Expression in Illinois Protein Strains 229 Regulatory Changes in FL2-mRFP Expression When Crossed to Illinois Protein Strains 230 Regulation of FL2-mRFP 232 Acknowledgments 233 References 234 Chapter 13 Machine Vision for Seed Phenomics 237 Jeffery L. Gustin and A. Mark Settles Introduction 237 High-Energy Imaging: X-ray Tomography and Fluorescence 238 Optical Imaging: Visible Spectrum 240 Resonance Absorption: Infrared Spectrum 242 Resonance Emission: Nuclear Magnetic Resonance 245 Conclusion 246 Acknowledgments 246 References 246 Color plate section found between pages 42 and 43. Index 253

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Book SynopsisPolyploidy plays an important role in biological diversity, trait improvement, and plant species survival. Understanding the evolutionary phenomenon of polyploidy is a key challenge for plant and crop scientists.Table of ContentsContributors xi Preface xvii Section I Genomics of Hybrids 1 1 Yeast Hybrids and Polyploids as Models in Evolutionary Studies 3 Avraham A. Levy, Itay Tirosh, Sharon Reikhav, Yasmin Bloch, and Naama Barkai 2 Transcriptome Profiling of Drosophila Interspecific Hybrids: Insights into Mechanisms of Regulatory Divergence and Hybrid Dysfunction 15 Jos´e M. Ranz, Shu-Dan Yeh, Kevin G. Nyberg, and Carlos A. Machado 3 cis- and trans-Regulation in Drosophila Interspecific Hybrids 37 Joseph D. Coolon and Patricia J. Wittkopp 4 Gene Expression and Heterosis in Maize Hybrids 59 Mei Guo and J. Antoni Rafalski 5 Integrating “Omics” Data and Expression QTL to Understand Maize Heterosis 85 Camille Rustenholz and Patrick S. Schnable 6 Genomics and Heterosis in Hexaploid Wheat 105 Zhongfu Ni, Yingyin Yao, Huiru Peng, Zhaorong Hu, and Qixin Sun 7 Progress of Genomics and Heterosis Studies in Hybrid Rice 117 Lei Zhang, Yonggang Peng, Yang Dong, Hongtao Li, Wen Wang, and Zhen Zhu 8 Heterosis: The Case for Single-Gene Overdominance 137 Katie L. Liberatore, Ke Jiang, Dani Zamir, and Zachary B. Lippman Section II Genomics of Polyploids 153 9 Genomics and Transcriptomics of Photosynthesis in Polyploids 155 Jeremy E. Coate and Jeff J. Doyle 10 Chromosomal and Gene Expression Changes in Brassica Allopolyploids 171 Eric Jenczewski, A.M. Ch`evre, and K. Alix 11 Dynamics of Duplicated Gene Expression in Polyploid Cotton 187 Keith L. Adams and Jonathan F. Wendel 12 Reprogramming of Gene Expression in the Genetically Stable Bread Allohexaploid Wheat 195 Dominique Arnaud, Houda Chelaifa, Joseph Jahier, and Boulos Chalhoub 13 Nucleocytoplasmic Interaction Hypothesis of Genome Evolution and Speciation in Polyploid Plants Revisited: Polyploid Species-Specific Chromosomal Polymorphisms inWheat 213 Bikram S. Gill and B. Friebe Section III Mechanisms for Novelty in Hybrids and Polyploids 223 14 Genes Causing Postzygotic Hybrid Incompatibility in Plants: A Window into Co-Evolution 225 Kirsten Bomblies 15 Meiosis in Polyploids 241 Graham Moore 16 Genomic Imprinting: Parental Control of Gene Expression in Higher Plants 257 Peter C. McKeown, Antoine Fort, and Charles Spillane 17 Seed Development in Interploidy Hybrids 271 Roderick J. Scott, Julia L. Tratt, and Ahmed Bolbol 18 Chromatin and Small RNA Regulation of Nucleolar Dominance 291 Pedro Costa-Nunes and Olga Pontes 19 Genetic Rules of Heterosis in Plants 313 James A. Birchler 20 Chromatin and Gene Expression Mechanisms in Hybrids 323 Guangming He and Xing-Wang Deng 21 Genetic and Epigenetic Mechanisms for Polyploidy and Hybridity 335 Z. Jeffrey Chen and Helen H. Yu Index 355 A color plate is located between pages 174 and 175.

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