In this timely new 2-volume treatise, experts from around the world have banded together to produce a first-of-its-kind synopsis of the exciting and fast moving field of plant evolutionary genomics. In Volume I of Plant Genome Diversity, an update is provided on what we have learned from plant genome sequencing projects. This is followed by more focused chapters on the various genomic "residents" of plant genomes, including transposable elements, centromeres, small RNAs, and the evolutionary dynamics of genes and non-coding sequences. Attention is drawn to advances in our understanding of plant mitochondrial and plastid genomes, as well as the significance of duplication in genic evolution and the non-independent evolution among sequences in plant genomes. Finally, Volume I provides an introduction to the vibrant new frontier of plant epigenomics, describing the current state of our knowledge and the evolutionary implications of the epigenomic landscape.

In 2001, first reports of the human draft genome were published. Since then, genomes of many other organisms have been sequenced, including several primate species: the chimpanzee, rhesus macaque, gorilla, orangutan, gibbon, baboon, marmoset, tarsier, galago, lemur, and more recently Neanderthals. In a new era of "post-genome biology", scientists now have the vast amount of information revealed by genome research to confront one of the most challenging, fundamental questions in primatology and anthropology: What makes us human? This volume comprises a collection of articles on a variety of topics relevant to primate genomes, including evolution, human origins, genome structure, chromosome genomics, and bioinformatics. The book covers the cutting-edge research in molecular primatology and provides great insights into the functional diversity of primates. This valuable collection will benefit researchers and students, including primatologists, anthropologists, molecular biologists, evolutionary biologists, and animal behaviorists.

Transcriptome Analysis, by Frank Stahl, Bernd Hitzmann, Kai Mutz, Daniel Landgrebe, Miriam Lubbecke, Cornelia Kasper, Johanna Walter und Thomas Scheper Transcriptome Data Analysis for Cell Culture Processes, by Marlene Castro-Melchor, Huong Le und Wei-Shou Hu Modeling Metabolic Networks for Mammalian Cell Systems: General Considerations, Modeling Strategies, and Available Tools, by Ziomara P. Gerdtzen Metabolic Flux Analysis in Systems Biology of Mammalian Cells, by Jens Niklas und Elmar Heinzle Advancing Biopharmaceutical Process Development by System-Level Data Analysis and Integration of Omics Data, by Jochen Schaub, Christoph Clemens, Hitto Kaufmann und Torsten W. Schulz Protein Glycosylation and Its Impact on Biotechnology, by Markus Berger, Matthias Kaup und Veronique Blanchard Protein Glycosylation Control in Mammalian Cell Culture: Past Precedents and Contemporary Prospects, by Patrick Hossler Modeling of Intracellular Transport and Compartmentation, by Uwe Jandt und An-Ping Zeng Genetic Aspects of Cell Line Development from a Synthetic Biology Perspective, by L. Botezatu, S. Sievers, L. Gama-Norton, R. Schucht, H. Hauser und D. Wirth."

"What underlying forces are responsible for the observed patterns of variability, given a collection of DNA sequences?" In approaching this question a number of probability models are introduced and anyalyzed.Throughout the book, the theory is developed in close connection with data from more than 60 experimental studies that illustrate the use of these results.

Transcription factors are the molecules that the cell uses to interpret the genome: they possess sequence-specific DNA-binding activity, and either directly or indirectly influence the transcription of genes. In aggregate, transcription factors control gene expression and genome organization, and play a pivotal role in many aspects of physiology and evolution.

This book provides a reference for major aspects of transcription factor function, encompassing a general catalogue of known transcription factor classes, origins and evolution of specific transcription factor types, methods for studying transcription factor binding sites in vitro, in vivo, and in silico, and mechanisms of interaction with chromatin and RNA polymerase."

This book provides an evolutionary conceptual framework for comparative genomics, with the ultimate objective of understanding the loss and gain of genes during evolution, the interactions among gene products, and the relationship between genotype, phenotype and the environment. The many examples in the book have been carefully chosen from primary research literature based on two criteria: their biological insight and their pedagogical merit. The phylogeny-based comparative methods, involving both continuous and discrete variables, often represent a stumbling block for many students entering the field of comparative genomics. They are numerically illustrated and explained in great detail. The book is intended for researchers new to the field, i.e., advanced undergraduate students, postgraduates and postdoctoral fellows, although professional researchers who are not in the area of comparative genomics will also find the book informative.

This book provides a broad introduction to all major aspects of quantum dot properties including fluorescence, electrochemical, photochemical and electroluminescence. Such properties have been produced for applications in biosensing, cell tracking, in vivo animal imaging and so on. It focuses on their special applications in DNA biosensing and provides readers with detailed information on the preparation and functionalization of quantum dots and the fabrication of DNA biosensors, using examples to show how these properties can be used in DNA biosensor design and the advantages of quantum dots in DNA biosensing. Further new emerging quantum dots such as metal nanoclusters and graphene dots and their applications in DNA biosensing have also been included.

One of the world's leading experts on genetics unravels one of the most important breakthroughs in modern science and medicine. If our genes are, to a great extent, our destiny, then what would happen if mankind could engineer and alter the very essence of our DNA coding? Millions might be spared the devastating effects of hereditary disease or the challenges of disability, whether it was the pain of sickle-cell anemia to the ravages of Huntington's disease. But this power to "play God" also raises major ethical questions and poses threats for potential misuse. For decades, these questions have lived exclusively in the realm of science fiction, but as Kevin Davies powerfully reveals in his new book, this is all about to change. Engrossing and page-turning, Editing Humanity takes readers inside the fascinating world of a new gene editing technology called CRISPR, a high-powered genetic toolkit that enables scientists to not only engineer but to edit the DNA of any organism down to the individual building blocks of the genetic code. Davies introduces readers to arguably the most profound scientific breakthrough of our time. He tracks the scientists on the front lines of its research to the patients whose powerful stories bring the narrative movingly to human scale. Though the birth of the "CRISPR babies" in China made international news, there is much more to the story of CRISPR than headlines seemingly ripped from science fiction. In Editing Humanity, Davies sheds light on the implications that this new technology can have on our everyday lives and in the lives of generations to come.

Designed as an introductory text the authors cover all core strategies in the application of modern recombinant DNA technology. The first chapters directly address the applications of polymerase chain reaction to a variety of problems in DNA cloning that are, or have been, extremely challenging using more traditional approaches and technologies. These include cDNA cloning and transcript mapping, mutagenesis as well as the cloning of very long transcripts and protocols using limiting amounts of total RNA. Further chapters describe approaches to subtractive cloning technologies as well as novel specialized expression cloning and library screening strategies. The handbook contains detailed step-by-step protocols and extensive hands-on advice.

Using genome sequencing, one can predict possible interactions among proteins. There are very few titles that focus on protein-protein interaction predictions in bacteria. The authors will describe these methods and further highlight its use to predict various biological pathways and complexity of the cellular response to various environmental conditions. Topics include analysis of complex genome-scale protein-protein interaction networks, effects of reference genome selection on prediction accuracy, and genome sequence templates to predict protein function.

Winner of the 2014 Diamond Anniversary Book Award Finalist for the 2014 National Communications Association Critical and Cultural Studies Division Book of the Year Award In 2000, the National Human Genome Research Institute announced the completion of a "draft" of the human genome, the sequence information of nearly all 3 billion base pairs of DNA. Since then, interest in the hereditary basis of disease has increased considerably. In The Material Gene, Kelly E. Happe considers the broad implications of this development by treating "heredity" as both a scientific and political concept. Beginning with the argument that eugenics was an ideological project that recast the problems of industrialization as pathologies of gender, race, and class, the book traces the legacy of this ideology in contemporary practices of genomics. Delving into the discrete and often obscure epistemologies and discursive practices of genomic scientists, Happe maps the ways in which the hereditarian body, one that is also normatively gendered and racialized, is the new site whereby economic injustice, environmental pollution, racism, and sexism are implicitly reinterpreted as pathologies of genes and by extension, the bodies they inhabit. Comparing genomic approaches to medicine and public health with discourses of epidemiology, social movements, and humanistic theories of the body and society, The Material Gene reworks our common assumption of what might count as effective, just, and socially transformative notions of health and disease.

Adenine Nucleotides play a major role in cellular metabolism and functions, serving as high-potential phosphate transfer compounds in energy metabolism and as substrates and co-factors for proteins involved in signal transduction. During the last few years definite advancement has been made in elucidating the molecular and genetic aspects of the enzyme involved in oxidative phosphorylation, the so-called FoFl H~-ATP synthase. Non-invasive NMR technologies have been developed to monitor in vivo the energy level of tissues based on determination of the concentrations of adenine nucleotides, phosphate and phosphate esters. Thus it became clear that the capacity of oxidative phosphorylation adapts itself to the ATP demand which changes continuously with the physiological state in various tissues. This is achieved by regulation of the enzyme activity as well as by regulation of its biogenesis. The reversible phosphorylation of proteins is re- cognised as a major regulatory mechanism in eukaryotic as well as in prokaryotic cells for cellular signal transduction and control of gene expression, cell growth, differentation and oncogenesis. The same applies to the role played by cAMP. A further topic of growing interest concerns the discovery of the ATP binding cassette (ABC) superfamily of transport proteins which includes systems of primary importance in medicine such as the multi-drug resistance P glycoprotein, the cystic fibrosis transmembrane conductance regulator (CFTR) and the 70 kd peroxisomal membrane protein. Finally, much attention is being devoted in many laboratories to the molecular structure and role of ATP- modulated channels.

PCR s simplicity as a molecular technique is, in some ways, responsible for the huge amount of innovation that surrounds it, as researchers continually think of new ways to tweak, adapt, and re-formulate concepts and applications. PCR Technology Current Innovations, Third Edition is a collection of novel methods, insights, and points of view that provides a critical and timely reference point for anyone wishing to use this technology.

Topics in this forward-thinking volume include:

• The purification and handling of PCR templates
• The effect of the manufacture and purification of the oligonucleotide on PCR behavior
• Optimum buffer composition
• Probe options
• The design and optimization of qPCR assays
• Issues surrounding the development and refinement of instrumentation
• Effective controls to protect against uncertainties due to reaction variability

Covering all aspects of PCR and real-time PCR, the book contains detailed protocols that make it suitable as both a reference and an instruction manual. Each chapter presents detailed guidelines as well as helpful hints and tips supplied by authors who are recognized experts in their fields. In addition to descriptions of current technology and best practices, the book also provides information about new developments in the PCR arena.

Depite the rapid expansion of the field of biophysics, there are very few books that comprehensively treat specific topics in this area. Recently, the field of single molecule biophysics has developed very quickly, and a few books specifically treating single molecule methods are beginning to appear. However, the promise of single molecule biophysics is to contribute to the understanding of specific fields of biology using new methods. This book would focus on the specific topic of the biophysics of DNA-protein interactions, and would include the use of new approaches, including both bulk methods as well as single molecule methods. This would make the book attractive to anyone working in the general area of DNA-protein interactions, which is of course a much wider market than just single molecule biophysicists or even biophysicists.

The subject of the book will be the biophysics of DNA-protein interactions, and will include new methods and results that describe the physical mechanism by which proteins interact with DNA. For example, there has been much recent work on the mechanism by which proteins search for specific binding sites on DNA. A few chapters will be devoted to experiments and theory that shed light on this important problem. We will also cover proteins that alter DNA properties to facilitate interactions important for transcription or replication. Another section of the book will cover the biophysical mechanism by which motor proteins interact with DNA. Finally, we will cover larger protein-DNA complexes, such as replication forks, recombination complexes, DNA repair interactions, and their chromatin context.

This volume provides a collection of robust protocols for molecular biologists studying comparative genomics. Each chapter includes detailed instructions for using a particular tool or method and an introduction to the theory behind the technique. Given the tremendous increase in available biosequence data over the past ten years, this volume is timely, comprehensive, and novel.

Colin Graham and a team of leading investigators and expert clinical scientists update the acclaimed first edition with a collection of powerful, up-to-date PCR-based methods for DNA sequencing, many suitable for human genome sequencing and mutation detection in human disease. This second edition offers new material on automated DNA sequencers, capillary DNA sequencers, heterozygote mutation detection, web-based sequencing databases and genome sequencing sites, and the human genome project. State-of-the-art and highly practical, DNA Sequencing Protocols, 2nd Edn. constitutes an essential laboratory handbook for geneticists and molecular biologists, offering concise, easy-to-follow methods that will work and impact today's genome sequencing projects.

Quantitative trait locus (QTL) mapping is used to discover the genetic and molecular architecture underlying complex quantitative traits. It has important applications in agricultural, evolutionary, and biomedical research. R/qtl is an extensible, interactive environment for QTL mapping in experimental crosses. It is implemented as a package for the widely used open source statistical software R and contains a diverse array of QTL mapping methods, diagnostic tools for ensuring high-quality data, and facilities for the fit and exploration of multiple-QTL models, including QTL x QTL and QTL x environment interactions. This book is a comprehensive guide to the practice of QTL mapping and the use of R/qtl, including study design, data import and simulation, data diagnostics, interval mapping and generalizations, two-dimensional genome scans, and the consideration of complex multiple-QTL models. Two moderately challenging case studies illustrate QTL analysis in its entirety.

The book alternates between QTL mapping theory and examples illustrating the use of R/qtl. Novice readers will find detailed explanations of the important statistical concepts and, through the extensive software illustrations, will be able to apply these concepts in their own research. Experienced readers will find details on the underlying algorithms and the implementation of extensions to R/qtl. There are 150 figures, including 90 in full color.

Through many recent remarkable developments, perhaps the most significant advancements in the study of transcriptional regulation are the development of genome-wide approaches for measuring gene expression, exemplified by gene chips (chip), and chromatin immunoprecipitation assays (ChIP) for measuring "in vivo" protein-DNA interactions at any genomic loci. "Transcriptional Regulation: Methods and Protocols" takes this progress and builds upon it with a collection of key protocols used in expert laboratories around the world. Divided into four convenient sections, this detailed volume explores promoter elements, transcription factors, and preinitiation complex (PIC) assembly, chromatin structure, chromatin modifying complexes, and RNA synthesis and regulation. Written in the highly successful "Methods in Molecular Biology " series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and vital tips on troubleshooting and avoiding known pitfalls.

Comprehensive and accessible, "Transcriptional Regulation: Methods and Protocols" equally serves senior researchers and scientists experienced in transcriptional regulation as well as graduate students and scientists who wish to study transcriptional regulation for the first time."

Advances in Botanical Research publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences. The series features several reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology, and ecology. Volume 78 focuses on the Genomes and Evolution of Charophytes, Bryophytes, Lycophytes, and Ferns. Sequencing of genomes of 'lower' animals such as sponges or hydrozoans has much informed our understanding of how metazoans evolved. On the plant side of things, sequencing and comparison of a moss and lycophyte genome with those of green algae and flowering plants has greatly informed our understanding of plant evolution. However, it has also become clear that we need to look into genomes of the closest algal relatives to land plants, the charophytes, and into further genomes of bryophytes, lycophytes, and ferns to unravel how land plants evolved.

DNA repair is a rapidly advancing field in biology. DNA repair systems represent a major defense mechanism against environmental and intracellular damaging agents, such as sunlight, ionizing radiation, and reactive oxygen species. With contributions from eminent researchers, this book explores the basics and current trends in this critical field. In particular, it provides essential information to scientists, pharmaceutical investigators, and clinicians interested in cancer therapy.

It will be some time beforewe see Relax, there's nothing wrong with the "slime, protoplasm, &c. "generating transpositionpaper. People aren't a new animal. ButI have long readyforthisyet. Istopped publishing regretted that I truckled to public in refereed journals in 1965 because opinion,andusedthePentateuchal therewas nointerest in themaize term of creation,by which I really controlling elements. meant "appeared" by some wholly Barbara McClintockto Mel Green, unknownprocess. It is mere rubbish, 1969 thinking at presentof theorigin of life; onemight as well think of the originof matter. Charles Darwin to James D. Hooker, March29, 1863 Sometimes my students and others have asked me: "what was ?rst in evo- tion - retroviruses or retrotransposons?" Since HowardTemin proposed that retrovirusesevolvedfromretrotransposons(Temin1980;Teminetal. 1995)the other alternative that retroviruses emerged ?rst and were the predecessors of LTR-retrotransposons has since been a controversial issue (Terzian et al. , this BOOK). While DNA-transposons could not have existed in an ancestral R- world by de?nition, sure enough, some arguments de?nitely point towards apre-DNAworldscenarioinwhichretroelementswerethedirectdescendants of the earliest replicators representing the emergence of life. First, these rep- cators likely catalyzed their own or other's replication cycles via the catalytic properties of RNA molecules. After translation had emerged some replicators possibly encoded an RNA polymerase ?rst. This later evolved into reverse transcriptase(RT),i. e. themostprominentkey-factoratthetransitionintothe DNA world. Simultaneously, replicators could also have encoded membrane protein-genessuchastheenvgeneofrecentDNA-proviruses. Membraneswere likely present muchearlier as prebioticoily ?lms that supported theevolution of a prebiotic-protometabolism (Dyson 1999; Grif?ths 2007).

Life's Greatest Secret is the story of the discovery and cracking of the genetic code. This great scientific breakthrough has had far-reaching consequences for how we understand ourselves and our place in the natural world. The code forms the most striking proof of Darwin's hypothesis that all organisms are related, holds tremendous promise for improving human well-being, and has transformed the way we think about life. Matthew Cobb interweaves science, biography and anecdote in a book that mixes remarkable insights, theoretical dead-ends and ingenious experiments with the pace of a thriller. He describes cooperation and competition among some of the twentieth century's most outstanding and eccentric minds, moves between biology, physics and chemistry, and shows the part played by computing and cybernetics. The story spans the globe, from Cambridge MA to Cambridge UK, New York to Paris, London to Moscow. It is both thrilling science and a fascinating story about how science is done.

This book facilitates the introduction of SAGE into the laboratory and provides a framework for interpreting and comparing data derived from SAGE experiments. SAGE studies encompass 50,000 tags and can provide detailed knowledge of the 2000 most highly expressed genes in the tissue sample. The SAGE protocols presented are detailed, fully annotated, and tested, and are all written by experienced SAGE researchers from around the world.

Combinatorial chemistry is used to find materials that form sensor microarrays. This book discusses the fundamentals, and then proceeds to the many applications of microarrays, from measuring gene expression (DNA microarrays) to protein-protein interactions, peptide chemistry, carbodhydrate chemistry, electrochemical detection, and microfluidics.

In recent years, high-density DNA microarrays have revolutionized biomedical research and drug discovery efforts by the pharmaceutical industry. Their efficacy in identifying and prioritizing drug targets based on their ability to confirm a large number of gene expression measurements in parallel has become a key element in drug discovery. Microarray Innovations: Technology and Experimentation examines the incredibly powerful nature of array technology and the ways in which it can be applied to understanding the genomic basis of disease. Explores a myriad of applications in use today This volume explores recent innovations in the microarray field and tracks the evolution of the major platforms currently used. The international panel of contributors presents a survey of the past five years' research and advancements in microarray methods and applications and their usage in drug discovery and biomedical research. The contributions discuss improvements in automation (array fabrication and hybridization), new substrates for printing arrays, platform comparisons and contrasts, experimental design, and data normalization and mining schemes. They also review epigenomic array studies, electronic microarrays, comparative genomic hybridization, microRNA arrays, and mutational analyzes. In addition, the book provides coverage of important clinical diagnostic arrays, protein arrays, and neuroscience applications. Examines improved methodologies As microarrays have evolved steadily over time from archetypical in-house complementary DNA (cDNA) arrays to robust commercial oligonucleotide platforms, there has been a migration to higher density biochips with increasing content and better analytical methodologies. This compendium summarizes the vast advances that have been made in this technology, highlighting the supreme advantages of microarray-based appro