Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP) which has become a world-wide effort and the Global Ocean Sampling (GOS) surveys. The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to receive seminal contributions from the leaders in the field and at the same time provide this information to a significant number of junior and senior scientists, via colleges, libraries, and just through online access. This format also allows scientists in the developing world to have continued access to this growing field. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.

This book describes how genomics has revolutionized our scientific understanding of agriculturally important plant-associated bacteria. Each chapter focuses on the genomics of particular bacteria: the first described plant pathogen, "Erwinia amylovora"; phytoplasmas lacking cell walls; fastidious, phloem-restricted liberibacters; "Pseudomonas syringae," which is a genetically tractable model system; "Xanthomonas citri," which causes a disease that can devastate citrus crops and "Pseudomonas fluorescens," which can protect plants from diseases.

Topics considered in this volume include the importance of horizontal gene transfer in originating new bacterial strains and species and advances in transcriptomics that allow us to describe the complex regulatory networks critical to plant-microbe interactions. The availability of the "Xanthomonas oryzae" genome has led to new technologies in genome editing, which will revolutionize approaches to genetic engineering, even in eukaryotes. The contributions show how genomics has greatly accelerated progress toward understanding the biology of these bacteria and how that understanding can be translated into novel crop protection methods.

The series Topics in Current Chemistry presents critical reviews of the present and future trends in modern chemical research. The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience. Each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field. Review articles for the individual volumes are invited by the volume editors. Readership: research chemists at universities or in industry, graduate students.

This book summarizes the latest information and the status quo of radish genome studies to stimulate innovations and improvements in breeding techniques and to promote further advances in the field. Radish (Raphanus sativus) is a member of the Brassicaceae family and is cultivated worldwide. Its varieties have been diversified in terms of size, shape, and the color of their roots and bio-components. Thanks to the development of high-throughput molecular techniques using next generation sequencers, complete genomes of cultivated and wild radish plants have been sequenced and published with annotations of predicted genes and single nucleotide polymorphism (SNP) information between radish cultivars and accessions. These, together with the construction of a high-density genetic map of radish and profiling of expression sequences in radish organs, have accelerated genetic studies, such as the identification of genes or loci associated with root development, pungent components, and plant disease resistance. Providing an overview of these advances, this book is a valuable resource for scientists involved in plant genetic research and crop breeding.

The discovery of stress-induced mutagenesis has changed ideas about mutation and evolution, and revealed mutagenic programs that differ from standard spontaneous mutagenesis in rapidly proliferating cells. The stress-induced mutations occur during growth-limiting stress, and can include adaptive mutations that allow growth in the otherwise growth-limiting environment. The stress responses increase mutagenesis specifically when cells are maladapted to their environments, i.e. are stressed, potentially accelerating evolution then. The mutation mechanism also includes temporary suspension of post-synthesis mismatch repair, resembling mutagenesis characteristic of some cancers. Stress-induced mutation mechanisms may provide important models for genome instability underlying some cancers and genetic diseases, resistance to chemotherapeutic and antibiotic drugs, pathogenicity of microbes, and many other important evolutionary processes. This book covers pathways of stress-induced mutagenesis in all systems. The principle focus is mammalian systems, but much of what is known of these pathways comes from non-mammalian systems.

This volume provides an overview on design PCR primers for successful DNA amplification. Chapters focus on primer design strategies for quantitative PCR, in silico PCR primer design, and primer design using software. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, PCR Primer Design, Second Edition seeks to aid molecular biology students, researchers, professors and PCR enthusiasts.

Burkholderia are a multi-faceted group of bacteria with considerable genetic and metabolic diversity and very versatile lifestyles. In this book leading international investigators review key advances in Burkholderia research to provide timely overview. The topics covered include: genomic taxonomy and biodiversity, comparative genomics, molecular epidemiology, transcriptomics, proteomics, molecular pathogenesis of virulence in B. mallei/B. pseudomallei and the Burkholderia cepacia complex. The theme underpinning each chapter is the use of DNA/protein sequence data and post-genomic technologies to understand Burkholderia biology.

* Comprehensive and an easily accessible reference volume for developing, running, and analyzing biomedical research using the rat as model system Grown exponentially by the genomic revolution, the use of the rat as a model of choice for physiological studies continues in popularity and at a much greater depth of understanding. In Rat Genomics: Methods and Protocols, world-wide experts provide both practical information for researchers involved in genomic research in the rat along with a more contextual discussion about the usefulness of the rat in physiological or translational research in different organs and systems. The volume extensively covers topics including genome sequencing, quantitative trait loci mapping, and the identification of single nucleotide polymorphisms as well as the development of transgenic technologies such as nuclear cloning, lentiviral-mediated transgenesis, gene knock-down using RNA interference, gene knock-out by mutagenesis, and zinc finger nucleases plus exciting advances in the obtention of rat embryonic cell lines. As a volume in the highly successful Methods in Molecular BiologyT series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Comprehensive and up-to-date, Rat Genomics: Methods and Protocols thoroughly covers the current techniques used in labs around the world and overviews the applications of the data obtained, making it certain to be useful to the scientific community as a key source of references and methods.

After the generation of genome sequence data from a wide variety of plants, databases are filled with sequence information of genes with no known biological function, and while bioinformatics tools can help analyze genome sequences and predict gene structures, experimental approaches to discover gene functions need to be widely implemented. In Plant Reverse Genetics: Methods and Protocols, leading researchers in the field describe cutting-edge methods, both high-throughput and genome-wide, involving the models Arabidopsis and rice as well as several other plants to provide comparative functional genomics information. With chapters on the analysis of high-throughput genome sequence data, the identification of non-coding RNA from sequence information, the comprehensive analysis of gene expression by microarrays, and metabolomic analysis, the thorough methods of the book are fully supported by scripts to aid their computational use. Written in the highly successful Methods in Molecular Biology (TM) series format, the chapters contain introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and essential, Plant Reverse Genetics: Methods and Protocols is an ideal guide for researchers seeking an understanding of how the complex web of plant genes work together in a systems biology view.

Transposable elements have played a major role in shaping plant genome structure and gene expression. Transposons not only drive sequence expansion, induce mutations and generate chromosome rearrangements, they also help to shape the epigenetic topology of the eukaryotic genome. In Plant Transposable Elements: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study transposons. These methods include computational approaches to study the ancient transposon remnants that comprise the bulk of plant genomes, as well as laboratory techniques to identify recent and ongoing transposition events. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Plant Transposable Elements: Methods and Protocols seeks to aid scientists in the further study of transposons by providing essential background information and specific experimental protocols.

This text explores the most recent advances in NGS instrumentation and data anlysis. It begins with a comprehensive description of current NSG platforms, their sequencing chemistries, instrument specifications, and general workflows and procedures. A separate chapter is dedicated to low-quanitity, single molecule sequencing technology. Further chapters explore the application of NSG technologies in various fields.

This book reflects more than three decades of research on Cellular Automata (CA), and nearly a decade of work on the application of CA to model biological strings, which forms the foundation of 'A New Kind of Computational Biology' pioneered by the start-up, CARLBio. After a brief introduction on Cellular Automata (CA) theory and functional biology, it reports on the modeling of basic biological strings with CA, starting with the basic nucleotides leading to codon and anti-codon CA models. It derives a more involved CA model of DNA, RNA, the entire translation process for amino acid formation and the evolution of protein to its unique structure and function. In subsequent chapters the interaction of Proteins with other bio-molecules is also modeled. The only prior knowledge assumed necessary is an undergraduate knowledge of computer programming and biology. The book adopts a hands-on, "do-it-yourself" approach to enable readers to apply the method provided to derive the CA rules and comprehend how these are related to the physical 'rules' observed in biology. In a single framework, the authors have presented two branches of science - Computation and Biology. Instead of rigorous molecular dynamics modeling, which the authors describe as a Bottoms-Up model, or relying on the Top-Down new age Artificial Intelligence (AI) and Machine Language (ML) that depends on extensive availability of quality data, this book takes the best from both the Top-Down and Bottoms-up approaches and establishes how the behavior of complex molecules is represented in CA. The CA rules are derived from the basic knowledge of molecular interaction and construction observed in biological world but mapped to a few subset of known results to derive and predict results. This book is useful for students, researchers and industry practitioners who want to explore modeling and simulation of the physical world complex systems from a different perspective. It raises the inevitable the question - 'Are life and the universe nothing but a collection of continuous systems processing information'.

Charge migration through DNA has been the focus of considerable interest in recent years. This book presents contributions from an international team of researchers active in this field. It contains a wide range of topics that includes the mathematical background of the quantum processes involved, the role of charge transfer in DNA radiation damage, a new approach to DNA sequencing, DNA photonics, and many others.

In DNA Cloning and Assembly Methods, expert researchers in the field detail many of the methods which are now commonly used for DNA cloning and make cloning procedures faster, more reliable and also suitable for high-throughput handling. These include methods and protocols that are based on several mechanisms including type II and IIS restriction enzymes, single stranded annealing, sequence overlap, and recombination. With additional chapters on software programs that are suitable for primer design, a feature crucial for the functionality of the described methods. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, DNA Cloning and Assembly Methods seeks to provide scientist with a valuable and useful resource for wet lab researchers within life sciences.

This volume includes, in an integrated way, modern computational studies of nucleic acids, ranging from advanced electronic structure quantum chemical calculations through explicit solvent molecular dynamics (MD) simulations up to mesoscopic modelling, with the main focus given to the MD field.It gives an equal emphasis to the leading methods and applications while successes as well as pitfalls of the computational techniques are discussed. The systems and problems studied include: Accurate calculations of base pairing energies; Electronic properties of nucleic acids and electron transfer, through various types of nucleic acid; and, Calculating DNA elasticity. This book is ideally suited to academics and researchers in organic and computational chemistry as well as biochemistry and particularly those interested in the molecular modelling of nucleic acids.Besides the state-of-the art science, the book also provides introductory information to non-specialists to enter this field.

DNA Repair and Human Disease highlights the molecular complexities of a few well-known human hereditary disorders that arise due to perturbations in the fidelity of diverse DNA repair machineries.

Microarray Technology, Volumes 1 and 2, present information in designing and fabricating arrays and binding studies with biological analytes. This is done while providing the reader with a broad description of microarray technology tools and their potential applications. The first volume deals with methods and protocols for the preparation of microarrays. The second volume details applications and data analysis, which is important in analyzing the enormous data coming out of microarray experiments. Microarray Technology, Volumes 1 and 2, provide ample information to all levels of scientists from novice to those intimately familiar with array technology.

This timely volume explores the use of CRISPR-Cas9 for genome editing, presenting cutting-edge techniques and their applications in treatment of disease. The chapters describe latest methods such as use of targetable nucleases, investigation of the non-coding genome, mouse genome editing, increasing of knock-in efficiency in mouse zygotes, and generation of reporter stem cells; the text contextualizes these methods in treatment of cardiovascular disease, diabetes mellitus, retinitis pigmentosa, and others. The final chapters round out the book with a discussion of controversies and future directions. Genome Editing is an essential, of-the-moment contribution to this rapidly growing field. Drawing from a wealth of international perspectives, it presents novel techniques and applications for the engineering of the human genome. This book is essential reading for all clinicians and researchers in stem cells, regenerative medicine, genomics, biochemical and biomedical engineering- especially those interested in learning more about genome editing and applying it in a targeted, specific way.

This book presents the foundations of key problems in computational molecular biology and bioinformatics. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. The book features a free download of the R software statistics package and the text provides great crossover material that is interesting and accessible to students in biology, mathematics, statistics and computer science. More than 100 illustrations and diagrams reinforce concepts and present key results from the primary literature. Exercises are given at the end of chapters.

This volume presents a valuable and readily reproducible collection of established and emerging techniques on modern genetic analyses. Chapters focus on statistical or data mining analyses, genetic architecture, the burden of multiple testing, genetic variance, measuring epistasis, multifactor dimensionality reduction, and ReliefF. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Epistasis: Methods and Protocols aids scientists in continuing to study elucidate epistasis in the context of modern data availability.

Epigenetics is a term in biology referring to heritable traits that do not involve changes in the underlying DNA sequence of the organism. Epigenetic traits exist on top of or in addition to the traditional molecular basis for inheritance. The "epigenome" is a parallel to the word "genome," and refers to the overall epigenetic state of a cell. Cancer and stem cell research have gradually focused attention on these genome modifications. The molecular basis of epigenetics involves modifications to DNA and the chromatin proteins that associate with it. Methylation, for example, can silence a nearby gene and seems to be involved in some cancers. Epigenetics is beginning to form and take shape as a new scientific discipline, which will have a major impact on Medicine and essentially all fields of biology. Increasingly, researchers are unearthing links between epigenetics and a number of diseases. Although in recent years cancer has been the main focus of epigenetics, recent data suggests that epigenetic plays a critical role in psychology and psychopathology. It is being realized that normal behaviors such as maternal care and pathologies such as Schizophrenia and Alzheimer's might have an epigenetic basis. It is also becoming clear that nutrition and life experiences have epigenetic consequences. Discover more online content in the Encyclopedia of Molecular Cell Biology and Molecular Medicine.

Mitochondrial DNA is one of the most closely explored genetic systems, because it can tell us so much about the human past. This book takes a unique perspective, presenting the disparate strands that must be tied together to exploit this system. From molecular biology to anthropology, statistics to ancient DNA, this first volume of three presents a comprehensive global picture and a critical appraisal of human mitochondrial DNA variation.

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."

The birth and the development of molecular biology and, subsequently, of genetic engineering and biotechnology cannot be separated from the advancements in our knowledge of the genetics, biochemistry and physiology of bacteria and bacter- phages. Also most of the tools employed nowadays by biotechnologists are of bacterial (or bacteriophage) origin and the playground for most of the DNA manipulations still remains within bacteria. The relative simplicity of the bacterial cell, the short gene- tion times, the well defined and inexpensive culturing conditions which characterize bacteria and the auto-catalytic process whereby a wealth of in-depth information has been accumulated throughout the years have significantly contributed to generate a large number of knowledge-based, reliable and exploitable biological systems. The subtle relationships between phages and their hosts have produced a large amount of information and allowed the identification and characterization of a number of components which play essential roles in fundamental biological p- cesses such as DNA duplication, recombination, transcription and translation. For instance, to remain within the topic of this book, two important players in the or- nization of the nucleoid, FIS and IHF, have been discovered in this way. Indeed, it is difficult to find a single fundamental biological process whose structural and functional aspects are better known than in bacteria.

Significant advancements have been made in the study of chromatin structure and function over the past fifty years but none as spectacular as those made in the last decade due to the development of novel techniques and the ability to sequence large stretches of DNA. In Chromatin Protocols, Second Edition, expert researchers delineate these cutting-edge techniques via step-by-step laboratory methods and protocols, which encompass a wide array of topics from the isolation of nucleosomes, assembly of nucleosomes and study of the basic chromatin structure to detailed analysis of histone modifications and chromatin function. Written in the highly successful Methods in Molecular Biology (TM) series style, chapters include brief introductions to the subjects, lists of the necessary materials and reagents, readily reproducible protocols, and Notes sections which highlight tips on troubleshooting and avoiding known pitfalls. Comprehensive and up-to-date, Chromatin Protocols, Second Edition is a valuable tool for scientists studying various aspects of chromatin function and an ideal guide to aid in the development of new techniques as well as new ideas in the field of chromatin biology.