This volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls. Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA.

Eminent scientists have contributed comprehensive reviews on all aspects of the genomics of Rhodococcus, Mycobacteria, Streptomyces and other organisms. The authors provide an insight into the many facets of large scale functional investigation in a variety of bacteria with the explicit goal to find common rules in the dynamic and structural organization of these organisms. This volume is the definitive guide to current research in this increasingly important area and is essential reading for all microbiologists, biotechnologists, and genome scientists.

This authoritative text/reference presents a review of the history, current status, and potential future directions of computational biology in molecular evolution. Gathering together the unique insights of an international selection of prestigious researchers, this must-read volume examines the latest developments in the field, the challenges that remain, and the new avenues emerging from the growing influx of sequence data. These viewpoints build upon the pioneering work of David Sankoff, one of the founding fathers of computational biology, and mark the 50th anniversary of his first scientific article. The broad spectrum of rich contributions in this essential collection will appeal to all computer scientists, mathematicians and biologists involved in comparative genomics, phylogenetics and related areas.

Advances in Botanical Research publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences. Currently in its 69th volume, the series features several reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology. This thematic volume features reviews on genomes of herbaceous land plants
Publishes in-depth and up-to-date reviews on a wide range of topics in plant sciencesFeatures a wide range of reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecologyVolume features reviews on genomes of herbaceous land plants

This volume provides broad coverage of computational and mathematical techniques and concepts related to the field of comparative genomics. The topics covered in the chapters range from those concerned with general techniques and concepts that apply to all organisms to others that are more specialized, covering specific biological systems such as viruses, Drosophila, and Homo sapiens. Written in the highly successful Methods in Molecular Biology series format, by authors who are active researchers in the field, many chapters include step-by-step procedures, which illustrate practical applications of the techniques described. Cutting-edge and thorough, Comparative Genomics: Methods and Protocols should be useful to students and researchers in the continually growing and exciting field of comparative genomics.

This volume presents a list of cutting-edge protocols for the study of CRISPR-Cas defense systems and their applications at the genomic, genetic, biochemical and structural levels. CRISPR: Methods and Protocols guides readers through techniques that have been developed specifically for the analysis of CRISPR-Cas and techniques adapted from standard protocols of DNA, RNA and protein biology. 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 cutting-edge, CRISPR: Methods and Protocols provides a broad list of tools and techniques to study the interdisciplinary aspects of the prokaryotic CRISPR-Cas defense systems.

Genomics is a new and fast expanding area of biology encompassing high throughput or large scale experimentation at the whole genome level, and the organization, analysis and interpretation of the huge amount of data emerging from genome projects. Major new technologies have evolved recently that enable experimentation at the whole genome level, and more novel technologies are currently being developed. This volume describes in detail the new technology necessary to study the entire genome in a holistic manner and all the high throughput and large-scale experimental methodologies currently being used in genomic science. In addition the authors describe the progress of the newest technologies that are currently being developed. Written by experts in the field, this concise yet informative volume covers all aspects of technology pertaining to genomic studies. It is an essential book for anyone involved in genomic science.

Current knowledge of the mechanisms that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens. The third edition of DNA Repair Protocols covers various aspects of the eukaryotic response to genomic insult including recent advanced protocols as well as standard techniques used in the field of DNA repair. Both mammalian and non-mammalian model organisms are covered in the book, and many of the techniques can be applied with only minor modifications to other systems than the one described. Written in the highly successful Methods in Molecular Biology? series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, DNA Repair Protocols, Third Edition provides expert guidance for DNA repair, recombination, and replication.

"Pharmacogenomics: Challenges and Opportunities in Therapeutic Implementation" includes discussions and viewpoints from the academic, regulatory, pharmaceutical, clinical, socio-ethical and economic perspectives. Each chapter presents an overview of the potential or opportunity within the areas discussed and also outlines foreseeable challenges and limitations in moving pharmacogenomics into drug development and direct therapeutic applications. This edited book contains review questions for a more in-depth analysis of the implications of pharmacogenomics and discussion points to generate ideas on best to move the field forward. Clinical pearls and case studies are used to illustrate real-life experiences and both successful and unsuccessful applications. Tables, figures, and annotations are included throughout the book to facilitate understanding and further reference.
Multi-contributed book and chapters are written by contributors who are experts in their fieldProvides perspectives from those involved in all aspects of pharmacogenomics-including academic, regulatory, economic, industry and medical-to illustrate how all of the pieces fit together and where the challenges may beIncludes case studies of both successful and unsuccessful applications so readers can consider the potential and challenges in moving the science into drug development and direct therapeutic applicationsChapters contain discussion questions and clinical pearls and enable readers to reflect on how to move pharmacogenomics forward and apply these observations and useful tips to their own work and research

A companion website offers an elaboration on key points and discussion questions and provides patient case scenarios that illustrate how pharmacogenomics may be applied to a clinical setting

Plasmids are fascinating entities which can replicate autonomously in bacterial, archaeal, and eukaryotic cells. They profit from the cellular environment of the host but can also carry a rich diversity of genes which can be beneficial for the host. Plasmids confer the ability to degrade organic compounds and to fix nitrogen. In addition, plasmids carry antibiotic resistance genes and their spread in pathogenic bacteria is of great medical importance. Plasmids are used in molecular studies of various organisms with ramifications in synthetic biology, medicine, ecology, and evolution, as well as basic research in molecular and structural biology. Written by acknowledged experts in the field, this volume provides an up-to-date treatment of the structure, function, and application of plasmids, with a particular emphasis on current and future trends. The book is aimed primarily at research scientists, graduate students, and professional scientists, but will also be of great interest to all

This new volume of "Current Topics in Developmental Biology" covers epigenetics and development, with contributions from an international board of authors. The chapters provide a comprehensive set of reviews covering such topics as epigenetic marking of the zebrafish developmental program, functions of DNA methylation and hydroxymethylation in mammalian development, and reprogramming and the pluripotent stem cell cycle.
Covers the area of epigenetics and developmentInternational board of authors Provides a comprehensive set of reviews covering such topics as epigenetic marking of the zebrafish developmental program, functions of DNA methylation and hydroxymethylation in mammalian development, and reprogramming and the pluripotent stem cell cycle

The application of modern genomic approaches to research on halophilic Archaea and Bacteria and their viruses in recent years has yielded fascinating insights into the adaptations and evolution of these unique organisms. This book highlights current genetics and genomics research to provide a timely overview.

DNA typing has revolutionized criminal investigations and has become a powerful tool in the identification of individuals in criminal and paternity cases. "Forensic DNA Biology: A Laboratory Manual" is comprised of up-to-date and practical experiments and step-by-step instructions on how to perform DNA analysis, including pipetting, microscopy and hair analysis, presumptive testing of body fluids and human DNA typing. Modern DNA typing techniques are provided, reflecting real life, where not all institutions and crime labs can afford the same equipment and software. Real case studies will be used throughout and the author will provide an Instructor Manual and PowerPoint lecture slides.
* Provides practical step-by-step instruction on how to perform forensic DNA analysis
* Includes analysis of hair, presumptive testing of body fluids, human DNA typing and statistics
* Covers techniques such as pipetting, microscopy and DNA extraction
* Pre- and post-lab exercises and questions assist the reader in learning the material
* Report writing templates assure the reader learns real world crime lab procedure

Innate DNA and RNA Recognition: Method and Protocols presents validated experimental strategies to dissect nucleic acid sensing in-vitro and in-vivo sources. 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 practical, Innate DNA and RNA Recognition: Method and Protocols provides a resource for immunologists, molecular biologists, virologists, microbiologists, and researchers studying how the innate immune system handles nucleic acids from endogenous or foreign sources.

"Advances in Botanical Research" publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences.
Features a wide range of reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology.
Thisthematic volume features reviews on Mitochondrial genome evolution.
Publishes in-depth and up-to-date reviews on a wide range of topics in plant sciencesFeatures a wide range of reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecologyThis thematic volume features reviews on mitochondrial genome evolution"

This volume of Methods in Enzymology aims to provide a reference for the diverse, powerful tools used to analyze RNA helicases. Thecontributions inthis volume cover the broad scope of methods in the research on these enzymes. Several chapters describe quantitative biophysical and biochemical approaches to study molecular mechanisms and conformational changes of RNA helicases. Further chapters cover structural analysis, examination of co-factor effects on several representative examples, and the analysis of cellular functions of select enzymes. Two chapters outline approaches to the analysis of inhibitors that target RNA helicases.
This volume of "Methods in Enzymology" aims to provide a reference for the diverse, powerful tools used to analyze RNA helicases The contributions in this volume cover the broad scope of methods in the research on these enzymes"

This new volume in the "Current topics in Developmental Biology" series concentrates on MicroRNAs in Development. It includes chapters on such topics as miRNA networks in neuronal development, let-7 in development, and Hox networks and miRNA. With an international team of authors, this volume is a must-have addition for researchers and students alike.
Concentrates on microRNAs in development Includes chapters on such topics as miRNA networks in neuronal development, let-7 in development, and Hox networks and miRNA With an international team of authors, this volume is a must-have addition for researchers and students alike"

DNA methylation is essential for the normal development and functioning of organisms. This volume discusses the latest developments in this very active field of research. It presents the evolution of DNA methylation, mammalian DNA methyltransferases, DNA methylation and demethlyation, DNA methylation and silencing and the role it plays in medicine including cancer.

* Discusses new discoveries, approaches, and ideas * Contributions from leading scholars and industry experts * Reference guide for researchers involved in molecular biology and related fields

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.

In recent years new discoveries have made this an exciting and important field of research. This comprehensive volume presents comprehensive chapters and detailed background information for researchers working with in the field of Nuclear Mechanics and Genome Regulation.

* Both classic and state-of-the-art methods readily adaptable and designed to last the test of time * Relevant to clinicians and scientists working in a wide range of fields

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.

Structural genomics is the systematic determination of 3-dimensional structures of proteins representative of the range of protein structure and function found in nature. The goal is to build a body of structural information that will predict the structure and potential function for almost any protein from knowledge of its coding sequence. This is essential information for understanding the functioning of the human proteome, the ensemble of tens of thousands of proteins specified by the human genome.
While most structural biologists pursue structures of individual proteins or protein groups, specialists in structural genomics pursue structures of proteins on a genome wide scale. This implies large scale cloning, expression and purification. One main advantage of this approach is economy of scale.
Key Features
*Examines the three dimensional structure of all proteins of a given organism, by experimental methods such as X-ray crystallography and NMR spectroscopy
* Looks at structural genomics as a foundation of drug discovery as discovering new medicines is becoming more challenging and the pharmaceutical industry is looking to new technologies to help in this mission

Appropriate for a wide range of disciplines, from biology to non-biology, law and nursing majors, "DNA and Biotechnology" uses a straightforward and comprehensive writing style that gives the educated layperson a survey of DNA by presenting a brief history of genetics, a clear outline of techniques that are in use, and highlights of breakthroughs in hot topic scientific discoveries.

Engaging and straightforward scientific writing style Comprehensive forensics chapter Parallel Pedagogic material designed to help both readers and teachers. Highlights in the latest scientific discoveries Outstanding full-color illustration that walk reader through complex concepts

Since the publication in 1859 of Darwin's Origin of Species, debate over the theory of evolution has been continuous and often impassioned. In recent years, opponents of "Darwin's dangerous idea" have mounted history's most sophisticated and generously funded attack, claiming that evolution is "a theory in crisis." Ironically, these claims are being made at a time when the explosion of information from genome projects has revealed the most compelling and overwhelming evidence of evolution ever discovered. Much of the latest evidence of human evolution comes not from our genes, but from so-called "junk DNA," leftover relics of our evolutionary history that make up the vast majority of our DNA.
Relics of Eden explores this powerful DNA-based evidence of human evolution. The "relics" are the millions of functionally useless but scientifically informative remnants of our evolutionary ancestry trapped in the DNA of every person on the planet. For example, the analysis of the chimpanzee and Rhesus monkey genomes shows indisputable evidence of the human evolutionary relationship with other primates. Over 95 percent of our genome is identical with that of chimpanzees and we also have a good deal in common with other animal species.
Author Daniel J. Fairbanks also discusses what DNA analysis reveals about where humans originated. The diversity of DNA sequences repeatedly confirms the archeological evidence that humans originated in sub-Saharan Africa (the "Eden" of the title) and from there migrated through the Middle East and Asia to Europe, Australia, and the Americas. In conclusion, Fairbanks confronts the supposed dichotomy between evolution and religion, arguing that both science and religion are complementary ways to seek truth. He appeals to the vast majority of Americans who hold religious convictions not to be fooled by the pseudoscience of Creationists and Intelligent Design advocates and to abandon the false dichotomy between religion and real science.
This concise, very readable presentation of recent genetic research is completely accessible to the nonspecialist and makes for enlightening and fascinating reading.

* 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.