Cellular editing of RNA can lead to the recoding of expressed sequences before they mature to their functional gene products - such as proteins or regulatory RNAs - and represents a hidden layer of genetic information and regulation. Often, the recoding events are essential for the normal function of the gene product (for example, creating an open reading frame). In other cases, RNA editing creates additional variation and phenotypic diversity since both the edited and the non-edited versions of the product are functional and co-exist. It is necessary to understand the mechanisms of RNA editing in order to elucidate the overall physiological impact of this phenomenon. This major new work presents an up-to-date overview of RNA editing. All chapters have been written by experts in the various research areas, describing key recent findings, as well as exploring current frontiers in the mechanisms and functional roles of RNA editing. The chapters span the editing of protein coding mRNAs, small regulatory RNAs, tRNAs, and non-coding sequences. Also included are studies employing bioinformatics to identify and predict RNA editing sites as well as the evolution of RNA modification. The book will be an essential text for anyone interested in RNA editing and modification, RNA structure and function, post-transcriptional regulation, and the regulation of gene expression. It is recommended for all molecular biology libraries.

Transposable elements are short lengths of DNA with the capacity to move between different points within a genome. This process can affect the function of genes at or near the insertion site. The present book gives an overview of the impact of transposable elements on plant genomes and explains how to recognize and study transposable elements, e.g. by using state-of-the-art strategies like "new generation sequencing." Moreover, the impact of transposable elements on plant genome structure and function is reviewed in detail, and also illustrated in examples and case studies. The book is intended both for readers familiar with the field and for newcomers. With large-scale sequencing becoming increasingly available, more and more people will come across transposable element sequences in their data, and this volume will hopefully help to convince them that they are not just "junk DNA."

GW bodies are novel cytoplasmic foci that were discovered and named by Dr. Chan's group in 2002. These bodies are now known to be active cytoplasmic foci involved with the new gene regulation process mediated by microRNA that leads to translational repression and mRNA degradation. The detailed biological functions of these cytoplasmic structures are still being uncovered and the idea for this book is to provide the history of the discovery and the major work from different laboratories that has led to the characterization and elucidation of the structure and function of these new multiple subcellular structures.

In recent years, a number of groundbreaking structural and mechanistic studies deepened our understanding of helicase mechanisms and established new approaches for their analyses. Many fundamental mechanistic questions ranging from the mechanism of force generation, mechanochemical coupling to distinct mechanisms by which the same enzyme translocates on DNA removing obstacles, unwinds DNA and/or remodels nucleoprotein complexes, however, remain to be answered. It is even less understood how the helicase motors are incorporated into a wide range of genome maintenance and repair machines. The field has reached a stage when the studies of molecular mechanisms and basic biology of helicases can and shall be integrated with the studies of development, cancer and longevity. The objective of this book is to provide the first systematic overview of structure, function and regulation of DNA helicases and related molecular motors. By integrating the knowledge obtained through the diverse technical approaches ranging from single-molecule biophysics to cellular and molecular biological studies the editors aim to provide a unified view on how helicases function in the cell, are regulated in response to different cellular stresses and are integrated into large macromolecular assemblies to form a complex and adaptive living system.

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.

Biolistic transfection represents a direct physical gene transfer approach in which nucleic acids are precipitated on biologically inert high-density microparticles (usually gold or tungsten) and delivered directly through cell walls and/or membranes into the nucleus of target cells by high-velocity acceleration using a ballistic device such as the gene gun. Biolistic DNA Delivery: Methods and Protocols provides a comprehensive collection of detailed protocols intended to provide the definitive practical guide for the novice as well as for the advanced gene transfer expert on how to introduce nucleic acids into eukaryotic cells using the biolistic technique. Split into six convenient sections, this detailed volume covers biolistic gene transfer into plants, nematodes, and mammalian cells, both in vitro and in vivo, as well as the use of gene gun-mediated DNA vaccination in various experimental animal models of human diseases, and the description of biolistic delivery of molecules other than nucleic acids. 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 tips on troubleshooting and avoiding known pitfalls. All-inclusive and cutting-edge, Biolistic DNA Delivery: Methods and Protocols brings together the knowledge and the experience of leading experts in the field of gene transfer in order to serve all researchers who wish to further our abilities in this vital field.

In this book, the authors present new research in the study of sex chromosomes. Topics discussed in this compilation include the evolution of mammalian X chromosomes and X chromosome inactivation; the role of sex chromosomes in mammalian female fertility; the fate of the Y chromosome; the role of Y chromosome genes on tumour development risk in disgenetic gonads; deletion of amelogenin Y-locus; non-invasive prenatal diagnosis for foetal sex determination; and application of X chromosomal STR polymorphisms to individual identification.

With the detailed genomic information that is now becoming available, we have a plethora of data that allows researchers to address questions in a variety of areas. Genome-wide association studies (GWAS) have become a vital approach to identify candidate regions associated with complex diseases in human medicine, production traits in agriculture, and variation in wild populations. Genomic prediction goes a step further, attempting to predict phenotypic variation in these traits from genomic information. Genome-Wide Association Studies and Genomic Prediction pulls together expert contributions to address this important area of study. The volume begins with a section covering the phenotypes of interest as well as design issues for GWAS, then moves on to discuss efficient computational methods to store and handle large datasets, quality control measures, phasing, haplotype inference, and imputation. Later chapters deal with statistical approaches to data analysis where the experimental objective is either to confirm the biology by identifying genomic regions associated to a trait or to use the data to make genomic predictions about a future phenotypic outcome (e.g. predict onset of disease). As part of the Methods in Molecular Biology series, chapters provide helpful, real-world implementation advice.

The genomes of cellular organisms are organized as double-stranded DNA, a structure that must be unwound to provide DNA replication, recombination, and repair machinery access to genomic information. However, DNA unwinding comes with inherent risks to genome stability. To help mediate these risks, bacterial, archael, and eukaryotic cells have evolved protective ssDNA-binding proteins (SSBs) that bind ssDNA with high affinity and specificity. SSBs also aid genome metabolic processes through direct interactions with key proteins in genome maintenance enzymes. Single-Stranded DNA Binding Proteins: Methods and Protocols assembles methods developed for examining the fundamental properties of SSBs and for exploiting the biochemical functions of SSBs for their use as in vitro and in vivo reagents. Clearly and concisely organized, the volume opens with an introduction to the structures and functions of SSBs, followed protocols for studying SSB/DNA complexes, methods for studying SSB/heterologous protein complexes, protocols for interrogating post-translational modifications of SSBs, and concludes with uses of fluorescently-labeled SSBs for in vitro and in vivo studies of genome maintenance processes. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Single-Stranded DNA Binding Proteins: Methods and Protocols provides a rich introduction for investigators who are interested in this fascinating family of DNA-binding proteins.

In this volume, internationally recognized 'Neurospora' experts critically review the most important research and demonstrate the breadth of applications to industrial biology, biofuels, agriculture, and human health.

Genomic imprinting, the process by which the non-equivalence of the paternal and maternal genomes is established, has been fascinating us for over three decades and has provided many emerging scientists with the chance to hit their stride in a frontier posing many unexpected questions and even more surprising answers. In Genomic Imprinting: Methods and Protocols, experts in the field provide a survey of the technologies that are being applied to advance the study of imprinting. This detailed volume features new technologies that are accelerating the pace of discovery of imprinted genes and characterization of their epigenetic profile, bioinformatic procedures for prediction and comparative analyses of imprinted genes, as well as methods in embryology and basic molecular biology that have been employed for many years, some appearing in new versions for small cell numbers. 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and easy to use, Genomic Imprinting: Methods and Protocols will aid scientists in unveiling both much awaited answers and all-new questions to keep this vital field busy for many exciting years to come.

This book offers an overview of state-of-the-art in non amplified DNA detection methods and provides chemists, biochemists, biotechnologists and material scientists with an introduction to these methods. In fact all these fields have dedicated resources to the problem of nucleic acid detection, each contributing with their own specific methods and concepts. This book will explain the basic principles of the different non amplified DNA detection methods available, highlighting their respective advantages and limitations. Non-amplified DNA detection can be achieved by adopting different techniques. Such techniques have allowed the commercialization of innovative platforms for DNA detection that are expected to break into the DNA diagnostics market. The enhanced sensitivity required for the detection of non amplified genomic DNA has prompted new strategies that can achieve ultrasensitivity by combining specific materials with specific detection tools. Advanced materials play multiple roles in ultrasensitive detection. Optical and electrochemical detection tools are among the most widely investigated to analyze non amplified nucleic acids. Biosensors based on piezoelectric crystal have been also used to detect unamplified genomic DNA. The main scientific topics related to DNA diagnostics are discussed by an outstanding set of authors with proven experience in this field.

With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.

Fully integrated and comprehensive in its coverage, "Root Genomics and Soil Interactions" examines the use of genome-based technologies to understand root development and adaptability to biotic and abiotic stresses and changes in the soil environment. Written by an international team of experts in the field, this timely review highlights both model organisms and important agronomic crops. Coverage includes: novel areas unveiled by genomics research basic root biology and genomic approaches applied to analysis of root responses to the soil environment. Each chapter provides a succinct yet thorough review of research.

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.

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.

Sequencing is often associated with the Human Genome Project and celebrated achievements concerning the DNA molecule. However, the history of this practice comprises not only academic biology, but also the world of computer-assisted information management. The book uncovers this history, qualifying the hype and expectations around genomics.

Recent progress in high-throughput technologies and genome wide transcriptome studies have lead to a significant scientific milestone of discovering non-coding RNAs (ncRNAs) which spans through a major portion of the genome. These RNAs most often act as riboregulators, and actively participate in the regulation of important cellular functions at the transcriptional and/or post-transcriptional levels rather than simply being an intermediated messenger between DNA and proteins. As the appreciation for the importance of ncRNAs continues to emerge, it is also increasingly clear that these play critical roles in gene regulatory processes during development and differentiation. Further, regulatory RNAs are useful biomarkers for diagnosis of diseases. Hence these RNA regulators are essential to the development of therapeutics. This book on "Regulatory RNAs" offers a comprehensive view on our current understanding of these regulatory RNAs viz. siRNA, miRNA, piRNA, snoRNA, long non-coding RNA, small RNA etc. It addresses both the biogenesis and mechanism of action of regulatory RNAs with a primary focus on their annotation, experimental methodologies (microarray, next-gen sequencing etc.) for their discovery, computational tools for their prediction, and above all, applications of these revolutionary regulatory molecules in understanding biological systems and diseases, including therapeutics. This comprehensive volume is intended for readers with research or teaching interests in ncRNA biology and will provide a major information resource on current research in the fast-moving fields of RNA and gene expression regulation. Cutting-edge and concise, "Regulatory RNAs: Basics, Methods and Applications" promises to support vital research in the field of regulatory RNAs, ever-continuing to grow rapidly and gain increasing importance in basic and translational biology.

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.

Over the last decade Life Science has undergone an accelerated evolution, culminating in the -omics era characterized by the development of a multitude of high throughput methods that are becoming more routinely applied in biochemistry labs. In Functional Genomics: Methods and Protocols, Second Edition expert researchers in the field detail many of the methods which are now commonly used for studies in the life sciences focusing on the dynamic aspects of the transcriptome, proteome and metabolome, respectively.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, Functional Genomics: Methods and Protocols, Second Edition seeks to aid scientists in establishing or extending technologies and techniques in their laboratories.

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."

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.

Small DNA tumour viruses are a group of double-stranded DNA viruses made up of the polyomavirus, the adenovirus, and the papillomavirus families. In this title, scientists from around the globe review current topics in this area, providing an overview of the molecular biology of these viruses and their interactions with the host.

Brucella is a genus of Gram-negative, facultative, intracellular bacteria that are highly pathogenic for a variety of mammals, including humans. Recently the WHO cited brucellosis to be the world's most widespread zoonosis. An important feature of the pathogenicity of these organisms is their ability to survive and replicate within the host macrophages. However the mechanism for this is unclear. In addition, none of the classical bacterial virulence factors found in other bacterial pathogens have been found in the genomes of the forty Brucella species and biovars analysed to date. Nevertheless the application of systems biology approaches in recent years has transformed research, permitting fascinating new insights into Brucella molecular biology and genomics. Written by highly acclaimed Brucella scientists, this book comprehensively reviews the most important advances in the field. Opening chapters focus on genetic diversity within Brucella, covering both classical and new species. Pa

The goal of this volume is to provide a comprehensive mechanistic and quantitative view of the processes that mediate or influence the quality control in translation. In addition to discussing processes with direct contribution to translation fidelity, such as aminoacylation of tRNAs and translation elongation itself, special attention is given to other processes with impact on quality control: detection and elimination of defective mRNAs, recycling and translation re-initiation, mRNA editing, and translational recoding through programmed frame-shifting.

Provides a comprehensive mechanistic and quantitative view of the processes that mediate or influence the quality control in translation.

Special attention is given to other processes with impact on quality control: detection and elimination of defective mRNAs, recycling and translation re-initiation, mRNA editing, and translational recoding through programmed frame-shifting.