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.

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.

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.

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.

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'.

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.

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.

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 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 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.

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.

Bioinformatics is a new and fast expanding area of biology encompassing the organization, analysis and interpretation of the huge amount of data emerging from sequencing and genome projects. Major new programs, software and internet facilities have evolved recently that enable bioinformatic analysis at the whole genome level and more novel technologies are currently being developed. Written by experts in the field, this concise yet informative volume covers all aspects of bioinformatics pertaining to genomic studies. It is an essential book for anyone involved in genomic science or bioinformatics.

MicroRNA research and development is the billion-dollar baby and most lucrative option for drug discovery in gene therapy industries worldwide. Personalized microRNA treatments are in many cases the only remedy for viral diseases that have no cure in conventional drugs and offer to bring us closer than ever to "personalized medicine." They also counteract cancer and other infectious and neuro-diseases. Early diagnosis, prognosis, staging, and sub-classification of various cancers can easily be facilitated by microRNA-based biomarkers. MicroRNA surveys recent advances in RNA and RNA-protein components that highlight RNA delivery, its stability, and applications of RNA-based drugs for the modulation of gene/protein expression and gene editing. The book not only focuses on the modern medicines of microRNA-based early diagnostic and therapy development, but also works as a hidden treasure for drug discovery of multiple rare diseases worldwide. It offers indispensable learning materials for academic researchers, graduate, and medical students, and offers a powerful practical guide for RNA-Pharma and gene therapy industries.

Structural Genomics and Drug Discovery: Methods and Protocols focuses on high throughput structure determination methods and how they can be applied to lay the groundwork for structure aided drug discovery. The methods and protocols that are described can be applied in any laboratory interested in using detailed structural information to advance the initial stages of drug discovery. 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, Structural Genomics and Drug Discovery: Methods and Protocols seeks to aid scientists in the further study into structural genomics approach as an efficient initial step toward drug discovery and the methods described will be useful to anyone interested in moving in this direction.

Eukaryotic DNA Damage Surveillance and Repair contains chapters from experts in the field of DNA damage detection, repair, and cell cycle control. The work reviews current understanding of how different types of DNA damage are detected and focuses on how these surveillance mechanisms are coupled to processes of DNA repair, cell cycle control, and apoptosis.
The title will be of interest to undergraduate/postgraduate students and academics alike.

After genomic sequencing, microarray technology has emerged as a widely used platform for genomic studies in the life sciences. Microarray technology provides a systematic way to survey DNA and RNA variation. With the abundance of data produced from microarray studies, however, the ultimate impact of the studies on biology will depend heavily on data mining and statistical analysis. The contribution of this book is to provide readers with an integrated presentation of various topics on analyzing microarray data.

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.

Fungal comparative genomics started in 2000 by the genome sequencing of several yeast species. Since then, over 30 fungal genome sequences have become available. This set represents a huge evolutionary divergence, but also contains closely related genomes. This volume describes how to use this set of genomes to trace events in genome evolution, to extract information about highly conserved and less conserved sequence elements, and to develop novel methods in genomics.

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.

As the emerging field of proteomics continues to expand at an extremely rapid rate, the relative quantification of proteins, targeted by their function, becomes its greatest challenge. Complex analytical strategies have been designed that allow comparative analysis of large proteomes, as well as in depth detection of the core proteome or the interaction network of a given protein of interest. In Functional Proteomics: Methods and Protocols, expert researchers describe the latest protocols being developed to address the problems encountered in high-throughput proteomics projects, with emphasis on the factors governing the technical choices for given applications. The case studies within the volume focus on the following three crucial aspects of the experimental design: 1) the strategy used for the selection, purification and preparation of the sample to be analyzed by mass spectrometry, 2) the type of mass spectrometer used and the type of data to be obtained from it, and 3) the method used for the interpretation of the mass spectrometry data and the search engine used for the identification of the proteins in the different types of sequence data banks available. As a part of the highly successful Methods in Molecular Biology (TM) series, the chapters compile step-by-step, readily reproducible laboratory protocols, lists of the necessary materials and reagents, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Functional Proteomics: Methods and Protocols is an ideal resource for all scientists pursuing this developing field and its multitudinous data.

This volume provides an overview of the methods currently employed for next-generation sequencing (NGS) data analysis, highlights their problems and limitations, demonstrates the applications and indicates the developing trends in various fields of genome research.