Clinical DNA Variant Interpretation: Theory and Practice, a new volume in the Translational and Applied Genomics series, covers foundational aspects, modes of analysis, technology, disease and disorder specific case studies, and clinical integration. This book provides a deep theoretical background, as well as applied case studies and methodology, enabling researchers, clinicians and healthcare providers to effectively classify DNA variants associated with disease and patient phenotypes. Practical chapters discuss genomic variant interpretation, terminology and nomenclature, international consensus guidelines, population allele frequency, functional evidence transcripts for RNA, proteins, and enzymes, somatic mutations, somatic profiling, and much more.

Leading scientists in gene expression methodology and bioinformatics data analysis describe readily reproducible methods for measuring RNA levels in cells and tissues. The techniques presented include new methods for applying the Affymetrix GeneChip (R), SAR-SAGE, StaRT-PCR, SSH, the Invader Assay (R), and ADGEM. The authors also provide critical bioinformatics insight and resources for data analysis and management. By distilling the basic underlying principles of many methods to a few straightforward concepts, investigators can easily choose the method most appropriate to their application.

Featuring current resources used to discover new legume family genes and to understand genes and their interactions, Legume Genomics: Methods and Protocols provides techniques from expert researchers to study these plants that are so vitally important for food, feed, human nutrition, bioenergy, and industrial purposes. This detailed volume covers genome characterization and analysis, transcriptome analysis and miRNA identification/analysis, forward and reverse genetics, molecular markers, as well as transformation strategies used to investigate gene function and many other topics. 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 useful, Legume Genomics: Methods and Protocols aims to serve plant molecular biologists, molecular breeders, plant physiologists and biochemists, developmental biologists, and those interested in plant-microbe interactions.

Microarray technology provides a highly sensitive and precise te- nique for obtaining information from biological samples, with the added advantage that it can handle a large number of samples simultaneously that may be analyzed rapidly. Researchers are applying microarray technology to understand gene expression, mutation analysis, and the sequencing of genes. Although this technology has been experimental, and thus has been through feasibility studies, it has just recently entered into widespread use for advanced research. The purpose of DNA Arrays: Methods and Protocols is to provide instruction in designing and constructing DNA arrays, as well as hybridizing them with biological samples for analysis. An additional purpose is to p- vide the reader with a broad description of DNA-based array technology and its potential applications. This volume also covers the history of DNA arrays-from their conception to their ready off-the-shelf availability-for readers who are new to array technology as well as those who are well versed in this field. Stepwise, detailed experimental procedures are described for constructing DNA arrays, including the choice of solid support, attachment methods, and the general conditions for hybridization. With microarray technology, ordered arrays of oligonucleotides or other DNA sequences are attached or printed to the solid support using au- mated methods for array synthesis. Probe sequences are selected in such a way that they have the appropriate sequence length, site of mutation, and T .

This book spans diverse aspects of modified nucleic acids, from chemical synthesis and spectroscopy to in vivo applications, and highlights studies on chemical modifications of the backbone and nucleobases. Topics discussed include fluorescent pyrimidine and purine analogs, enzymatic approaches to the preparation of modified nucleic acids, emission and electron paramagnetic resonance (EPR) spectroscopy for studying nucleic acid structure and dynamics, non-covalent binding of low- and high-MW ligands to nucleic acids and the design of unnatural base pairs. This unique book addresses new developments and is designed for graduate level and professional research purposes.

Handbook of Clinical Adult Genetics and Genomics: A Practice-Based Approach provides a thorough overview of genetic disorders that are commonly encountered in adult populations and supports the full translation of adult genetic and genomic modalities into clinical practice. Expert chapter authors supplement foundational knowledge with case-based strategies for the evaluation and management of genetic disorders in each organ system and specialty area. Topics discussed include employing genetic testing technologies, reporting test results, genetic counseling for adult patients, medical genetics referrals, issues of complex inheritance, gene therapy, and diagnostic and treatment criteria for developmental, cardiovascular, gastrointestinal, neuropsychiatric, pulmonary issues, and much more.

Disorders of Protein Synthesis, Volume 132 in the Advances in Protein Chemistry and Structural Biology series, highlights new advances in the field, with this new volume presenting interesting chapters written by an international board of authors.

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.

Applied Genomics and Public Health examines the interdisciplinary and growing area of how evidence-based genomic knowledge can be applied to public health, population health, healthcare and health policies. The book gathers experts from a variety of disciplines, including life sciences, social sciences, and health care to develop a comprehensive overview of the field. In addition, the book delves into subjects such as pharmacogenomics, genethics, big data, data translation and analysis, economic evaluation, genomic awareness and education, sociology, pricing and reimbursement, policy measures and economic evaluation in genomic medicine. This book is essential reading for researchers and students exploring applications of genomics to population and public health. In addition, it is ideal for those in the biomedical sciences, medical sociologists, healthcare professionals, nurses, regulatory bodies and health economists interested in learning more about this growing field.

2 On the Early History of 5-mC In the fall of 1966, Norton D. Zinder of Rockefeller University in New York City presented the Harvey Lecture on "Phage RNA as Genetic Material" (Zinder 1966). Frankly,I do not remember manydetailsofhis talk. However, one ofhis concluding remarks, in which he thanked his teacher Rollin Hotchkiss, stuck in my mind andbecame an important leitmotiffor much of my own scienti?c career. Norton's relevant passages went somethinglikethis (approximate quotation): When we hope to have made a scienti?c discovery, we better spend much of our time immediately after this fortunate event in trying to counter our own beliefsand interpretations. Onlyafter a lot of painstaking scrutiny involving many control experiments when our discoveryhas stood the test of careful consideration, can one hope that our colleagues will beabletocon?rm the new ?ndings. Of course, it is a major task of the scienti?c community to respectfully meet supposedly novel announ- ments withdisbelief and skepticism and in turn commence the process of disproving these concepts. Consistent con?rmations, with plenty of modi?cations to be sure, will providethe encouragement necessary to continue and to improve the initial observations and conclusions. Apparently, the scienti?c tradition re?ected in this overall cautious attitude had emanatedfrom the laboratory of Oswald Avery that Rollin Hotchkiss had been trained in. This certainly most important of scienti?ccredos seems tocontradict intuitively held notions and might bethought to run counter to general practice.

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.

Sequence-specific DNA binding ligands, amongst which triple helix forming oligonucleotides are the most efficient as yet, represent promising tools in a number of fields. One of their most promising applications is as antiviral tools: they can specifically target a viral gene, even if it is integrated into the host genome, and be used to specifically inactivate the viral gene or even destroy the cells harboring this gene. However, from science fiction to science there remains a gap; and we are at the moment on the threshold of this fascinating field. Triple Helix Forming Oligonucleotides considers the different aspects of the design and improvement, current or future, of these molecules and their structural analysis, as well as their applications, with special emphasis on the attempts to obtain biological effects of these potentially important tools. What emerges is that the current state of the research is encouraging, and that these molecules are already useful in some biotechnology applications.

The first edition of this book, published in 1999 and called DNA Repair Protocols: Eukaryotic Systems, brought together laboratory-based methods for studying DNA damage and repair in diverse eukaryotes: namely, two kinds of yeast, a nematode, a fruit fly, a toad, three different plants, and human and murine cells. This second edition of DNA Repair Protocols covers mammalian cells only and hence its new subtitle, Mammalian Systems. There are two reasons for this fresh emphasis, both of them pragmatic: to cater to the interests of what is now a largely mammalocentric DNA repair field, and to expedite editing and prod- tion of this volume. Although DNA Repair Protocols: Mammalian Systems is a smaller book than its predecessor, it actually contains a greater variety of methods. Fourteen of the book's thirty-two chapters are entirely new and areas of redundancy present in the first edition have been eliminated here (for example, now just two chapters describe assays for nucleotide excision repair [NER], rather than seven). All eighteen returning chapters have been revised, many of them ext- sively. In order to maintain a coherent arrangement of topics, the four-part p- titioning seen in the first edition was dispensed with and chapters concerned with ionizing radiation damage and DNA strand breakage and repair were re- cated to near the front of the book. Finally, an abstract now heads each chapter.

This book introduces some key problems in bioinformatics, discusses the models used to formally describe these problems, and analyzes the algorithmic approaches used to solve them. After introducing the basics of molecular biology and algorithmics, Part I explains string algorithms and alignments; Part II details the field of physical mapping and DNA sequencing; and Part III examines the application of algorithmics to the analysis of biological data. Exciting application examples include predicting the spatial structure of proteins, and computing haplotypes from genotype data. Figures, chapter summaries, detailed derivations, and examples, are provided.

In Tiling Arrays: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study tiling microarrays in genomic discovery . These include methods and applications for transcriptional regulation, expression, genetic and epigenetic regulation, as well as techniques and skills on tiling microarray data analysis. 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, Tiling Arrays: Methods and Protocols seeks to provide scientists with a comprehensive and down to earth approach to maximize results.

Our ever-increasing knowledge of whole genome sequences is unveiling a variety of structures and mechanisms that impinge on current evolutionary theory. The origin of species, the evolution of form, and the evolutionary impact of transposable elements are just a few of the many processes that have been revolutionized by ongoing genome studies. These novelties, among others, are examined in this book in relation to their general significance for evolution, emphasising their human relevance. The predominance of non-coding DNA in the human genome, the long-term adaptive role of so called "junk DNA" in the evolution of new functions, and the key evolutionary differences that define our humanity are just some of the controversial issues that this book examines in the context of Darwinian evolution. The author's principle intention is to show that whilst genomics is revealing new and previously unanticipated mechanisms and sources of variability that must be incorporated into evolutionary theory, there is no reason to dismiss the role of natural selection as the mechanism that sorts out these potentialities. In other words, this genome potential provides new possibilities (and also constraints) for evolution, but the realization of this potential is driven by natural selection.

Microarray technology is a major experimental tool for functional genomic explorations, and will continue to be a major tool throughout this decade and beyond. The recent explosion of this technology threatens to overwhelm the scientific community with massive quantities of data. Because microarray data analysis is an emerging field, very few analytical models currently exist. Methods of Microarray Data Analysis II is the second book in this pioneering series dedicated to this exciting new field. In a single reference, readers can learn about the most up-to-date methods, ranging from data normalization, feature selection, and discriminative analysis to machine learning techniques.

Currently, there are no standard procedures for the design and analysis of microarray experiments. Methods of Microarray Data Analysis II focuses on a single data set, using a different method of analysis in each chapter. Real examples expose the strengths and weaknesses of each method for a given situation, aimed at helping readers choose appropriate protocols and utilize them for their own data set. In addition, web links are provided to the programs and tools discussed in several chapters. This book is an excellent reference not only for academic and industrial researchers, but also for core bioinformatics/genomics courses in undergraduate and graduate programs.

The aim of molecular diagnostics is preferentially to detect a developing disease before any symptoms appear. There has been a significant increase, fueled by technologies from the human genome project, in the availability of nucleic acid sequence information for all living organisms including bacteria and viruses. When combined with a different type of instrumentation applied, the resulting diagnostics is specific and sensitive. Nucleic acid-based medical diagnosis detects specific DNAs or RNAs from the infecting organism or virus and a specific gene or the expression of a gene associated with a disease. Nucleic acid approaches also stimulate a basic science by opening lines of inquiry that will lead to greater understanding of the molecules at the center of life. One can follow Richard Feynman's famous statement "What I cannot create, I do not understand."

Depite the rapid expansion of the field of biophysics, there are very few books that comprehensively treat specific topics in this area. Recently, the field of single molecule biophysics has developed very quickly, and a few books specifically treating single molecule methods are beginning to appear. However, the promise of single molecule biophysics is to contribute to the understanding of specific fields of biology using new methods. This book would focus on the specific topic of the biophysics of DNA-protein interactions, and would include the use of new approaches, including both bulk methods as well as single molecule methods. This would make the book attractive to anyone working in the general area of DNA-protein interactions, which is of course a much wider market than just single molecule biophysicists or even biophysicists. The subject of the book will be the biophysics of DNA-protein interactions, and will include new methods and results that describe the physical mechanism by which proteins interact with DNA. For example, there has been much recent work on the mechanism by which proteins search for specific binding sites on DNA. A few chapters will be devoted to experiments and theory that shed light on this important problem. We will also cover proteins that alter DNA properties to facilitate interactions important for transcription or replication. Another section of the book will cover the biophysical mechanism by which motor proteins interact with DNA. Finally, we will cover larger protein-DNA complexes, such as replication forks, recombination complexes, DNA repair interactions, and their chromatin context.

Corepressors are newly discovered assemblies of proteins that play essential roles in eukaryotic gene regulation. Recent discoveries about corepressors have provided new insights into the molecular basis of gene regulation, and have established surprising connections between the mechanisms of action of a wide variety of transcriptional regulators. The reviews in this volume critically discuss the nature, mechanisms of action, and physiological roles of corepressors in a diverse assortment of biological systems. Both basic and clinical investigators will be able to find relevant information. The comprehensive nature of the compilation, and the breadth of the reviews, are intended to provide the reader with an excellent introduction to the newly emergent and rapidly-growing field of corepressor research. A valuable and detailed reference guide.

Protein Interactions as Targets in Drug Discovery, Volume 121, is dedicated to the design of therapeutics, both experimental and computational, that target protein interactions. Chapters in this new release include Trends in structure based drug design with protein targets, From fragment- to peptide-protein interaction: addressing the structural basis of binding using Supervised Molecular Dynamics (SuMD), Protein-protein and protein-ligand interactions: identification of potential inhibitors through computational analysis, Aromatic-aromatic interactions in protein-drug and protein-protein interactions, Role of protein-protein interaction in allosteric drug design within the human methyltransferome, and much more.

This volume provides readers with wide-ranging coverage of CRISPR systems and their applications in various plant species. The chapters in this book discuss topics such as plant DNA repair and genome editing; analysis of CRISPR-induced mutations; multiplexed CRISPR/Cas9 systems; CRISPR-Cas12a (Cpf1) editing systems; and non-agrobacterium based CRISPR delivery systems. 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. Comprehensive and thorough, Plant Genome Editing with CRISPR Systems: Methods and Protocols is a valuable resource for any researcher interested in learning about and using CRISPR systems in plants.

DNA Microarrays is intended for scientists who are entering the field, as well as those already familiar with the technology, but interested in new applications and methods. All up-to-date microarray platforms and their various applications are introduced, presenting the successive stages of microarray technology, from array production to the data analysis. There is extensive discussion of array applications in a broad range of studied organisms from yeast to humans

Clinical Precision Medicine: A Primer offers clinicians, researchers and students a practical, up-to-date resource on precision medicine, its evolving technologies, and pathways towards clinical implementation. Early chapters address the fundamentals of molecular biology and gene regulation as they relate to precision medicine, as well as the foundations of heredity and epigenetics. Oncology, an early adopter of precision approaches, is considered with its relationship to genetic variation in drug metabolism, along with tumor immunology and the impact of DNA variation in clinical care. Contributions by Stephanie Kramer, a Clinical Genetic Counselor, also provide current information on prenatal diagnostics and adult genetics that highlight the critical role of genetic counselors in the era of precision medicine.

Inflammation is a biological response triggered by different stimuli that has in the body a potentially damaging effect. In certain conditions, such as injury or infection, inflammation is a normal, healthy response. However, inflammatory disorders that result in the immune system attacking the body's own cells or tissues may cause abnormal inflammation, which results in chronic pain, redness, swelling, stiffness, and damage to normal tissues. Mechanisms involved in promoting a number of different inflammatory disorders and their targeting for therapeutic benefit have been one of the hottest topics in last few decades. The two consecutive volumes (119 and 120) dedicated to this subject cover a wide spectrum of inflammatory disorders, mechanisms that are believed to cause them and different strategies for managing the inflammatory diseases.