Post-transcriptional Gene Regulation in Human Disease, a new volume in the Translational Epigenetics book series, offers a thorough overview and discussion of post-transcriptional genetic control mechanisms and their roles across various pathologies and human developmental outcomes, along with regulatory mechanisms targeted for therapeutic approaches. The book is broadly divided in two parts: early chapters describe the basics of post-transcriptional gene regulation, associated epigenetic mechanisms, the role of RNA binding proteins, the evolution of post-transcriptional gene regulation, and methods to study these mechanisms. The second half of the book includes deeper discussion of post-transcriptional gene regulation across specific diseases and therapeutics targets. Various post-transcriptional events, including alternative splicing and polyadenylation, mRNA stability, and miRNAs and their involvement in the disease progression, are examined in detail.

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.

Genomic Medicine Skills and Competencies discusses core and practical aspects of genetic and genomic education and training for medical field. Many aspects of genomic applications in science, biotechnology, clinical medicine and healthcare require core and specialist knowledge, skills development and competencies for carrying out diverse tasks. Several knowledge-based courses and opportunities for skills and competencies development and assessment are now available and the main required subjects are discussed in this volume. The book focuses on all major aspects of genetic and genomic education training that are currently offered and evaluated and is a valuable resource for researchers, clinicians, physicians, nurses, genetic counselors, bioinformatics technicians, and other professionals who are interested in learning more about such promising field.

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.

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 .

The purpose of this primer is to provide students, teachers as well as academic and industry researchers with a succinct account of the chemical and structural features of chromatin and the role that these features play in the maintenance and function of the genetic material.It is universally accepted that DNA is the carrier of the genetic information that is transmitted from parents to their offspring and that it is responsible for the anatomy, physiology and behavior of all individuals throughout development and adult life. Yet, how this information is retrieved and used selectively to allow a fertilized egg to become an organism made up of myriads of different cells and tissues is not as evident and easily understood.Dr Lucchesi, an internationally known researcher and teacher, provides an easily opened window into the role that the complex of proteins and nucleic acids that are associated with the DNA play in mediating gene expression and in responding to environmental circumstances.

The purpose of this primer is to provide students, teachers as well as academic and industry researchers with a succinct account of the chemical and structural features of chromatin and the role that these features play in the maintenance and function of the genetic material.It is universally accepted that DNA is the carrier of the genetic information that is transmitted from parents to their offspring and that it is responsible for the anatomy, physiology and behavior of all individuals throughout development and adult life. Yet, how this information is retrieved and used selectively to allow a fertilized egg to become an organism made up of myriads of different cells and tissues is not as evident and easily understood.Dr Lucchesi, an internationally known researcher and teacher, provides an easily opened window into the role that the complex of proteins and nucleic acids that are associated with the DNA play in mediating gene expression and in responding to environmental circumstances.

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.

Genomics in Biosecurity: Principles and Applications of Genomic Technologies in Expanded Biosecurity Concepts, in the Translational and Applied Genomics series, explains in definite and practical terms the applicability of genomic technologies in every aspect of biosecurity, from emergent diagnostics to bioterrorism, agroterrorism, next generation biowarfare, biosurveillance and risk assessment. This book offers an integrated discussion of genomics and GCBR (global catastrophic biological risks) events, considering both basic aspects of biosecurity genomics and application of genomic technologies to drive new solutions. Readers will find evidence-based strategies to apply genomics in disease and pathogen monitoring and diagnosis, and more. Social aspects of GCBR events and genomic biosecurity, such as issues of terrorism, policy ethics, and practice, are also considered in-depth.

Progress in Genomic Medicine: From Research to Clinical Application provides a careful synthesis of the foundations, current trends and translational challenges in genomic medicine, clarifying pathways forward and enabling genomic medicine research and implementation across clinical settings and treatment development. Sections address the history and growth of genetic medicine, with a discussion of key studies in syndrome delineations, inherited diseases, biochemical genetics, and chromosome abnormalities, overview clinical applications made possible through genomic advances, with chapters on DNA sequencing for clinical genetic diagnosis, genotype-phenotype correlations in individuals and across populations, new-born screening for treatable genetic disorders, and more. In addition, social, ethical and public health aspects of applying genomic technologies are included throughout. Here, Dr. Smith applies her experience and participation in the field, across its major milestones, to put current research, clinical advances, and ongoing questions in context.

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.

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.

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.

Rigor and Reproducibility in Genetics and Genomics: Peer-reviewed, Published, Cited provides a full methodological and statistical overview for researchers, clinicians, students, and post-doctoral fellows conducting genetic and genomic research. Here, active geneticists, clinicians, and bioinformaticists offer practical solutions for a variety of challenges associated with several modern approaches in genetics and genomics, including genotyping, gene expression analysis, epigenetic analysis, GWAS, EWAS, genomic sequencing, and gene editing. Emphasis is placed on rigor and reproducibility throughout, with each section containing laboratory case-studies and classroom activities covering step-by-step protocols, best practices, and common pitfalls. Specific genetic and genomic technologies discussed include microarray analysis, DNA-seq, RNA-seq, Chip-Seq, methyl-seq, CRISPR gene editing, and CRISPR-based genetic analysis. Training exercises, supporting data, and in-depth discussions of rigor, reproducibility, and ethics in research together deliver a solid foundation in research standards for the next generation of genetic and genomic scientists.

Epigenetics of Exercise and Sports: Concepts, Methods, and Current Research explains fundamental epigenetic processes and how these are altered by exercise and sports. After a brief review of fundamental epigenetic biology, this all-new volume in the Translational Epigenetics series offers step-by-step instruction in how epigenetic factors are investigated for their influence over exercise related traits of human physiology, disease, and injury. The current state of knowledge in the field and recent findings are discussed in-depth, illuminating how exercise and sports performance may epigenetically modify our physiology, disease and injury risks, and how this knowledge can be applied in personalized exercise approaches, diagnostics, and treatment. This book also explores the shortcomings of explaining exercise related phenomena using only genomics and traditional biochemical techniques, setting the scene for a paradigm shift in exercise biology. In addition, over a dozen international specialists contribute chapters on exercise and sports epigenetics, and their influence over metabolism, obesity, aging, immunity, and neurological disease, as well as the epigenetic impacts of concussions and sports doping. A concluding chapter discusses ongoing themes in the field and outlooks for future research.

In recent times, the boundary between living and non-living has been blurred by advances in genomics, cell biology, and molecular neuroscience, whereby humans are repaired, enhanced, or made anew. Scientists and physicians are now able to keep cells, organs, and bodies alive indefinitely and can return cells or DNA to our bodies and make new cells for the purpose of treating disease or growing new tissue. Meanwhile, transhuman technologies create illusions of immortality. Immortal: Our Cells, DNA, and Bodies synthesizes what we know about life and death from a genetic, molecular, and cellular perspective, demarcates limits of knowledge, and poses new questions. Award-winning researcher and writer David Goldman examines in-depth three keys to understanding the nature and continuity of life: 1) epigenetic (ephemeral) vs genetic (durable) transgenerational memory; 2) life's cellular nature, and the ability to make bodies from cells; and 3) the distinction between bodies and persons. Grounded in recent scientific evidence and real-life cases that test our historical understanding of life and death, Goldman probes the nature of molecular continuity in the face of mortal extinction, encompassing how changes to the DNA code can be both long-lasting and transgenerational, and the continuous nature of cellular and molecular information transmission. In tying these themes together, Immortal asks us to apply fresh scientific concepts to examine, for ourselves, the continuity of being in the face of mortality.

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.

This book provides an introduction to the latest gene mapping techniques and their applications in biomedical research and evolutionary biology. It especially highlights the advances made in large-scale genomic sequencing. Results of studies that illustrate how the new approaches have improved our understanding of the genetic basis of complex phenotypes including multifactorial diseases (e.g., cardiovascular disease, type 2 diabetes, and obesity), anatomic characteristics (e.g., the craniofacial complex), and neurological and behavioral phenotypes (e.g., human brain structure and nonhuman primate behavior) are presented. Topics covered include linkage and association methods, gene expression, copy number variation, next-generation sequencing, comparative genomics, population structure, and a discussion of the Human Genome Project. Further included are discussions of the use of statistical genetic and genetic epidemiologic techniques to decipher the genetic architecture of normal and disease-related complex phenotypes using data from both humans and non-human primates.

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.

Genomics in the Clinic: A Practical Guide to Genetic Testing, Evaluation, and Counseling illustrates the current scope of the practice of genetics for healthcare professionals, so they can understand principles applicable to genetic testing and consultation. Written by an authoritative well-balanced team, including experienced clinical geneticists, genetic counselors, and medical subspecialists, this book adopts an accessible, easy-to-follow format. Sections are dedicated to basic genetic principles; clinical genetic and genomic testing; prenatal, clinical and cancer genetic diagnosis and counseling; and ethical and social implications in genomic medicine. Over 100 illustrative cases examine a range of prenatal, pediatric and adult genetic conditions and testing, putting these concepts and approaches into practice. Genomics in the Clinic: A Practical Guide to Genetic Testing, Evaluation, and Counseling is important for primary care providers, as patient care evolves in the current genomic-influenced world of precision medicine.

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."

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.

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.