This volume provides established approaches for identifying, characterizing, and manipulating circRNAs in vitro, in vivo, and in silico. Chapters highlight the breakthroughs and the challenges in this new field of research. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Circular RNAs: Methods and Protocols aims to useful and informative for further study into this vital field.

Life's Greatest Secret is the story of the discovery and cracking of the genetic code. This great scientific breakthrough has had far-reaching consequences for how we understand ourselves and our place in the natural world. The code forms the most striking proof of Darwin's hypothesis that all organisms are related, holds tremendous promise for improving human well-being, and has transformed the way we think about life. Matthew Cobb interweaves science, biography and anecdote in a book that mixes remarkable insights, theoretical dead-ends and ingenious experiments with the pace of a thriller. He describes cooperation and competition among some of the twentieth century's most outstanding and eccentric minds, moves between biology, physics and chemistry, and shows the part played by computing and cybernetics. The story spans the globe, from Cambridge MA to Cambridge UK, New York to Paris, London to Moscow. It is both thrilling science and a fascinating story about how science is done.

'Species' are central to understanding the origin and dynamics of biological diversity; explaining why lineages split into multiple distinct species is one of the main goals of evolutionary biology. However the existence of species is often taken for granted, and precisely what is meant by species and whether they really exist as a pattern of nature has rarely been modelled or critically tested. This novel book presents a synthetic overview of the evolutionary biology of species, describing what species are, how they form, the consequences of species boundaries and diversity for evolution, and patterns of species accumulation over time. The central thesis is that species represent more than just a unit of taxonomy; they are a model of how diversity is structured as well as how groups of related organisms evolve. The author adopts an intentionally broad approach, stepping back from the details to consider what species constitute, both theoretically and empirically, and how we detect them, drawing on a wealth of examples from microbes to multicellular organisms.

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.

Oligonucleotides represent one of the most significant pharmaceutical breakthroughs in recent years, showing great promise as diagnostic and therapeutic agents for malignant tumors, cardiovascular disease, diabetes, viral infections, and many other degenerative disorders. The Handbook of Analysis of Oligonucleotides and Related Products is an essential reference manual on the practical application of modern and emerging analytical techniques for the analysis of this unique class of compounds. A strong collaboration among thirty leading analytical scientists from around the world, the book provides readers with a comprehensive overview of the most commonly used analytical techniques and their advantages and limitations in assuring the identity, purity, quality, and strength of an oligonucleotide intended for therapeutic use. Topics discussed include: Strategies for enzymatic or chemical degradation of chemically modified oligonucleotides toward mass spectrometric sequencing Purity analysis by chromatographic or electrophoretic methods, including RP-HPLC, AX-HPLC, HILIC, SEC, and CGE Characterization of sequence-related impurities in oligonucleotides by mass spectrometry and chromatography Structure elucidation by spectroscopic methods (IR, NMR, MS) as well as base composition and thermal melt analysis (Tm) Approaches for the accurate determination of molar extinction coefficient of oligonucleotides Accurate determination of assay values Assessment of the overall quality of oligonucleotides, including microbial analysis and determination of residual solvents and heavy metals Strategies for determining the chemical stability of oligonucleotides The use of hybridization techniques for supporting pharmacokinetics and drug metabolism studies in preclinical and clinical development Guidance for the presentation of relevant analytical information towards meeting current regulatory expectations for oligonucleotide therapeutics This resource provides a practical guide for applying state-of-the-art analytical techniques in research, development, and manufacturing settings.

Assembling the work of an international panel of researchers, Mass Spectrometry of Nucleosides and Nucleic Acids summarizes and reviews the latest developments in the field and provides a window on the next generation of analysis. Beginning with an overview of recent developments, the book highlights the most popular ionization methods and illustrates the diversity of strategies employed in the characterization and sequencing of DNA and RNA oligomers, nucleosides, nucleotides, and adducts. It describes studies performed on deoxyinosine and its analogues and provides an introduction to tandem mass spectrometry (MS/MS).

Next, the contributors examine mass spectrometric application in the study of cyclic nucleotides in biochemical signal transduction. They analyze urinary modified nucleosides and explore DNA adducts. They discuss isotope labeling of DNA-mass spectrometry (ILD-MS) and examine various uses of electrospray ionization mass spectrometry (ESI-MS). The book reviews recent progress in the direct MS characterization of noncovalent nucleic acid-protein complexes, explores the interaction and ionization of guanidine-derived compounds with highly acidic biomolecules, and examines quantitative identification of nucleic acids via signature digestion products detected using mass spectrometry.

The book describes a direct-infusion ESI-MS approach that can serve as a screening technique for the presence of modified nucleosides from small RNAs. Lastly, it discusses the LC-MS/MS method for the in vitro replication studies on damage-containing DNA substrates, and concludes with an examination of the influence of metal ions on the structure and reactivity of nucleic acids.

The exciting developments in mass spectrometry technology have fueled incredible advances in our understanding of nucleic acids and their complexes. The contributions presented in this volume capture the range of these advances, helping to inspire new findings and avenues of research.

"Genomic Control Process" explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes.

This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual frameworkProvides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literatureIncludes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant typeDemonstrates the causal power of system-level understanding of genomic control process
Conceptually organizes a constellation of complex and diverse biological phenomenaInvestigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual modelsExplores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome"

Evolution is one of the most important processes in life. It not only explains the detailed history of life on earth, but its scope also extends into many aspects of our own contemporary behavior-who we are and how we got to be here, our psychology, our cultures-and greatly impacts modern advancements in medicine and conservation biology. Perhaps its most important claim for science is its ability to provide an overarching framework that integrates the many life sciences into a single unified whole. Yet, evolution-evolutionary biology in particular-has been, and continues to be, regarded with suspicion by many. Understanding how and why evolution works, and what it can tell us, is perhaps the single most important contribution to the public perception of science. This book provides an overview of the basic theory and showcases how widely its consequences reverberate across the life sciences, the social sciences and even the humanities. In this book, Robin Dunbar uses examples drawn from plant life, animals and humans to illustrate these processes. Evolutionary science has important advantages. Most of science deals with the microscopic world that we cannot see and invariably have difficulty understanding, but evolution deals with the macro-world in which we live and move. That invariably makes it much easier for the lay audience to appreciate, understand and enjoy. Evolution: What Everyone Needs to Know (R) takes a broad approach to evolution, dealing both with the core theory itself and its impact on different aspects of the world we live in, from the iconic debates of the nineteenth century, to viruses and superbugs, to human evolution and behavior.

Given this pervasiveness and importance of miRNA-mediated gene regulation, it should come as little surprise that miRNAs themselves are also highly regulated. However, the recent explosion of knowledge on this topic has been remarkable, providing a primary motivation for publication of this book. As miRNAs are transcribed by RNA polymerase II, the enzyme that also generates mRNAs, it was perhaps not unexpected that miRNA transcription would be subject to regulation, and we have willfully mitted this aspect from this monograph. However, what has been unexpected is the extent of post-transcriptional regulation of miRNAs that is illustrated in this book.

DNA Repair, Volume 115, the latest release in the Advances in Protein Chemistry and Structural Biology series, provides an overview of current developments in mechanisms underlying DNA repair, their involvement in maintaining chromatin repair, the balance between chromosome breaks repair pathways, tumorigenesis, immune signaling and infection-induced inflammation. Specific chapters cover the Structure and function of the multi-subunit TFIIH with insights into nucleotide excision repair, Chromatin repair: how DNA packaging controls double-strand break repair, Controlling the balance between chromosome breaks repair pathways, The targeting of DNA repair pathways in the era of precision oncology, and much more.

What are the genomic signatures of adaptations in DNA? How often does natural selection dictate changes to DNA? How does the ebb and flow in the abundance of individuals over time get marked onto chromosomes to record genetic history? Molecular population genetics seeks to answer such questions by explaining genetic variation and molecular evolution from micro-evolutionary principles. It provides a way to learn about how evolution works and how it shapes species by incorporating molecular details of DNA as the heritable material. It enables us to understand the logic of how mutations originate, change in abundance in populations, and become fixed as DNA sequence divergence between species. With the revolutionary advances in genomic data acquisition, understanding molecular population genetics is now a fundamental requirement for today's life scientists. These concepts apply in analysis of personal genomics, genome-wide association studies, landscape and conservation genetics, forensics, molecular anthropology, and selection scans. This book introduces, in an accessible way, the bare essentials of the theory and practice of molecular population genetics.

Although less than a decade old, the field of microarray data analysis is now thriving and growing at a remarkable pace. Biologists, geneticists, and computer scientists as well as statisticians all need an accessible, systematic treatment of the techniques used for analyzing the vast amounts of data generated by large-scale gene expression studies. And there is arguably no group better qualified to do so than the authors of this book.

Statistical Analysis of Gene Expression Microarray Data promises to become the definitive basic reference in the field. Under the editorship of Terry Speed, some of the world's most pre-eminent authorities have joined forces to present the tools, features, and problems associated with the analysis of genetic microarray data. These include::

· Model-based analysis of oligonucleotide arrays, including expression index computation, outlier detection, and standard error applications
· Design and analysis of comparative experiments involving microarrays, with focus on \ two-color cDNA or long oligonucleotide arrays on glass slides
· Classification issues, including the statistical foundations of classification and an overview of different classifiers
· Clustering, partitioning, and hierarchical methods of analysis, including techniques related to principal components and singular value decomposition

Although the technologies used in large-scale, high throughput assays will continue to evolve, statistical analysis will remain a cornerstone of their success and future development. Statistical Analysis of Gene Expression Microarray Data will help you meet the challenges of large, complex datasets and contribute to new methodological and computational advances.

The Anthropocene defines the here-and-now time period on Earth of indelible (and possibly irreversible) human disturbance to the natural world, from habitat destruction and mass extinction to global climate change. To ameliorate and repair the damage that threatens the world's dwindling resources and our very existence, humanity is enacting massive interventions to fuse modern technologies with long established natural processes. Advances in genetic engineering have put us on the cusp of directly shaping the DNA of every living organism (including ourselves), as well as determining the evolution of completely novel species. The author invites the reader to explore how humans have manipulated the ancient forces of evolution and the future possibilities of genetic engineering for conservation and rewilding, de-extinction, and even the creation of viable populations of entirely new species. To entertain such possibilities of synthetic biology, he forces us to wrestle with the threats and ethical conundrums that surround the unintended consequences, as well as the values that humanity places on authenticity in nature. In so doing, this accessible and thought-provoking book explores the potential future of life on planet Earth.

Forensic DNA analysis plays a central role in the judicial system. A DNA sample can change the course of an investigation with immense consequences. Because DNA typing is recognized as the epitome of forensic science, increasing public awareness in this area is vital. Through several cases, examples and illustrations, this book explains the basic principles of forensic DNA typing, and how it integrates with law enforcement investigations and legal decisions. Written for a general readership, Understanding Forensic DNA explains both the power and the limitations of DNA analysis. This book dispels common misunderstandings regarding DNA analysis and shows how astounding match probabilities such as one-in-a-trillion are calculated, what they really mean, and why DNA alone never solves a case.

Forensic DNA analysis plays a central role in the judicial system. A DNA sample can change the course of an investigation with immense consequences. Because DNA typing is recognized as the epitome of forensic science, increasing public awareness in this area is vital. Through several cases, examples and illustrations, this book explains the basic principles of forensic DNA typing, and how it integrates with law enforcement investigations and legal decisions. Written for a general readership, Understanding Forensic DNA explains both the power and the limitations of DNA analysis. This book dispels common misunderstandings regarding DNA analysis and shows how astounding match probabilities such as one-in-a-trillion are calculated, what they really mean, and why DNA alone never solves a case.

Single Molecule Science (SMS) has emerged from developing, using and combining technologies such as super-resolution microscopy, atomic force microscopy, and optical and magnetic tweezers, alongside sophisticated computational and modelling techniques. This comprehensive, edited volume brings together authoritative overviews of these methods from a biological perspective, and highlights how they can be used to observe and track individual molecules and monitor molecular interactions in living cells. Pioneers in this fast-moving field cover topics such as single molecule optical maps, nanomachines, and protein folding and dynamics. A particular emphasis is also given to mapping DNA molecules for diagnostic purposes, and the study of gene expression. With numerous illustrations, this book reveals how SMS has presented us with a new way of understanding life processes. A must-have for researchers and graduate students, as well as those working in industry, primarily in the areas of biophysics, biological imaging, genomics and structural biology.

The past few years have seen a revolution in our ability to map whole genome DNA from ancient humans. With the ancient DNA revolution, combined with rapid genome mapping of present human populations, has come remarkable insights into our past. This important new data has clarified and added to our knowledge from archaeology and anthropology, helped resolve long-existing controversies, challenged long-held views, and thrown up some remarkable surprises. The emerging picture is one of many waves of ancient human migrations, so that all populations existing today are mixes of ancient ones, as well as in many cases carrying a genetic component from Neanderthals, and, in some populations, Denisovans. David Reich, whose team has been at the forefront of these discoveries, explains what the genetics is telling us about ourselves and our complex and often surprising ancestry. Gone are old ideas of any kind of racial 'purity', or even deep and ancient divides between peoples. Instead, we are finding a rich variety of mixtures. Reich describes the cutting-edge findings from the past few years, and also considers the sensitivities involved in tracing ancestry, with science sometimes jostling with politics and tradition. He brings an important wider message: that we should celebrate our rich diversity, and recognize that every one of us is the result of a long history of migration and intermixing of ancient peoples, which we carry as ghosts in our DNA. What will we discover next?

The technique of DNA Sequencing lies at the heart of modern molecular biology. Since current methods were first introduced, sequence databases have grown exponentially, and are now an indispensable research tool. This up-to-date, practical guide is unique in covering all aspects of the methodology of DNA sequencing, as well as sequence analysis. It describes the basic methods (both manual and automated) and the more advanced techniques (for example, those based on PCR) before moving on to key applications. The final section focuses on the analysis of sequence data; it details the software available, and explains how the Internet can be used for accessing software and major databases. By explaining the options available and their merits, DNA Sequencing allows newcomers to the field to decide which method is the most suitable for their application. For experienced sequencers the book is a useful reference source for details of the less common techniques and as a means of updating knowledge.

The release of the complete version of the human genome sequence in 2003 has paved the way for defining gene function and genetic background for phenotypic variation in humans and allowed us to study the aging process in a new light. This new volume results from that research and focuses on the genetic and epigenetic process of aging. While the interpretation of the genome data is still in its initial stages, this new volume looks at the evolving understanding of molecular mechanisms involved in cellular processes, gene function associated with complex traits, epigenetic components involve in gene control and the creation of hypothesis-free genome-wide approaches. Longevity Genes: A Blueprint for Aging explores the genetic and genomic elements that can maintain a long life such as DNA damage mechanisms, epigenetics and the way we can use this knowledge to generate customized treatments. It touches on some of the multidisciplinary approaches as well as genomic-wide association technology used to analyze complex traits. This book describes the hunt for genes affecting complex traits using a high throughput technology, with adequate consideration for the selection of an appropriate population, applications of statistical genetics and computational biology, and most importantly, considering phenotype-genotype association studies. Longevity Genes provides coverage of not only established aspects of genetics and aging, but also new approaches and perceptions in this important area of research.

Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

In 1962, Maurice Wilkins, Francis Crick, and James Watson received the Nobel Prize, but it was Rosalind Franklin's data and photographs of DNA that led to their discovery.

Brenda Maddox tells a powerful story of a remarkably single-minded, forthright, and tempestuous young woman who, at the age of fifteen, decided she was going to be a scientist, but who was airbrushed out of the greatest scientific discovery of the twentieth century.

Combinatorial chemistry is used to find materials that form sensor microarrays. This book discusses the fundamentals, and then proceeds to the many applications of microarrays, from measuring gene expression (DNA microarrays) to protein-protein interactions, peptide chemistry, carbodhydrate chemistry, electrochemical detection, and microfluidics.

A Primer of Population Genetics and Genomics has been completely revised and updated to provide a concise but comprehensive introduction to the basic concepts of population genetics and genomics. Recent textbooks have tended to focus on such specialized topics as the coalescent, molecular evolution, human population genetics, or genomics. This primer bucks that trend by encouraging a broader familiarity with, and understanding of, population genetics and genomics as a whole. The overview ranges from mating systems through the causes of evolution, molecular population genetics, and the genomics of complex traits. Interwoven are discussions of ancient DNA, gene drive, landscape genetics, identifying risk factors for complex diseases, the genomics of adaptation and speciation, and other active areas of current research. The principles are illuminated by numerous examples from a wide variety of animals, plants, microbes, and human populations. The approach also emphasizes learning by doing, which in this case means solving numerical or conceptual problems. The rationale behind this is that the use of concepts in problem-solving lead to deeper understanding and longer knowledge retention. This accessible, introductory textbook is aimed principally at students of various levels and abilities (from senior undergraduate to postgraduate) as well as practising scientists in the fields of population genetics, ecology, evolutionary biology, computational biology, bioinformatics, biostatistics, physics, and mathematics.

Phenotypic Switching: Implications in Biology and Medicine provides a comprehensive examination of phenotypic switching across biological systems, including underlying mechanisms, evolutionary significance, and its role in biomedical science. Contributions from international leaders discuss conceptual and theoretical aspects of phenotypic plasticity, its influence over biological development, differentiation, biodiversity, and potential applications in cancer therapy, regenerative medicine and stem cell therapy, among other treatments. Chapters discuss fundamental mechanisms of phenotypic switching, including transition states, cell fate decisions, epigenetic factors, stochasticity, protein-based inheritance, specific areas of human development and disease relevance, phenotypic plasticity in melanoma, prostate cancer, breast cancer, non-genetic heterogeneity in cancer, hepatitis C, and more. This book is essential for active researchers, basic and translational scientists, clinicians, postgraduates and students in genetics, human genomics, pathology, bioinformatics, developmental biology, evolutionary biology and adaptive opportunities in yeast.

Legumes in the Omic Era provides a timely review of recent advances in legume genomics research and application. In this post-genomic era enormous amount of biological information is available which could be of huge potential use for crop improvement applications. This aspect of genomics assisted plant breeding is focused throughout the book for all the important grain legume crops. Role of functional genomics and importance of bioinformatics tools in present day genomics and molecular breeding research is also discussed in detail. Use of molecular tools for nutritional fortification of grain legume is briefly presented. A chapter also been contributed on fungal disease resistance to elucidate potential application of genomic tools in molecular breeding of grain legume species. The book contains fifteen chapters contributed by 50 scientists from different countries who are actively involved in analyzing and improving particular legume genome. This book will serve as reference resource to legumes researchers for use of genome information in improvement of major legume crops.

Dr Sanjeev Gupta is Principal Scientist/Project Coordinator-All India Coordinated Research Project on "Vigna" Crops at Indian Institute of Pulses Research (IIPR), Kanpur. He has more than two decades of research experience in grain legume breeding and developed a number of high yielding cultivars in grain legumes. He is authored numerous research papers published in peer-reviewed journals and edited several books in plant breeding aspects. He was the Organizing Secretary of the International Grain Legume Conference, 2009 held in the Indian Institute of Pulses Research, Kanpur, India. He has travelled across the continents to present his research several times. He is recipient of several awards for his research and literary contributions Dr. Nagasamy Nadarajan is the Director of the Indian Institute of Pulses Research (IIPR), Kanpur. He has more than three decades of teaching and research experience and developed more than fifteen legume and cereal cultivars. He has to his credits more than 200 peer-reviewed research publications. He has guided several graduate students for Masters and Doctoral degrees in food legume breeding and genetics research. He has authored a book in biometrics which is one of the most popular books among the agriculture graduate students in India. He is the recipient of three international and six national awards and honours for his outstanding contributions Mr. Debjyoti Sen Gupta is the ICAR International Fellow and Ph.D. candidate at North Dakota State University (NDSU), Fargo, USA. Recently, he visited Department of Crop and Soil Sciences, Washington State University, Pullman, USA for high throughput genotyping work. Before joining at NDSU he was serving as the Scientist in the Indian Institute of Pulses Research (IIPR). He has authored several research articles, review articles and book chapters in the peer-reviewed journals and books from reputed publishers like Springer, CABI etc. He is recipient of several fellowships like CSIR-JRF, New Delhi; ICAR-JRF, New Delhi throughout his graduate study programs. "