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.

Are you considering to test your own DNA? Do you want to learn more about your health and ancestry? Understand your DNA - A Guide is about what you can use genetics for. For a few hundred dollars, you can now scan your own genes. Millions of people all over the world have already done so. Everyone wants to see what they can get to know about themselves, and the market growing rapidly. But what does it require from you? And what can you really use a DNA test for? Understand your DNA - A Guide helps you put the plots and charts of consumer genetics into perspective and enables you to figure out what's up and down in the media headlines. The book is also a key input for today's debate about what we as a society can and want to do with medical genetics. Genetics will play a growing role in the future. Understand your DNA - A Guide is an easy-to-read and necessary guide to that future. The book is provided with a foreword by Professor Sham Pak-Chung of Hong Kong University.While there are many books about genetics, they typically take the perspective of a scientist wanting to understand the molecular levels. At the same time, direct-to-consumer genetics is a booming market, with millions of people already tested. Very little has been published that will guide them for real, because the need here is more focused on medical and practical understanding, than focussed on molecules.This book therefore aims to hit that vacant spot in the market. It's a walk-through of all concepts that are necessary to understand in your own analysis. Meanwhile, it is also limited in scope to only those concepts - thus distinguishing it from broader works.The book is appropriate for the readerships in modern multi-ethnic metropolises because it mixes European and Asian examples, both from the collaboration between the author from Europe and the foreword-writer, Prof. Pak Sham of Hong Kong University. But also, because many of the examples in the book concerns differences and similarities between Asian and European ethnicities, something the author believes is a trend in time.Related Link(s)

This book comprehensively discusses our current understanding of the role and biological mechanisms of horizontal transfer of genetic elements in the environment, which has been important in the evolution of prokaryotes (archaea and bacteria). Horizontal transfer of genetic elements generates variations of prokaryotes and their genomes. Comparative studies of genomes revealed that it frequently occurred during archaeal and bacterial evolution. The book introduces a variety of studies related to horizontal gene transfer, gene silencing, plasmids, phages, transposons, and the emergence of microbes that degrade man-made xenobiotics and have antimicrobial resistance. Written by leading researchers in DNA traffic, the book is a valuable guide to horizontal transfer for both young scientists and experts in the field.

Epigenetics is the study of heritable changes in gene function that do not involve changes in the DNA sequence. These changes, consisting principally of DNA methylation, histone modifications, and non-coding RNAs, maintain or modulate the initial impact of regulatory factors that recognize and associate with particular genomic sequences. Epigenetic modifications are manifest in all aspects of normal cellular differentiation and function, but they can also have damaging effects that result in pathologies such as cancer. Research is continuously uncovering the role of epigenetics in a variety of human disorders, providing new avenues for therapeutic interventions and advances in regenerative medicine. This book's primary goal is to establish a framework that can be used to understand the basis of epigenetic regulation and to appreciate both its derivation from genetics and interdependence with genetic mechanisms. A further aim is to highlight the role played by the three-dimensional organization of the genetic material itself (the complex of DNA, histones and non-histone proteins referred to as chromatin), and its distribution within a functionally compartmentalized nucleus. This architectural organization of the genome plays a major role in the subsequent retrieval, interpretation, and execution of both genetic and epigenetic information.

This monograph presents a new disciplinecultural genomicsas a complex approach for studying the interrelation between genomic data and culture and the impact of culture on genomic evolution in human history. It analyzes three basic components of cultural genomicsarchaeology, genealogy, and genomics. The author explores the classifications of archaeology and genealogy as traditional disciplines and tests their peculiarities against the limitations and delimitations of genomics to resolve the problems of human origin and historical demography. The main thesis in the book is that cultural genomics as a complex discipline has been changing the dynamics of exploring the human cultural identity in revolutionary ways and the problems of personal origin and lineage. Additionally, this book analyzes the evolution of human civilization and its requirement for close integration of genomics, archaeology, genetic genealogy, traditional genealogy, and other related social and cultural disciplines. Cultural identity is the basic constructor of the progress of human civilization. Cultural genomics allows researchers to personalize human history and embed new parameters of identity from the perspective of origin. However, the success of the scholarly results depends on how well genomics is blended with related branches of the science of humanity to produce quality results. Many topics of cultural identity still dwell only in the domain of traditional archaeology and genealogy, although genomics has expanded the opportunity to learn not only how cultural identity evolved, but also to create platforms of global networks of interrelatedness that have no analogies in the previous human scholarly experience. The innovative scholarly problems that the author addresses and the general attempt to constitute cultural genomics as a leading complex discipline of human cultural identity in the 21st century connect the book to the interests of the global scholarly community and all who are interested in cultural identity, genomic archaeology, genetic genealogy, and human origin as well as the evolution of human civilization. The author of this study, Dr. Lolita Nikolova, is a globally renowned scientist who has conducted an in-depth and complex original research; she uniquely combines expertise in the fields of prehistoric archaeology, genealogy, and cultural genomics.

This volume details a collection of state-of-art methods including identification of novel ncRNAs and their targets, functional annotation and disease association in different biological contexts. Chapters guide readers through an overview of disease-specific ncRNAs, computational methods and workflows for ncRNA discovery, annotation based on high-throughput sequencing data, bioinformatics tools and databases for ncRNA analyses, network-based methods, and kinetic modelling of ncRNA-mediated gene regulation. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Biology of Non-Coding RNA: Methods and Protocols aims to provide a state-of-the-art collection of computational methods and approaches that will be of value to researchers interested in ncRNA field.

Analysis of the equine genome began just over a decade ago, culminating in the recent complete sequencing of the horse genome. The availability of the equine whole genome sequence represents the successful completion of an important era of equine genome analysis, and the beginning of a new era where the sequence information will catalyze the development of new tools and resources that will permit study of a range of traits that are economically important and are significant to equine health and welfare."Equine Genomics" provides a timely comprehensive overview of equine genomic research. Chapters detail key accomplishments and the current state of research, as well as looking forward to possible applications of genomic technologies to horse breeding, health, and welfare. "Equine Genomics" delivers a global overview of the topic and is seamlessly edited by a leading equine genomics researcher. "Equine Genomics" is an indispensible source of information for anyone with an interest in this increasingly important field of study, including equine genomic researchers, clinicians, animal science professionals and equine field veterinarians.

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.

This book constitutes the proceedings of the 15th International Workshop Comparative Genomics, RECOMB-CG 2017, held in Barcelona, Spain, in October 2017. The 16 full papers presented were carefully reviewed and selected from 32 submissions. The papers report original research in all areas of Comparative Genomics.

Over a decade ago, as the Human Genome Project completed its mapping of the entire human genome, hopes ran high that we would rapidly be able to use our knowledge of human genes to tackle many inherited diseases, and understand what makes us unique among animals. But things didn't turn out that way. For a start, we turned out to have far fewer genes than originally thought - just over 20,000, the same sort of number as a fruit fly or worm. What's more, the proportion of DNA consisting of genes coding for proteins was a mere 2%. So, was the rest of the genome accumulated 'junk'? Things have changed since those early heady days of the Human Genome Project. But the emerging picture is if anything far more exciting. In this book, John Parrington explains the key features that are coming to light - some, such as the results of the international ENCODE programme, still much debated and controversial in their scope. He gives an outline of the deeper genome, involving layers of regulatory elements controlling and coordinating the switching on and off of genes; the impact of its 3D geometry; the discovery of a variety of new RNAs playing critical roles; the epigenetic changes influenced by the environment and life experiences that can make identical twins different and be passed on to the next generation; and the clues coming out of comparisons with the genomes of Neanderthals as well as that of chimps about the development of our species. We are learning more about ourselves, and about the genetic aspects of many diseases. But in its complexity, flexibility, and ability to respond to environmental cues, the human genome is proving to be far more subtle than we ever imagined.

The book gives an overview of developments in Quantitative Genetics and variance component analysis in an era of Big Data and Sequenced Genomes. It provides a detailed description of a direct method of estimation that will be a useful means of extracting information from a large set of data that was inconceivable 10 to 20 years ago.The book is a combination of a history of variance component analysis and a forward looking view as to how direct methods of estimation arise from the availability of big data sets and sequenced genomes of each individual in the sample.Many papers and books on quantitative genetics versions of the general linear model from statistics are useful for analyzing the data, using relatively small sets of data. In this book, new methods of direct estimation are introduced and analyzed that are appropriate for an era of big sets of data and sequences genomes. These direct methods of estimation are based on taking conditional expectations rather the methods of least squares that characterize many applications of the general linear model of statistics.

The book gives an overview of developments in Quantitative Genetics and variance component analysis in an era of Big Data and Sequenced Genomes. It provides a detailed description of a direct method of estimation that will be a useful means of extracting information from a large set of data that was inconceivable 10 to 20 years ago.The book is a combination of a history of variance component analysis and a forward looking view as to how direct methods of estimation arise from the availability of big data sets and sequenced genomes of each individual in the sample.Many papers and books on quantitative genetics versions of the general linear model from statistics are useful for analyzing the data, using relatively small sets of data. In this book, new methods of direct estimation are introduced and analyzed that are appropriate for an era of big sets of data and sequences genomes. These direct methods of estimation are based on taking conditional expectations rather the methods of least squares that characterize many applications of the general linear model of statistics.

The problem of unraveling two intertwined strands during the duplication of DNA was recognized shortly after the proposal of the DNA double helix structure in 1953. A group of enzymes called DNA topoisomerases solve this problem by breaking and rejoining DNA molecules in a controlled manner, thereby allowing strands to be passed through each other and thus untangled not just during DNA replication, but also during many other basic cellular processes. Because of their intimate involvement in the workings of the cell, topoisomerases are also the logical targets of many antibiotics (including Cipro) and anticancer agents. This book, written by James Wang, the discoverer of the first topoisomerase and a leader in the field since, presents ten chapters covering the historical backdrop of the DNA entanglement problem and the discovery of the DNA topoisomerases, how DNA topoisomerases perform their magic in DNA replication, transcription, genetic recombination and chromosome condensation, and how they are targets of therapeutic agents. The book should appeal to readers from undergraduates upwards with interests in the biological and clinical aspects of topoisomerase function, or in the mathematics and physics of topology.

This volume covers the latest protocols designed to identify and characterize TEs in genomes, ancient or recently inserted. Additionally, this book includes a series of protocols designed to understand how host genomes act to regulate the activity of TEs, from elegant genetic mobilization assays to key biochemical methods. Finally, this book also includes chapters that describe how TEs can be used for biotechnological applications. Written for the Methods in Molecular Biology series, 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, Transposons and Retrotransposons: Methods and Protocols aims to ensure successful results in the further study of this vital field.

How unassuming government researcher Marshall Nirenberg beat James Watson, Francis Crick, and other world-famous scientists in the race to discover the genetic code. The genetic code is the Rosetta Stone by which we interpret the 3.3 billion letters of human DNA, the alphabet of life, and the discovery of the code has had an immeasurable impact on science and society. In 1968, Marshall Nirenberg, an unassuming government scientist working at the National Institutes of Health, shared the Nobel Prize for cracking the genetic code. He was the least likely man to make such an earth-shaking discovery, and yet he had gotten there before such members of the scientific elite as James Watson and Francis Crick. How did Nirenberg do it, and why is he so little known? In The Least Likely Man, Franklin Portugal tells the fascinating life story of a famous scientist that most of us have never heard of. Nirenberg did not have a particularly brilliant undergraduate or graduate career. After being hired as a researcher at the NIH, he quietly explored how cells make proteins. Meanwhile, Watson, Crick, and eighteen other leading scientists had formed the "RNA Tie Club" (named after the distinctive ties they wore, each decorated with one of twenty amino acid designs), intending to claim credit for the discovery of the genetic code before they had even worked out the details. They were surprised, and displeased, when Nirenberg announced his preliminary findings of a genetic code at an international meeting in Moscow in 1961. Drawing on Nirenberg's "lab diaries," Portugal offers an engaging and accessible account of Nirenberg's experimental approach, describes counterclaims by Crick, Watson, and Sidney Brenner, and traces Nirenberg's later switch to an entirely new, even more challenging field. Having won the Nobel for his work on the genetic code, Nirenberg moved on to the next frontier of biological research: how the brain works.

This volume presents a series of protocols and methods, some of which are not widely used by researchers/practitioners, and will aid in the execution of different laboratory techniques. Forensic DNA Typing Protocols, Second Edition is arranged into a series of related chapters. Chapter 1-3 examines two different aspects of RNA analysis for body fluid identification. Chapters 4-7 focuses on the storage of biological materials and the extraction of DNA from hard tissues. Chapters 8-10 present methods for monitoring the quality of DNA extracts, and steps to aid in the purification of DNA. Chapters 11-16 talk about methods on non-standard markers, such as INDELs, Y chromosome STRs, and mitochondrial DNA. Detailed procedures and data analysis for phenotypes and ancestry are explored in Chapter 17-19. The last chapter (20) looks at the application of DNA typing to the identification of non-human material to species level. 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. Practical and thorough, Forensic DNA Typing Protocols, Second Edition, is a valuable resource for forensic specialists, researchers, and anyone interested in the field of forensic science.

This book explores the double coding property of DNA, which is manifested in the digital and analog information types as two interdependent codes. This double coding principle can be applied to all living systems, from the level of the individual cell to entire social systems, seen as systems of communication. Further topics discussed include the ubiquitous problem of logical typing, which reflects our inherent incapacity to simultaneously perceive discontinuity and continuity, the problem of time, and the peculiarities of autopoietic living systems. It is shown that the scientific "truths" that appear to be coherent constructions connecting the scientifically verified observations by the rules of logic are in fact always relative and never absolute.

Inferring the precise locations and splicing patterns of genes in DNA is a difficult but important task, with broad applications to biomedicine. The mathematical and statistical techniques that have been applied to this problem are surveyed and organized into a logical framework based on the theory of parsing. Both established approaches and methods at the forefront of current research are discussed. Numerous case studies of existing software systems are provided, in addition to detailed examples that work through the actual implementation of effective gene-predictors using hidden Markov models and other machine-learning techniques. Background material on probability theory, discrete mathematics, computer science, and molecular biology is provided, making the book accessible to students and researchers from across the life and computational sciences. This book is ideal for use in a first course in bioinformatics at graduate or advanced undergraduate level, and for anyone wanting to keep pace with this rapidly-advancing field.

Inferring the precise locations and splicing patterns of genes in DNA is a difficult but important task, with broad applications to biomedicine. The mathematical and statistical techniques that have been applied to this problem are surveyed and organized into a logical framework based on the theory of parsing. Both established approaches and methods at the forefront of current research are discussed. Numerous case studies of existing software systems are provided, in addition to detailed examples that work through the actual implementation of effective gene-predictors using hidden Markov models and other machine-learning techniques. Background material on probability theory, discrete mathematics, computer science, and molecular biology is provided, making the book accessible to students and researchers from across the life and computational sciences. This book is ideal for use in a first course in bioinformatics at graduate or advanced undergraduate level, and for anyone wanting to keep pace with this rapidly-advancing field.

Metagenomic analysis has extraordinary potential to improve our understanding of microbial populations in their natural environment and identify novel genes of interest. The key feature of such analyses is that they are performed using metagenomic libraries constructed from total DNA isolated from a particular niche rather than a laboratory culture. Thus, metagenomic analyses potentially allow access to all the genetic resources present in an environment, regardless of whether or not they belong to micro-organisms that can be cultured in the laboratory. Sequence-based metagenomic analyses rely on comparisons with databases of known genomic sequences whilst functional analyses rely on screening libraries on the basis of the phenotypes cloned DNA can confer to host bacteria. Therefore, functional analysis allows the identification of novel genes with functions that could not have been predicted from their DNA sequence. This book discusses metagenomics' methods, applications and perspectives.

The nitrogen (N) cycle is one of the most important nutrient cycles on the planet, and many of its steps are performed by microbial organisms. During the cycling process, greenhouse gases are formed, including nitrous oxide and methane. In addition, the use of nitrogen fertilizers increases freshwater nitrate levels, causing pollution and human health problems. A greater knowledge of the microbial communities involved in nitrogen transformations is necessary to understand and counteract nitrogen pollution. This book - written by renowned researchers who are specialized in the most relevant and emerging topics in the field - provides comprehensive information on the new theoretical, methodological, and applied aspects of metagenomics and other 'omics' approaches used to study the microbial N cycle. The book provides a thorough account of the contributions of metagenomics to microbial N cycle background theory. It also reviews state-of-the-art investigative methods and explores new applications in water treatment, agricultural practices, climate change, among others. The book is recommended for microbiologists, environmental scientists, and anyone interested in microbial communities, metagenomics, metatranscriptomics, and metaproteomics of the microbial N cycle.

Understanding mechanisms of gene regulation that are independent of the DNA sequence itself - epigenetics - has the potential to overthrow long-held views on central topics in biology, such as the biology of disease or the evolution of species. High throughput technologies reveal epigenetic mechanisms at a genome-wide level, giving rise to epigenomics as a new discipline with a distinct set of research questions and methods. Leading experts from academia, the biotechnology and pharmaceutical industries explain the role of epigenomics in a wide range of contexts, covering basic chromatin biology, imprinting at a genome-wide level, and epigenomics in disease biology and epidemiology. Details on assays and sequencing technology serve as an up-to-date overview of the available technological tool kit. A reliable guide for newcomers to the field as well as experienced scientists, this is a unique resource for anyone interested in applying the power of twenty-first-century genomics to epigenetic studies.

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. "

Through the use of dramatic narratives, The Drama of DNA brings to life the complexities raised by the application of genomic technologies to health care and diagnosis. This creative, pedagogical approach shines a unique light on the ethical, psychosocial, and policy challenges that emerge as comprehensive sequencing of the human genome transitions from research to clinical medicine. Narrative genomics aims to enhance understanding of how we evaluate, process, and share genomic information, and to cultivate a deeper appreciation for difficult decisions encountered by health care professionals, bioethicists, families, and society as this technology reaches the bedside.
This innovative book includes both original genomic plays and theatrical excerpts that illuminate the implications of genomic information and emerging technologies for physicians, scientists, counselors, patients, blood relatives, and society. In addition to the plays, the authors provide an analytical foundation to frame the many challenges that often arise.

Scientoonics is a new discipline in science that disseminate scientific knoweldge through the medium of comics and cartoons (called scientoons). These are essentially cartoons based on scientific concepts, discoveries, results, and their applications. This book takes an entirely novel approach in communicating scientific facts. It will not only help the layman to acquaint himself with the scientific jargon but also allow him to understand how we can make use of such facts in our day-to-day life. Recent advances in scientific research, in fact, demand pro-active efforts from the scientists to ensure that complex ideas reach to the public effectively. Through scientoons this book aims to depict present concerns brought forward by the recent explosion of knowledge, especially in areas such as DNA, DNA fingerprinting, the human genome, conservation of wildlife, etc. The authors have taken the opportunity to provide information that will not only entertain the readers but also enrich their knowledge about the scientific advances taking place around the world. Each scientoon is therefore associated with a text that narrates the formal aspects of the science or its applications. This book is an endeavor to reduce the gap between the excitement of the advances in modern scientific world and the curious readers who want to know more about science.