This volume presents protocols for Brachypodium genomics in numerous areas ranging from marker development, trait evolution, functional genomics, metabolomics, transcriptomics, genomics, and tilling. This book also explores techniques to study the widening genetic base of Brachypodium that will help researchers better understand the model plant using NGS technologies. 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. Cutting-edge and comprehensive, Brachypodium Genomics: Methods and Protocols is a valuable resource for bench-oriented molecular biologists and computational biologists working towards further evolving this field.

This book provides an overview of the latest advancements in the field of alien introgression in wheat. The discovery and wide application of molecular genetic techniques including molecular markers, in situ hybridization, and genomics has led to a surge in interspecific and intergeneric hybridization in recent decades. The work begins with the taxonomy of cereals, especially of those species which are potential gene sources for wheat improvement. The text then goes on to cover the origin of wheat, breeding in connection with alien introgressions, and the problems of producing intergeneric hybrids and backcross derivatives. These problems can include crossability, sterility, and unequal chromosome transmission. The work then covers alien introgressions according to the related species used, as well as new results in the field of genomics of wild wheat relatives and introgressions.

This book is a comprehensive understanding of the evolution of pre-malignant disease, emphasizing common themes in the field, including stem cell biology and histologic modes of cancer progression between the distal esophagus and stomach. Its sixteen chapters discuss metaplastic tissue change in the upper GI, clonalexpansion of early neoplasia, stem cell dynamics in experimental models, pathology of early esophageal squamous cell carcinoma, therapeutic modalities for esophageal squamous cell carcinoma, pathology of Barrett's esophagus, screening, early detection and novel diagnostic tools for Barrett's esophagus, clonal evolution of Barrett's esophagus, endoscopic therapeutic modalities of early esophageal cancer, pathology of early gastric cancer, and experimental models for gastric cancer. Stem Cells, Pre-neoplasia and Early Cancer of the Upper Gastrointestinal Tract is an integrative text on both the current state of translational research on every cancer development of the upper gastrointestinal tract as well as on novel clinical diagnostic and therapeutic modalities. It highlights a rapidly growing field within cancer research and is essential reading for oncologists, biochemists and advanced graduate students alike. Springer's Advances in Experimental Medicine and Biology series presents multidisciplinary and dynamic findings in the broad fields of experimental medicine and biology. The wide variety in topics it presents offers readers multiple perspectives on a variety of disciplines including neuroscience, microbiology, immunology, biochemistry, biomedical engineering and cancer research.

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.

Our genetic markers have come to be regarded as portals to the past. Analysis of these markers is increasingly used to tell the story of human migration; to investigate and judge issues of social membership and kinship; to rewrite history and collective memory; to right past wrongs and to arbitrate legal claims and human rights controversies; and to open new thinking about health and well-being. At the same time, in many societies genetic evidence is being called upon to perform a kind of racially charged cultural work: to repair the racial past and to transform scholarly and popular opinion about the "nature" of identity in the present. Genetics and the Unsettled Past considers the alignment of genetic science with commercial genealogy, with legal and forensic developments, and with pharmaceutical innovation to examine how these trends lend renewed authority to biological understandings of race and history. This unique collection brings together scholars from a wide range of disciplines-biology, history, cultural studies, law, medicine, anthropology, ethnic studies, sociology-to explore the emerging and often contested connections among race, DNA, and history. Written for a general audience, the book's essays touch upon a variety of topics, including the rise and implications of DNA in genealogy, law, and other fields; the cultural and political uses and misuses of genetic information; the way in which DNA testing is reshaping understandings of group identity for French Canadians, Native Americans, South Africans, and many others within and across cultural and national boundaries; and the sweeping implications of genetics for society today.

This detailed volume explores the continuing techniques of studying RNA-protein complexes and interactions as research in these areas expand. After an introductory chapter, the book continues with ways to purify RNA-protein complexes assembled in cells or in isolated cellular extracts, methods for measuring various biochemical activities of RNA-interacting proteins or ribonucleoproteins, biochemical methods for measuring direct RNA-protein contact, as well as various new or innovative methods pertinent to the subject. Written for the highly successful Methods in Molecular Biology series, chapters contain brief 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 up-to-date, RNA-Protein Complexes and Interactions: Methods and Protocols provides a set of useful protocols, both basic and advanced, designed to inspire researchers working with RNA and RNA-interacting proteins.

Much research has focused on the basic cellular and molecular biological aspects of stem cells. Much of this research has been fueled by their potential for use in regenerative medicine applications, which has in turn spurred growing numbers of translational and clinical studies. However, more work is needed if the potential is to be realized for improvement of the lives and well-being of patients with numerous diseases and conditions. With a goal to accelerate advances by timely information exchange, this new book series 'Cell Biology and Translational Medicine (CBTMED)' as part of SpringerNature's longstanding and very successful Advances in Experimental Medicine and Biology book series is launched. Emerging areas of regenerative medicine and translational aspects of stem cells will be covered in each volume. Outstanding researchers are recruited to highlight developments and remaining challenges in both the basic research and clinical arenas. This current book is the first volume of a continuing series.

This volume opens by covering two main types of approaches widely used to determine essential genes: single-gene knockouts and transposon mutagenesis, in both prokaryotes and Candida albicans. Given the significant advancement in the computational predictions of microbial essential genes, the second half of the book examines four main types of approaches: comparative genomics, supervised machine learning, constraint-based methods, and corrections of transposon mutagenesis data, as well as databases and servers that are often used in studying gene essentiality. Written in the highly successful Methods in Molecular Biology series format, chapters include an introduction 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 up-to-date, Gene Essentiality: Methods and Protocols will aid researchers who wish to further our knowledge in this vital field of study.

Updated and revised, this thorough volume covers a range of methods focusing on systems, including mammalian, yeast, bacterial and archaeal. This second edition of DNA Replication: Methods and Protocols describes approaches to analyze whole genomes to single molecules, as well as both in vivo and in vitro experiments. As a volume in the highly successful Methods in Molecular Biology series, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, DNA Replication: Methods and Protocols, Second Edition provides a collections of methods intended for newcomers to this research field and for established laboratories.

Advances in Cancer Research, Volume 148, the latest release in this ongoing, well-regarded serial, provides invaluable information on the exciting and fast-moving field of cancer research.

Since its discovery in 1998, RNA interference (RNAi) has heralded the advent of novel tools for biological research and drug discovery. This exciting new technology is emerging as a powerful modality for battling some of the most notoriously challenging viral clinical targets, such as the hepatitis C virus (HCV) and the human immunodeficiency virus (HIV). However, several critical issues associated with this novel technology must be resolved before it can progress to testing in human clinical trials, and these have been the target of intensive research in recent years. In this book, expert RNAi specialists from around the world have teamed up to produce a timely and thought-provoking review of the area. The two central themes are: 1) the latest findings on RNAi-virus interactions and 2) progress in the development of RNAi-based antiviral therapeutics. A number of chapters explain general concepts concerned with the role of RNAi in natural antiviral defense mechanisms. Other chapters discuss how to improve the efficacy and safety of RNAi-based antiviral drugs, as well as describe how this technology is being developed as a new therapeutic tool for fighting specific viruses, including HIV, HCV, and respiratory viruses. The book also outlines potential new avenues for research. RNA Interference and Viruses is essential reading for researchers involved in RNAi or antiviral research and is a recommended text for all virology laboratories.

Stem cells hold great promise for cell therapy, tissue engineering, regenerative medicine and pharmaceutical and biotechnological applications. This book highlights the potency of stem cells, their property of self-renewal and their ability to differentiate into different cell lineages. It further describes the different markers to identify stem cells, sources, methods of isolation, culture including 2D, 3D and beyond and their cryopreservation. This is among the first books to discuss glycosylation and sialylation in stem cells. Chapters describe application of stem cells in regenerative medicine and therapy, and highlight their application in cancer therapy and spinal cord injury. The book talks about the important patents on stem cells. The book also highlights the plant stem cells, discussing their pluoripotent nature, role in organ regeneration after injury, specific stem cell niches, that signals to block differentiation studied in plants shoot, root, and vascular meristems, differentiation of plant stem cell, transcriptional regulation and epigenetic modification of plant stem cells. This book is exciting and cutting edge. It will be of great interest to doctors, students and researchers in the field of regenerative medicine, cancer , biotechnology and plant sciences.

By identifying the structure of DNA, the molecule of life, Francis Crick and James Watson revolutionized biochemistry and won themselves a Nobel Prize. At the time, Watson was only twenty-four, a young scientist hungry to make his mark. His uncompromisingly honest account of the heady days of their thrilling sprint against other world-class researchers to solve one of science's greatest mysteries gives a dazzlingly clear picture of a world of brilliant scientists with great gifts, very human ambitions, and bitter rivalries. With humility unspoiled by false modesty, Watson relates his and Crick's desperate efforts to beat Linus Pauling to the Holy Grail of life sciences, the identification of the basic building block of life. Never has a scientist been so truthful in capturing in words the flavor of his work.

This book presents a guide to building computational gene finders, and describes the state of the art in computational gene finding methods, with a focus on comparative approaches. Fully updated and expanded, this new edition examines next-generation sequencing (NGS) technology. The book also discusses conditional random fields, enhancing the broad coverage of topics spanning probability theory, statistics, information theory, optimization theory and numerical analysis. Features: introduces the fundamental terms and concepts in the field; discusses algorithms for single-species gene finding, and approaches to pairwise and multiple sequence alignments, then describes how the strengths in both areas can be combined to improve the accuracy of gene finding; explores the gene features most commonly captured by a computational gene model, and explains the basics of parameter training; illustrates how to implement a comparative gene finder; examines NGS techniques and how to build a genome annotation pipeline.

This new edition captures the advances made in the field of evolutionary systems biology since the publication of the first edition. The first edition focused on laying the foundations of evolutionary systems biology as an interdisciplinary field, where a way of thinking and asking questions is combined with a wide variety of tools, both experimental and theoretical/computational. Since publication of the first edition, evolutionary systems biology is now a well-known term describing this growing field. The new edition provides an overview of the current status and future developments of this interdisciplinary field. Chapters highlight several key achievements from the last decade and outline exciting new developments, including an understanding of the interplay between complexity and predictability in evolutionary systems, new viewpoints and methods to study organisms in evolving populations at the level of the genome, gene regulatory network, and metabolic network, and better analysis and modeling techniques that will open new avenues of scientific inquiry.

The technical advances in molecular biology have endowed us with a wealth of knowledge, which has allowed us to identify the cause of diseases not only at a single gene level but at a greater magnitude, where a substitution or deletion of a single base pair can be identified. Our present task is to establish a clear link between phenotype and nucleotide sequence. Obviously, a gene is no longer an imaginary entity. Recent discoveries in a number of bewildering traits, whose inheritance do not follow simple mendelian rules, have caused much amazement. For example, fragile X-syndrome, spine and bulbar muscular atrophy and myotic dystrophy arise from "triples repeat mutation" and amplification in future generations. Genetic diseases which are inherited, can now be diagnosed prenatally; an idea that was once inconceivable.
The aim of the second volume, entitled Morbid Anatomy of the Genome, is to reflect on the importance of molecular genetics in modern medicine. The field has expanded so as to warrant a volume dedicated exclusively toward understanding those who wish to know the cause, detection and in turn treatment of such diseases. In this volume, I have commissioned several scientists to contribute 12 chapters. A chapter describing a special role of molecular genetics in combating genetic diseases through gene therapy has also been included, while chapter 13 is a commentary.
A complete account of all diseases whose genetic basis is well established would be a herculean task and is not within the scope of a single volume format. Therefore a few specific topics have been chosen which may be of the greatest interest to scientists and clinicians. The purpose of this issue is to keep abreast of the latest developments in a select group of genetic diseases.

This book describes how epigenetic context, in a large sense, affects gene expression and the development of an organism, using the asymptotic limit theorems of information theory to construct statistical models useful in data analysis. The approach allows deep understanding of how embedding context affects development. We find that epigenetic information sources act as tunable catalysts, directing ontogeny into characteristic pathways, a perspective having important implications for epigenetic epidemiology. In sum, environmental stressors can induce a broad spectrum of developmental dysfunctions, and the book explores a number of pandemic chronic diseases, using U.S. data at different scales and levels of organization. In particular, we find the legacy of slavery has been grossly compounded by accelerating industrial decline and urban decay. Individual chapters are dedicated to obesity and its sequelae, coronary heart disease, cancer, mental disorders, autoimmune dysfunction, Alzheimer's disease, and other conditions. Developmental disorders are driven by environmental factors channeled by historical trajectory and are unlikely to respond to medical interventions at the population level in the face of persistent individual and community stress. Drugs powerful enough to affect deleterious epigenetic programming will likely have side effects leading to shortened lifespan. Addressing chronic conditions and developmental disorders requires significant large-scale changes in public policy and resource allocation.

In the past half century, filamentous fungi have grown in commercial importance not only in the food industry but also as sources of pharmaceutical agents for the treatment of infectious and metabolic diseases and of specialty proteins and enzymes used to process foods, fortify detergents, and perform biotransformations. The commercial impact of molds is also measured on a negative scale since some of these organisms are significant as pathogens of crop plants, agents of food spoilage, and sources of toxic and carcinogenic compounds. Recent advances in the molecular genetics of filamentous fungi are finding increased application in the pharmaceutical, agricultural, and enzyme industries, and this trend promises to continue as the genomics of fungi is explored and new techniques to speed genetic manipulation become available.

This volume focuses on the filamentous fungi and highlights the advances of the past decade, both in methodology and in the understanding of genomic organization and regulation of gene and pathway expression.

This volume covers the global history of the Lysenko controversy, while exploring in greater depth the background of D. Lysenko's career and influence in the USSR. By presenting the rise and fall of T.D. Lysenko in a variety of aspects-his influence upon art, unrecognized predecessors, and the extent to which genetics continued in the USSR even while he was in power, and the revival of his reputation today-the authors provide a fresh perspective on one of the most notorious episodes in the history of science.

This book explores the regenerative properties of fetal stem cells, from feto-maternal cell traffic through perinatal stem cells, with a discussion of key topics including stem cell banking, drug screening, in utero stem cell transplantation and ethical considerations. The expertly authored chapters also delve into embryonic, amniotic membrane, and umbilical cord blood stem cells; fetal development models; fetal cell reprogramming; culture methods; disease models; perinatal gene therapy, and more. These chapters are grouped into four sections, each discussing a separate prenatal stem cell population and providing fascinating historical contexts for our knowledge of these systems. Featuring a foreword written by the renowned Dr. Joseph Vacanti of the Harvard Stem Cell Institute, Fetal Stem Cells in Regenerative Medicine: Principles and Translational Strategies is a welcome and timely contribution to the Stem Cell Biology and Regenerative Medicine series. It is essential reading for scientists and researchers, clinicians and residents, and advanced students involved in stem cells, regenerative medicine, tissue engineering, and related disciplines such as embryology.

This text highlights the endogenous regenerative potential of the central nervous system in neonates and juveniles and discusses possible ways it might be manipulated for medical purposes. The first section provides a descriptive summary of the salient steps of human brain development with a discussion of comparisons with other mammalian brains. It also provides a historical perspective on our understanding of ongoing brain development throughout the lifespan and serve to introduce the concept of brain plasticity following injury. The second part is devoted to the endogenous reparative potential of the brain, including its limitations, and articles focusing on defined pathologies (e.g. anoxia/hypoxia, epilepsy, traumatic brain injury and stress) in animal models and in humans pinpoint eventual ways these pathologies might be manipulated. The third and final focuses on the "dark side" of stem cells for brain repair or of the manipulation of spontaneous adaptive events after injury (e.g. genomic instability, sensitization to cancerous transformation and defective neural networks).

Metagenomics is a rapidly growing field of research that has had a dramatic effect on the way we view and study the microbial world. By permitting the direct investigation of bacteria, viruses, and fungi, irrespective of their culturability and taxonomic identities, metagenomics has changed microbiological theory and methods and has also challenged the classical concept of species. This new field of biology has proven to be rich and comprehensive and is making important contributions in many areas including ecology, biodiversity, bioremediation, bioprospection of natural products, and medicine. This book addresses, in a coherent manner, the diverse and multiple aspects of metagenomics and the multiplicity of its potential applications. Renowned authors from around the world have contributed chapters covering the new theoretical insights, the more recent applications, and the dynamically developing methods of data acquisition and analysis. Topics include: conceptual frameworks * tools and methods * integration of complementary approaches * horizontal gene transfer * analysis of complex microbial communities * public data resources * plant-microbe interactions * bioremediation * industrial bioproducts * archaeal metagenomics * bioprospecting novel genes * the human microbiome * and philosophical themes in metagenomics. The book is essential reading for all researchers currently performing metagenomics studies and it is highly recommended for all students and scientists wishing to increase their understanding of this field.