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 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.

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 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).

Bryan Sykes brings together a world-class set of contributors to debate just what the links between genes, language, and the archaeological record can tell us about human evolution. The eight lively essays offer widely differing opinions, pose more questions than they offer answers, eschew jargon, and pursue controversy. Guaranteed to fascinate anyone who has ever wondered how the fossil record, the incredible diversity of human language, and our genetic inheritance might combine to give a glimpse of human origins.

This volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls. Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA.

This well-established international series examines major areas of basic and clinical research within neuroscience, as well as emerging and promising subfields. This volume concentrates on Epigenetics

This book looks atEpigeneticsinthe light of the newest scholarly discoveries and insights."

"Stem Cell Biology and Tissue Engineering in Dental Sciences" bridges the gap left by many tissue engineering and stem cell biology titles to highlight the importance of research in this field in the dental sciences.It compiles basic embryology and developmental biology with keen focus on stem cells, basic cell and matrix biology with relevance to tissue regeneration and repair, biomaterials (including nanotechnology) and current applications in various disciplines of dental science.Tissue engineering is an interdisciplinary field of biomedical research which combines life, engineering, and materials sciences to further the maintenance, repair, and replacement of diseased and damaged tissues. This emerging area of research applies an understanding of normal tissue physiology to develop novel biomaterial, acellular, and cell-based therapies for clinical application. These strategies are being developed and evaluated as potential treatments of dental conditions, particularly periodontology, endodontics, dental implantology, and oral-maxillofacial surgery.
Covers all aspects related to stem cell biology and tissue engineering in dental sciences: basic science, research, clinical application and commercializationDescribes stem cell biology with details focused on dental stem cells and their potential research application throughout medicine Describes new technologies and fabrication techniques in the fields of stem cells and biomaterial and tissue engineering research, including the latest advances in nanotechnology"

This volume presents a list of cutting-edge protocols for the study of CRISPR-Cas defense systems and their applications at the genomic, genetic, biochemical and structural levels. CRISPR: Methods and Protocols guides readers through techniques that have been developed specifically for the analysis of CRISPR-Cas and techniques adapted from standard protocols of DNA, RNA and protein biology. 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, CRISPR: Methods and Protocols provides a broad list of tools and techniques to study the interdisciplinary aspects of the prokaryotic CRISPR-Cas defense systems.

The field of genetics is rapidly evolving, and new medical breakthroughs are occurring as a result of advances in our knowledge of genetics. "Advances in Genetics" continually publishes important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines.

Volume 85 presents an eclectic mix of articles of use to all human and molecular geneticists on topics including: association mapping in crop plants; miRNA-mediated crosstalk between transcripts; unisexual reproduction; and more.
Includes methods for testing with ethical, legal, and social implicationsCritically analyzes future directionsWritten and edited by recognized leaders in the field

A TIMES ENVIRONMENT AND SCIENCE BOOK OF THE YEAR 2022 'The ideal guide to what is not just a fiendishly complex area of science but also an ethical minefield' Mail on Sunday A new gene editing technology, invented just seven years ago, has turned humanity into gods. Enabling us to manipulate the genes in virtually any organism with exquisite precision, CRISPR has given scientists a degree of control that was undreamt of even in science fiction. But CRISPR is just the latest, giant leap in a long journey to master genetics. The Genetic Age shows the astonishing, world-changing potential of the new genetics and the possible threats it poses, sifting between fantasy and the reality when it comes to both benefits and dangers. By placing each phase of discovery, anticipation and fear in the context of over fifty years of attempts to master the natural world, Matthew Cobb, the Baillie-Gifford-shortlisted author of The Idea of the Brain, weaves the stories of science, history and culture to shed new light on our future. With the powers now at our disposal, it is a future that is almost impossible to imagine - but it is one we will create ourselves.

This volume presents the current state of laser-assisted bioprinting, a cutting edge tissue engineering technology. Nineteen chapters discuss the most recent developments in using this technology for engineering different types of tissue. Beginning with an overview, the discussion covers bioprinting in cell viability and pattern viability, tissue microfabrication to study cell proliferation, microenvironment for controlling stem cell fate, cell differentiation, zigzag cellular tubes, cartilage tissue engineering, osteogenesis, vessel substitutes, skin tissue and much more. Because bioprinting is on its way to becoming a dominant technology in tissue-engineering, Bioprinting in Regenerative Medicine is essential reading for those researching or working in regenerative medicine, tissue engineering or translational research. Those studying or working with stem cells who are interested in the development of the field will also find the information invaluable.

Providing expert coverage of all major events in early embryogenesis and the organogenesis of specific systems, and supplemented with representative clinical syndromes, "Principles of Developmental Genetics, Second Edition" discusses the processes of normal development in embryonic and prenatal animals, including humans. The new edition of this classic work supports clinical researchers developing future therapies with its all-new coverage of systems biology, stem cell biology, new technologies, and clinical disorders. A crystal-clear layout, exceptional full-color design, and bulleted summaries of major takeaways and clinical pathways assist comprehension and readability of the highly complex content.
All-new coverage of systems biology and stem cell biology in context of evolving technologies places the work squarely on the modern sciencesChapters are complemented with a bulleted summary for easy digestion of the major points, with a clinical summary for therapeutic applicationClinical highlights provides a bridge between basic developmental biology and clinical sciences in embryonic and prenatal syndromes

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.

With the discovery of stem cells capable of multiplying indefinitely in culture and differentiating into many other cell types in appropriate conditions, new hopes were born in repair and replacement of damaged cells and tissues. The features of stem cells may provide treatment for some incurable diseases with some therapies are already in clinics, particularly those from adult stem cells. Some treatments will require large number of cells and may also require multiple doses, generating a growing demand for generating and processing large numbers of cells to meet the need of clinical applications. With this in mind, our aim is to provide a book on the subject of stem cells and cell therapy for researchers and students of cell biotechnology, bioengineering and bioproduction. This book is exceptional as it teaches researchers stem cells and cell therapy in that it covers the concepts and backgrounds necessary so that readers get a good understanding of the production of stem cells. The book covers three topics: The basics of stem cells and cell therapy, the use of stem cells for the treatment of human diseases, and stem cell processing. It includes chapters on neural and vascular stem vascular stem cell therapy, expansion engineering of embryonic stem cells, stem cell based production of blood cells and separation technologies for stem cells and cell therapy products. It is an informed and informative presentation of what modern research, science and engineering have learned about stem cells and their production and therapies. Addressing both the medical and production issues, this book is an invaluable contribution to having an academic and industrial understanding with respect to R&D and manufacturing of clinical grade stem cells.

This volume contains protocols specifically designed for studying programmed cell death, and also discusses recent advances in techniques that span broader areas of biology that have been recently used or that have potential to be incorporated into cell death research. The protocols are mostly described in the context of mammalian systems, but also cover other systems such as plants, Drosophila, and yeast. Programmed Cell Death: Methods and Protocols is comprised of 20 chapters: Chapters 1-5 describe apoptosis detection techniques; Chapter 6-9 describe methods for studying apoptosis associated with various pathologies in different organs including the lymphoid compartment, intestinal epithelium, granulocytes, and cardiomyocytes; Chapter 11-13 cover protocols and techniques for studying apoptosis in non-mammalian systems; Chapters 14-16 cover biochemical and biophysical methods for studying Bcl-2 family protein dynamics and protein-protein interactions during apoptosis; and the last four chapters explore protocols that are useful not only in apoptosis research but in wider areas of biological research, such as genome editing, inducible transgenes, and proteomics. Written in the highly successful Methods in Molecular Biology aeries format, chapters include introductions to their respective topics, lists of the necessary material and reagents, step-by-step, readily reproducible laboratory protocol, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Programmed Cell Death: Methods and Protocols is a comprehensive and valuable resource for researchers, ranging from beginner to expert, in their studies on programmed cell death.

A biologist and a Christian theologian examine the scientific and philosophical implications and potential impacts of genetic technologies. God, Science, and Designer Genes: An Exploration of Emerging Technologies provides a unique approach to the central ethical dilemma in contemporary science, offering both an up-to-date account of the current state of genetic technologies and insightful discussions of the moral/theological questions these technologies raise. Coauthored by professors of biology and theology, God, Science, and Designer Genes examines a range of from-the-headlines issues, including the relationship between science and religion, "designing" our children, stem-cell research, cloning, genetics and behavior, genetics and privacy, and using genetic technologies for social justice. Who should benefit-personally and financially-from DNA technology? Who might be harmed? How do we protect individual rights and guard against discrimination? How will embryo modification affect the identity of those so modified? God, Science, and Designer Genes gives readers an eloquent, thoughtful, and objective foundation for considering these and other questions about the potential conflict between scientific achievement, personal faith, and social responsibility. A series of chapters combining basic scientific discussions of DNA technologies with ethical discussions of the social issues they are raising Five hypothetical case studies that provide realistic contexts for exploring specific issues related to genetic technologies An extensive bibliography of current and significant books, journals and websites with regard to genetic technologies A comprehensive index

This authoritative text/reference presents a review of the history, current status, and potential future directions of computational biology in molecular evolution. Gathering together the unique insights of an international selection of prestigious researchers, this must-read volume examines the latest developments in the field, the challenges that remain, and the new avenues emerging from the growing influx of sequence data. These viewpoints build upon the pioneering work of David Sankoff, one of the founding fathers of computational biology, and mark the 50th anniversary of his first scientific article. The broad spectrum of rich contributions in this essential collection will appeal to all computer scientists, mathematicians and biologists involved in comparative genomics, phylogenetics and related areas.

Plant genomics and biotechnology have recently made enormous strides, and hold the potential to benefit agriculture, the environment and various other dimensions of the human endeavor. It is no exaggeration to claim that the twenty-first century belongs to biotechnology. Knowledge generation in this field is growing at a frenetic pace, and keeping abreast of the latest advances and calls on us to double our efforts. Volume II of this two-part series addresses cutting-edge aspects of plant genomics and biotechnology. It includes 37 chapters contributed by over 70 researchers, each of which is an expert in his/her own field of research. Biotechnology has helped to solve many conundrums of plant life that had long remained a mystery to mankind. This volume opens with an exhaustive chapter on the role played by thale cress, Arabidopsis thaliana, which is believed to be the Drosophila of the plant kingdom and an invaluable model plant for understanding basic concepts in plant biology. This is followed by chapters on bioremediation, biofuels and biofertilizers through microalgal manipulation, making it a commercializable prospect; discerning finer details of biotic stress with plant-fungal interactions; and the dynamics of abiotic and biotic stresses, which also figure elsewhere in the book. Breeding crop plants for desirable traits has long been an endeavor of biotechnologists. The significance of molecular markers, marker assisted selection and techniques are covered in a dedicated chapter, as are comprehensive reviews on plant molecular biology, DNA fingerprinting techniques, genomic structure and functional genomics. A chapter dedicated to organellar genomes provides extensive information on this important aspect. Elsewhere in the book, the newly emerging area of epigenetics is presented as seen through the lens of biotechnology, showcasing the pivotal role of DNA methylation in effecting permanent and transient changes to the genome. Exclusive chapters deal with bioinformatics and systems biology. Handy tools for practical applications such as somatic embryogenesis and micropropagation are included to provide frontline information to entrepreneurs, as is a chapter on somaclonal variation.Overcoming barriers to sexual incompatibility has also long been a focus of biotechnology, and is addressed in chapters on wide hybridization and hybrid embryo rescue. Another area of accomplishing triploids through endosperm culture is included as a non-conventional breeding strategy. Secondary metabolite production through tissue cultures, which is of importance to industrial scientists, is also covered. Worldwide exchange of plant genetic material is currently an essential topic, as is conserving natural resources in situ. Chapters on in vitro conservation of extant, threatened and other valuable germplasms, gene banking and related issues are included, along with an extensive account of the biotechnology of spices - the low-volume, high-value crops. Metabolic engineering is another emerging field that provides commercial opportunities. As is well known, there is widespread concern over genetically modified crops among the public. GM crops are covered, as are genetic engineering strategies for combating biotic and abiotic stresses where no other solutions are in sight. RNAi- and micro RNA- based strategies for crop improvement have proved to offer novel alternatives to the existing non-conventional techniques, and detailed information on these aspects is also included. The book's last five chapters are devoted to presenting the various aspects of environmental, marine, desert and rural biotechnology. The state-of-the-art coverage on a wide range of plant genomics and biotechnology topics will be of great interest to post-graduate students and researchers, including the employees of seed and biotechnology companies, and to instructors in the fields of plant genetics, breeding and biotechnology.

" Principles of Cloning, Second Edition" is the fully revised edition of the authoritative book on the science of cloning. The book presents the basic biological mechanisms of how cloning works and progresses to discuss current and potential applications in basic biology, agriculture, biotechnology, and medicine. Beginning with the history and theory behind cloning, the book goes on to examine methods of micromanipulation, nuclear transfer, genetic modification, and pregnancy and neonatal care of cloned animals. The cloning of various species-including mice, sheep, cattle, and non-mammals-is considered as well. The Editors have been involved in a number of breakthroughs using cloning technique, including the first demonstration that cloning works in differentiated cells done by the Recipient of the 2012 Nobel Prize for Physiology or Medicine - Dr John Gurdon; the cloning of the first mammal from a somatic cell - Drs Keith Campbell and Ian Wilmut; the demonstration that cloning can reset the biological clock - Drs Michael West and Robert Lanza; the demonstration that a terminally differentiated cell can give rise to a whole new individual - Dr Rudolf Jaenisch and the cloning of the first transgenic bovine from a differentiated cell - Dr Jose Cibelli. The majority of the contributing authors are the principal investigators on each of the animal species cloned to date and are expertly qualified to present the state-of-the-art information in their respective areas.
First and most comprehensive book on animal cloning, 100% revisedDescribes an in-depth analysis of current limitations of the technology and research areas to exploreOffers cloning applications on basic biology, agriculture, biotechnology, and medicine "

This invaluable resource discusses the saftey, ethics, and regulations of developing stem cell clinical applications. Each chapter is contributed by a preeminent scientist in the field and covers such topics as clinical safety of stem cell gene therapy, the patentability of hESC technologies, international guidelines, challenges to international stem cell clinical trials, worldwide regulations including in emerging markets like China and Taiwan. Saftey, Ethics, and Regulations and the other books in the Stem Cells in Clinical Applications series will be invaluable to scientists, researchers, advanced students and clinicians working in stem cells, regenerative medicine or tissue engineering.

Advances in Botanical Research publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences. Currently in its 69th volume, the series features several reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology. This thematic volume features reviews on genomes of herbaceous land plants
Publishes in-depth and up-to-date reviews on a wide range of topics in plant sciencesFeatures a wide range of reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecologyVolume features reviews on genomes of herbaceous land plants