This book reviews how the release of the citrus genome facilitates the investigation of ancestral species, the study of their complex biological features, and the genetic basis of agronomic traits of paramount importance for their sustainable cultivation. The first chapters discuss citrus origin and distribution, and the economic importance and varietal composition of the cultivated species, providing an overview of citrus and related genera genetic resources. The book then describes the role of traditional breeding techniques (for scion and rootstocks) as well as the potential of genomic breeding and innovative protocols for biotechnological approaches. The second part provides essential information on the genus Citrus, the attributes of pure citrus species, genetic admixtures, hybrids and citrus relatives, and on the horticultural classification of cultivated species, varieties and rootstocks. The third part then focuses on the different molecular mechanisms, covering various aspects of citrus biology, including the role of beneficial compounds of citrus fruits. In addition, it examines the molecular responses of citrus to abiotic stresses and to field and post-harvest diseases. Providing insights gained in recent years, it is a valuable guide for those who are interested in gene discovery, comparative genomics, molecular breeding and new breeding techniques. It is particularly useful for scientists, breeders and students at universities and public sector institutes involved in research for the citrus industry.

This book highlights the uses for underutilized crops, presenting the state-of-the-art in terms of genome sequencing for over 30 crops, previously understudied and under-researched. In a changing climate and with significant pressure on the land, it is the ideal time to be discussing novel crops, with significant biotic and abiotic tolerances and/or rich nutrient profiles for consumers. Previously, the only species with sequenced genomes were high-profile internationally recognized crops, but in the current era genomes are being sequenced for dozens of crops, including those previously classified as underutilized, now being investigated. This book covers food crops, from fruits to tubers, and from grasses to legumes, as well as crops with non-food applications. Some of these crops have draft genomes, and others have polished genomes with extensive resequencing panels. Each chapter tells the story of an individual crop or crop group, written by experts, focusing on the genome data available, revealing more about crop domestication and genetic variation, and the current and future prospects given that this data is now becoming available. It also highlights how even small sequencing projects can provide draft genome sequences suitable for gene discovery, comparative genomics, and identification of molecular markers for understanding these crops further.

The book highlights the therapeutic applications of various stem cells, and introduces readers to thymus stem cells and their applications in the reconstitution of thymic structure and function. It also discusses the significant role of mesenchymal stem cells (MSCs) in the treatment of autoimmune diseases and the use of MSC-derived exosomes in cell-free therapy. Moreover, it explores the application of hematopoietic stem cells in the vasculoprotection of the ischemially injured heart. Further topics include the regenerative potential of ovarian germline stem cells and the significance of endometrial stem cells in the pathogenesis of female reproductive tract diseases. Lastly, the book addresses stem cells from perinatal tissues and their immunoregulatory and differentiation potentials, and summarizes new strategies for targeting cancer stem cells to treat tumors.

This second edition provides new and updated chapters detailing recent advances in MYC research and current techniques. Chapters guide readers through protocols on how to express and purify MYC protein, X-ray crystallography, NMR, techniques to study how MYC is modified, apoptosis, senescence, proliferation, metabolic changes, translation, tumorigenesis,reprogramming, and clinical application of MYC studies.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, The Myc Gene: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

Interest in a specialized microenvironment or "niche" regulating hemopoietic stem cell function has been steadily growing since the idea was first proposed by Ray Schofield over three decades ago. This growing interest, as well as more recently the interest in cellular-molecular-biochemical characterization of not only the hemopoietic stem cell niche but the niches for other stem cells, incited the compilation of Stem Cell Niche: Methods and Protocols. In this volume, scientists have provided protocols that will provide both a flavor of the field and hopefully stimulate new approaches and methodologies by those interested in the stem cell niche. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Stem Cell Niche: Methods and Protocols seeks to serve both experts and novices in the stem cell field with well-established protocols on this exciting subject.

This volume provides detailed methods and key approaches used to mechanistically study DNA damage, as well as the factors involved in the damage response. Chapters guide readers through proteomics and biophysical approaches, analyzing protein function, quantifying DNA replication dynamics and nucleic acid base damage, as well as biochemical reconstitution of key pathways involved in DNA repair. 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, DNA Damage Responses: Methods and Protocols aims to be a useful practical guide to researches to help further their study in this field.

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. This 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, has the goal to accelerate advances by timely information exchange. Emerging areas of regenerative medicine and translational aspects of stem cells are 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 eight volume of a continuing series.

This book introduces some key problems in bioinformatics, discusses the models used to formally describe these problems, and analyzes the algorithmic approaches used to solve them. After introducing the basics of molecular biology and algorithmics, Part I explains string algorithms and alignments; Part II details the field of physical mapping and DNA sequencing; and Part III examines the application of algorithmics to the analysis of biological data. Exciting application examples include predicting the spatial structure of proteins, and computing haplotypes from genotype data. Figures, chapter summaries, detailed derivations, and examples, are provided.

This detailed edition reflects the significant new findings in the components of permeability barriers and how they work in different tissues with a collection of cutting-edge techniques. Chapters explore the formation, maintenance, regulation, and dynamics of permeability barriers in an effort to push the boundaries of the field. Written for the highly successful 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 up-to-date, Permeability Barrier: Methods and Protocols, Second Edition serves as an invaluable guide for both experts but novices in the stem cell field and other related areas of research.

The reproduction and spread of a virus during an epidemic proceeds when the virus attaches to a host cell and viral genetic material (VGM) (protein, DNA, RNA) enters the cell, then replicates, and perhaps mutates, in the cell. The movement of the VGM across the host cell outer membrane and within the host cell is a spatiotemporal dynamic process that is modeled in this book as a system of ordinary and partial differential equations (ODE/PDEs). The movement of the virus proteins through the cell membrane is modeled as a diffusion process expressed by the diffusion PDE (Fick's second law). Within the cell, the time variation of the VGM is modeled as ODEs. The evolution of the dependent variables is computed by the numerical integration of the ODE/PDEs starting from zero initial conditions (ICs). The departure of the dependent variables from zero is in response to the virus protein concentration at the outer membrane surface (the point at which the virus binds to the host cell). The numerical integration of the ODE/PDEs is performed with routines coded (programmed) in R, a quality, open-source scientific computing system that is readily available from the Internet. Formal mathematics is minimized, e.g., no theorems and proofs. Rather, the presentation is through detailed examples that the reader/researcher/analyst can execute on modest computers. The ODE/PDE dependent variables are displayed graphically with basic R plotting utilities. The R routines are available from a download link so that the example models can be executed without having to first study numerical methods and computer coding. The routines can then be applied to variations and extensions of the ODE/PDE model, such as changes in the parameters and the form of the model equations.

This wide-ranging book introduces information as a key concept not only in physics, from quantum mechanics to thermodynamics, but also in the neighboring sciences and in the humanities. The central part analyzes dynamical processes as manifestations of information flows between microscopic and macroscopic scales and between systems and their environment. Quantum mechanics is interpreted as a reconstruction of mechanics based on fundamental limitations of information processing on the smallest scales. These become particularly manifest in quantum chaos and in quantum computing. Covering subjects such as causality, prediction, undecidability, chaos, and quantum randomness, the book also provides an information-theoretical view of predictability. More than 180 illustrations visualize the concepts and arguments. The book takes inspiration from the author's graduate-level topical lecture but is also well suited for undergraduate studies and is a valuable resource for researchers and professionals.

This detailed volume focuses on the CRISPR-associated guide RNA and how it can be designed, modified, and validated for a broad repertoire of purposes. Beginning with a section on computational design of target-specific guide RNAs, the book continues by covering chemical modifications to alter guide RNA stability, specificity, and efficiency, as well as to create inducible guide RNAs, append additional functional domains, and express guide RNAs in a conditional manner. It concludes with methods for measuring off-target guide RNA activity. Written for the highly successful Methods in Molecular Biology series, chapters include 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 essential, CRISPR Guide RNA Design: Methods and Protocols provides a comprehensive pipeline for guide RNA design and aims to be an invaluable resource in applying this powerful technology to basic research and therapeutic applications.

It is now 10 years since the first edition of YAC Protocols was published in 1996. YAC Protocols was first produced to address the huge demand within the research community for a lab-based text that described in detail the wide range of uses for large insert yeast artificial chromosome (YAC) DNA clones. In doing this, the original editor, David Markie, and the many different contri- tors who provided descriptions of the protocols they used and developed, did a magnificent job. Indeed many of the techniques described within the first e- tion require little change and have stood up admirably to the test of time. Since the first edition, the use of YACs has proved invaluable for addressing a wide range of new biological problems ranging from those of basic biochemistry to assisting in the mapping and sequencing of the human genome. The requirement for a second edition of YAC Protocols was prompted by a number of major advances in biology since the publication of the first edition. These advances have included the sequencing of the human genome, and the genomes of a wide variety of other organisms, and the increased use of transgenic animals for understanding the molecular basis of human and animal disease.

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

This comprehensive volume discusses in vitro laboratory development of insulin-producing cells. It encompasses multiple aspects of islet biology-from embryonic development and stem cell differentiation to clinical studies in islet transplantation, regulation of islet beta-cell regeneration, pancreatic progenitors, mathematical modelling of islet development, epigenetic regulation, and much more. The chapter authors represent leading laboratories from around the world who contribute their international perspectives and global expertise. Collectively, they provide the reader with a concise yet detailed knowledge of processes and current developments in islet regenerative biology. Pancreatic Islet Biology, part of the Stem Cell Biology and Regenerative Medicine series, is essential reading for researchers and clinicians in stem cells or endocrinology, especially those focusing on diabetes.

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

Biostimulants for crops from seed germination to plant development focuses on the effects and roles of natural biostimulants in every aspect of plant growth development to reduce the use of harmful chemical fertilizers and pesticides. Biostimulants are a group of substances of natural origin that offer a potential to reduce the dependency on harmful chemical fertilizers causing environmental degradation. While there is extensive literature on biostimulants, there remains a gap in understanding how natural biostimulants work and their practical application. This book fills that gap, presenting the ways in which biostimulants enhance seed vigor and plant productivity by looking into their mode of action, an area still being researched for deeper understanding. Exploring the roles of seed germination, pollen tube formation, pollen-pistil interaction, flower and fruit setting, to plant pigments, rhizospheric and soil microorganisms, the book also sheds light on the challenges and realistic opportunities for the use of natural biostimulants.

This book presents applications of bioinformatics tools that experimental research scientists use in "daily practice." Its interdisciplinary approach combines computational and experimental methods to solve scientific problems. The book begins with reviews of computational methods for protein sequence-structure-function analysis, followed by methods that use experimental data obtained in the laboratory to improve functional predictions.

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

Nature has long used nucleic acid aptamers and enzymes for regulatory activities, such as the recently discovered riboswitches involved in gene expression. The existence of a large array of natural and artificial functional nucleic acids has generated tremendous enthusiasm and new opportunities for molecular scientists from diverse disciplines to devise new concepts and real applications that take advantage of those nucleic acids for sensing and other analytical applications. This book provides a timely and comprehensive overview of recent advances in the field, from leading experts in biology, chemistry, and engineering. A variety of topics are covered, from fundamentals of functional nucleic acids, to their applications as sensors, to nanotechnologies; as well as integration of functional nucleic acids into practical analytical systems.

Recent advances in genome analysis and transformation have made rice a model monocot for molecular biologists. This volume covers four areas of rice molecular biology in which exciting progress has been made recently: genome analysis and gene isolation, development, regulation of gene expression, and transformation and rice improvement. It will be of great interest to researchers who work in traditional agricultural sciences using rice, as well as to those who have an interest in using rice as an experimental model for basic research. The book gives an overall view on what has already been done, as well as what will be possible in rice. It presents chapters on development and gene regulation - exciting new research area in the future, and explores potentials in rice improvement using various molecular biological methods.

Chemical Biology of the Genome provides a comprehensive overview of essential concepts and principles of genomic and epigenomics dynamics as explored through the lens of chemical biology. Key examples and case studies illustrate chemical biology methods for study and analysis of the genome and epigenome, with an emphasis on relevance to physiological and pathophysiological processes and drug discovery. Authors and international leaders in biochemical studies of the genome, Drs. Siddhartha Roy and Tapas Kundu, adopt an integrated, interdisciplinary approach throughout, demonstrating how fast evolving chemical and mass-scale sequencing tools are increasingly used to interpret biochemical processes of the genome. Later sections discuss chemical modifications of the genome, DNA sequence recognition by proteins and gene regulation, GWAS and EpiGWAS studies, 3D architecture of the genome, and functional genome architecture. In-depth, discovery focused chapters examine intervention in gene networks using SiRNA/ShRNA, miRNA, and anti-miR, small molecule modulation of iPS, drug resistance pathways altered DNA methylation as drug targets, anti-miR as therapeutics, and nanodelivery of drugs.

This volume provides basic and advanced protocols on somatic cell nuclear transfer, induced pluripotent stem cells, and direct reprogramming of somatic cells into different functional cells. Chapters guide readers through methods on standardized procedures for characterization of induced pluripotent stem cells, as well as those for preparation of materials required for induction of pluripotent stem cells. 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, Nuclear Reprogramming: Methods and Protocols aims to ensure successful results in the further study of this vital field.

This detailed book serves as a systematic examination of the analytical methods to study the transcription factor NF- B in physiology and disease. It provides an up-to-date guidebook to navigate both conventional and highly specialized methods to detect and analyze the different signaling pathways of NF- B activation and contextualize them within organismal physiology and disease pathogenesis, using genetic and biochemical techniques and some of the most advanced computational and systems biology methods. Additionally, the volume includes several examples of approaches utilized by leading experts in the NF- B field to analyze and modulate NF- B signaling in specific physiological and disease contexts, along with some of the most promising approaches to pharmacologically target the NF- B pathway in human disease. Written for the highly successful 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, NF- B Transcription Factors: Methods and Protocols is an up-to-date guide intended for both basic and translational scientists who are working in the dynamic NF- B field.