The new edition of Gene Control has been updated to include significant advances in the roles of the epigenome and regulatory RNAs in gene regulation. The chapter structure remains the same: the first part consists of pairs of chapters that explain the mechanisms involved and how they regulate gene expression, and the second part deals with specific biological processes (including diseases) and how they are controlled by genes. Coverage of methodology has been strengthened by the inclusion more explanation and diagrams. The significant revision and updating will allow Gene Control to continue to be of value to students, scientists and clinicians interested in the topic of gene control.

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.

The 'Adaptive Landscape' has been a central concept in population genetics and evolutionary biology since this powerful metaphor was first formulated by Sewall Wright in 1932. Eighty years later, it has become a central framework in evolutionary quantitative genetics, selection studies in natural populations, and in studies of ecological speciation and adaptive radiations. Recently, the simple concept of adaptive landscapes in two dimensions (genes or traits) has been criticized and several new and more sophisticated versions of the original adaptive landscape evolutionary model have been developed in response. No published volume has yet critically discussed the past, present state, and future prospect of the adaptive landscape in evolutionary biology. This volume brings together prominent historians of science, philosophers, ecologists, and evolutionary biologists, with the aim of discussing the state of the art of the Adaptive Landscape from several different perspectives.

The book presents comprehensive information on fundamental, and applied knowledge for developing varieties resistant individually as well as to all the major pathogens of crucifers, such as Albugo, Alternaria, Erysiphe, Hyaloperonospora, Plasmodiophora, Leptosphaeria, Sclerotinia, Turnip mosaic virus, Verticillium, and Xanthomonas through the use of latest biotechnological approaches including identification of R genes and their incorporation into agronomically superior varieties. The chapters include the information's viz., principles of host resistance, identification of R-genes sources, inheritance of disease resistance, host resistance signaling network system to multiple stresses. The book also covers transfer of disease resistance, and management of disease resistance. Standardized, reproducible techniques are also included for the researchers of cruciferous crops for developing resistant cultivars. The book deals with the gaps in understanding, knowledge of genomics, and offers suggestions for future research priorities in order to initiate the advance research on disease resistance. This book is immensely useful to the researchers especially Brassica breeders, teachers, extension specialists, students, industrialists, farmers, and all others who are interested to grow healthy, and profitable cruciferous crops all over the world.

This volume details protocols emphasizing systems-level approaches that can be applied to genomic analyses. Chapters detail techniques for optimized application in in vivo systems, spatial, physiological, environmental contexts, imaging-based techniques, single-molecule approaches, CRISPR systems, new genomic approaches, and measurements of kinetics governing. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, DNA-Protein Interactions: Methods and Protocols aims to present genome-wide techniques that will complement the biochemistry-based protocols to aid researchers in their studies.

Codon-based models of evolution are a relatively new addition to the toolkit of computational biologists, and in recent years remarkable progress has been made in this area. The study of evolution at the codon level captures information contained in both amino acid and synonymous DNA substitutions. By combining these two types of information, codon analyses are more powerful than those of either amino acid or DNA evolution alone. This is a clear benefit for most evolutionary analyses, including phylogenetic reconstruction, detection of selection, ancestral sequence reconstruction, and alignment of coding DNA. Despite the theoretical advantages of codon based models, their relative complexity delayed their widespread use. Only in recent years, when large-scale sequencing projects produced sufficient genomic data and computational power increased, did their usage become more common. In Codon Evolution, leading researchers in the field of molecular evolution provide the latest insights from codon-based analyses of genetic sequences. The first part of the book provides comprehensive coverage of the developments of various types of codon substitution models such as parametric and empirical models used in maximum likelihood as well as Bayesian frameworks. Subsequent chapters examine the use of codon models to infer selection and other applications of codon models to biological systems. The second part of the book focuses on codon usage bias. Both the underlying mechanisms as well as current methods to analyse codon usage bias are presented.

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.

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.

Now in its second edition, Forensic DNA Evidence Interpretation is the most comprehensive resource for DNA casework available today. Written by leaders in the fields of biology and statistics, including a contribution from Peter Gill, the father of DNA analysis, the book emphasizes the interpretation of test results and provides the necessary formulae in an easily accessible manner. This latest edition is fully updated and includes current and emerging techniques in this fast-moving field. The book begins by reviewing all pertinent biology, and then provides information on every aspect of DNA analysis. This includes modern interpretation methods and contemporary population genetic models available for estimating DNA frequencies or likelihood ratios. Following a chapter on procedures for validating databases, the text presents overviews and performance assessments of both modern sampling uncertainty methods and current paternity testing techniques, including new guidelines on paternity testing in alignment with the International Society for Forensic Genetics. Later chapters discuss the latest methods for mixture analysis, LCN (ultra trace) analysis and non-autosomal (mito, X, and Y) DNA analysis. The text concludes with an overview of procedures for disaster victim identification and information on DNA intelligence databases. Highlights of the second edition include: New information about PCR processes, heterozygote balance and back and forward stuttering New information on the interpretation of low template DNA, drop models and continuous models Additional coverage of lineage marker subpopulation effects, mixtures and combinations with autosomal markers This authoritative book provides a link among the biological, forensic, and interpretative domains of the DNA profiling field. It continues to serve as an invaluable resource that allows forensic scientists, technicians, molecular biologists and attorneys to use forensic DNA evidence to its greatest potential.

The genomics revolution has expanded from its origins in molecular biology to impact upon every discipline in the life sciences, including ecology. Several lines of ecological research can now be profitably addressed using genomics technology, including issues of nutrient cycling, population structure, life-history variation, trophic interaction, stress responses, and adaptation to environmental change. This new edition addresses a series of fundamental ecological questions: the relationship between community structure and ecological function in ecosystems; how variation in life-history patterns among species can be explained from interaction between the genome and the environment; the molecular responses to changing and toxic environmental conditions; adaptive phenotypes and their relationship to genetic variation. Each of these questions is evaluated in the light of recent advances in genomics research, paying particular attention to data obtained from sequencing and screening of environmental genomes (metagenomics), microarray-based transcription profiling, gene expression directed by signal-transduction pathways, and the analysis of genomic polymorphisms. The chapters covering these key areas are preceded by discussions of genomics methodology (including an overview of next-generation sequencing technologies) and comparative genomics, and the book concludes with a chapter on integrative approaches such as ecological control analysis. The authors also provide a comparative survey of the properties of genomes (genome size, gene families, synteny, and polymorphism) for prokaryotes as well as the main eukaryotic models. An Introduction to Ecological Genomics incorporates a balance of plant, animal, and microbial examples, and continues to define the new and exciting field of ecological genomics.

This detailed book brings together a new set of protocols to arm cell biologists with techniques that are currently being used in a number of well-established laboratories around the world. The contents represent the great strides made in the field of cell-cell communications with respect to the identification and characterization of key components of the communication apparatus, assembly and maintenance of the communications structures, and concomitantly their roles in not only tissue formation and maintenance but also regeneration and repair. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective chapters, 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, Stem Cell Renewal and Cell-Cell Communication: Methods and Protocols, Second Edition serves as an ideal guide for experts and newcomers alike seeking to increase our understanding of the crucial biological and physiological roles of cell-cell communications in tissue function and organismal integrity.

Pillars of Evolution provides a fresh and provocative perspective on adaptive evolution. Readers new to the study of evolution will find a refreshing new insight that establishes evolutionary biology as a rigorous and predictive science, whilst practicing biologists will discover a provocative book that challenges traditional approaches.
The book begins by leading readers through the mechanics of heredity, reproduction, movement, survival, and development. With that framework in place, it then explores the numerous ways that traits emerge from the interactions between genetics, development, and the environment. The key message is that adaptive changes in traits (and their underlying allelic frequencies) evolve through the traits' functions and their connection with fitness. The complex mappings from genes-to-traits-to-fitness are characterized in the structure of evolution. A single "structure matrix" describes why individuals vary in the values of adaptive traits, their ability to perform the function of those traits, and in the fitness they accrue. Fitness depends on how organisms interact with and perceive their environment in time and space. These relationships are made explicit in spatial, temporal, and organizational scale that also sets the stage for the crucially important role that ecology always plays in evolution. The ecological hallmarks of density- and frequency-dependent interactions allow the authors to explore new and exciting insights into evolution's dynamics. The theories and principles are then brought together in a final synthesis on adaptation.
The book's unique approach unites genetic, development, and environmental influences into a single comprehensive treatment of the eco-evolutionary process.

The present book is an attempt to describe the most recent developments in the area of pericyte biology which is one of the emergent hot topics in the field of molecular and cellular biology today. Here, we present a selected collection of thirteen detailed chapters on what we know so far about pericytes in distinct organs in physiological and pathological conditions. Further, it provides an update on the most novel functions attributed to these cells and will introduce a newer generation of researchers and scientists to the importance of these cells, ranging from their discovery in different organs through current state-of-the-science. It will be invaluable for both advanced cell biology students as well as researchers in cell biology, stem cells and vascular research. This volume explores pericytes' physiologic roles in different tissues, ranging from the pancreas, lungs and liver through skeletal muscle, gut, retina and more. Together with its companion volumes Pericyte Biology in Disease and Pericyte Biology - Novel Concepts, Pericyte Biology in Different Organs presents a comprehensive update on the latest information and most novel functions attributed to pericytes. To those researchers newer to this area, it will be useful to have the background information on these cells' unique history. It will be invaluable for both advanced cell biology students as well as researchers in cell biology, stem cells and researchers or clinicians involved with specific organs.

For more than two decades the concept of phenotypic plasticity has allowed researchers to go beyond the nature-nurture dichotomy to gain deeper insights into how organisms are shaped by the interaction of genetic and ecological factors. "Phenotypic Plasticity: Beyond Nature and Nurture" is the first work to synthesize the burgeoning area of plasticity studies, providing a conceptual overview as well as a technical treatment of its major components.

Phenotypic plasticity integrates the insights of ecological genetics, developmental biology, and evolutionary theory. Plasticity research asks foundational questions about how living organisms are capable of variation in their genetic makeup and in their responses to environmental factors. For instance, how do novel adaptive phenotypes originate? How do organisms detect and respond to stressful environments? What is the balance between genetic or natural constraints (such as gravity) and natural selection? The author begins by defining phenotypic plasticity and detailing its history, including important experiments and methods of statistical and graphical analysis. He then provides extended examples of the molecular basis of plasticity, the plasticity of development, the ecology of plastic responses, and the role of costs and constraints in the evolution of plasticity. A brief epilogue looks at how plasticity studies shed light on the nature/nurture debate in the popular media.

"Phenotypic Plasticity: Beyond Nature and Nurture" thoroughly reviews more than two decades of research, and thus will be of interest to both students and professionals in evolutionary biology, ecology, and genetics.

Life history theory seeks to explain the evolution of the major features of life cycles by analyzing the ecological factors that shape age-specific schedules of growth, reproduction, and survival and by investigating the trade-offs that constrain the evolution of these traits. Although life history theory has made enormous progress in explaining the diversity of life history strategies among species, it traditionally ignores the underlying proximate mechanisms.
Mechanisms of Life History Evolution argues that many fundamental problems in life history evolution, including the nature of trade-offs, can only be fully resolved if we begin to integrate information on developmental, physiological, and genetic mechanisms into the classical life history framework. Each chapter is written by an established or up-and-coming leader in their respective field; they not only represent the state of the art but also offer fresh perspectives for future research. The text is divided into 7 sections that cover basic concepts (Part 1), the mechanisms that affect different parts of the life cycle (growth, development, and maturation; reproduction; and aging and somatic maintenance) (Parts 2-4), life history plasticity (Part 5), life history integration and trade-offs (Part 6), and concludes with a synthesis chapter written by a prominent leader in the field and an editorial postscript (Part 7).

Statistical genomics is a rapidly developing field, with more and more people involved in this area. However, a lack of synthetic reference books and textbooks in statistical genomics has become a major hurdle on the development of the field. Although many books have been published recently in bioinformatics, most of them emphasize DNA sequence analysis under a deterministic approach.

"Principles of Statistical Genomics" synthesizes the state-of-the-art statistical methodologies (stochastic approaches) applied to genome study. It facilitates understanding of the statistical models and methods behind the major bioinformatics software packages, which will help researchers choose the optimal algorithm to analyze their data and better interpret the results of their analyses. Understanding existing statistical models and algorithms assists researchers to develop improved statistical methods to extract maximum information from their data.

Resourceful and easy to use, "Principles of Statistical Genomics" isa comprehensive reference for researchers and graduate students studying statistical genomics. "

This book focuses on the discoveries in M. truncatula genomic research which has been undertaken in the last two decades. Legumes are important for their economic values as food, feed, and fodder and also serve as the pillar of sustainable agriculture because of its biological nitrogen fixation capacity. Medicago truncatula was established as a model legume in the 1990s and has been well adopted as a model internationally since then. M. truncatula is an autogamous, diploid (2n = 16) species with a short generation time, and relatively small genome size (~375 Mbp). The M. truncatula genome was initially sequenced by the International Medicago Genome Annotation Group (IMGAG) in 2011 and has been well-annotated. M. truncatula research benefits from the availability of several genetic and genomic tools, such as gene expression atlas (MtGEA), insertion and neutron bombardment mutant populations, and a HapMap panel containing 384 sequenced inbred lines for genome-wide association studies. This book covers the current status and latest advancements of the M. truncatula genomics and transcriptomics resources along with a glimpse of newly developed tools that makes M. truncatula a front runner model in functional genomic studies.

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 volume provides protocols and methods on techniques to study plant gametogenesis. Chapters are divided into four sections covering omics, cytological, molecular approaches, plant transformation, genome editing, bioinformatics, and data analysis. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Plant Gametogenesis: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.

Beginning with the Escherichia coli ? protein, or bacterial DNA topoisomerase I, an ever-increasing number of enzymes have been identified that catalyze changes in the linkage of DNA strands. DNA topoisomerases are ubiquitous in nature and have been shown to play critical roles in most p- cesses involving DNA, including DNA replication, transcription, and rec- bination. These enzymes further constitute the cellular targets of a number of clinically important antibacterial and anticancer agents. Thus, further studies of DNA topology and DNA topoisomerases are critical to advance our und- standing of the basic biological processes required for cell cycle progression, cell division, genomic stability, and development. In addition, these studies will continue to provide critical insights into the cytotoxic action of drugs that target DNA topoisomerases. Such mechanistic studies have already played an important role in the development and clinical application of antimicrobial and chemotherapeutic agents. The two volumes of DNA Topoisomerase Protocols are designed to help new and established researchers investigate all aspects of DNA topology and the function of these enzymes. The chapters are written by prominent investigators in the field and provide detailed background information and st- by-step experimental protocols. The topics covered in Part I: DNA Topology and Enzymes, range from detailed methods to analyze various aspects of DNA structure, from linking number, knotting/unknotting, site-specific recombi- tion, and decatenation to the overexpression and purification of bacterial and eukaryotic DNA topoisomerases from a variety of cell systems and tissues.

This book presents a comprehensive discussion on the novel concepts in stem cell heterogeneity, from pluripotent stem cells to human mesenchymal stem cells, adult and cancer stem cells of the thyroid, sarcoma, and more. Thus, Stem Cell Heterogeneity - Novel Concepts starts from a timely update on the current information on stem cells heterogeneity in various tissues and discusses new concepts and future directions. It also provides a solid foundation of the history of stem cells from specific tissues and the current applications of this knowledge in regenerative medicine. When taken as a whole, alongside its companion volumes Stem Cells Heterogeneity in Different Organs, and Stem Cells Heterogeneity in Cancer, these three books present a comprehensive reference on stem cell heterogeneity in various tissues and current and future applications for regenerative medicine. It is essential reading for advanced cell biology students as well as researchers in stem cells and clinicians.

The present volume focuses on microbial invasion strategies of pathogen uptake. An accompanying volume (Vol. 5) in the series presents the phagocytic process from the viewpiont of the host cell.
This field of study is growing rapidly after a somewhat slow start over recent decades. This collection of invited chapters attempts to reflect current research and brings together cell biologists, microbiologists, and immunologists wiht disthemes, hopefully like a symphony rather than a boring catalogue. It will be evident that editorial bias favors intracellular parasitism and medically important organisms. The neutrophil is far more than a supporting player to the macrophage and some attempt is made to remind the reader of some of its unique skills. To retain a manageable size, the emphasis is on relatively early events such as mutual recognition, cell entry, and response, rather than on longterm changes in gene expression by either host cell or pahtogen. Viruses are excluded not because of lack of importance but because of somewhat different research approaches, although it is becoming increasingly clear that large viruses (e.g. "Vaccinia") and "Listeria monocytogenes," share common strategies in invasion and intercellular spread.

This book presents an authoritative review of the most significant findings about all the epigenetic targets (writers, readers, and erasers) and their implication in physiology and pathology. The book also covers the design, synthesis and biological validation of epigenetic chemical modulators, which can be useful as novel chemotherapeutic agents. Particular attention is given to the chemical mechanisms of action of these molecules and to the drug discovery prose which allows their identification. This book will appeal to students who want to know the extensive progresses made by epigenetics (targets and modulators) in the last years from the beginning, and to specialized scientists who need an instrument to quickly search and check historical and/or updated notices about epigenetics.

This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book's respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.

This book provides an overview of methods and experimental protocols that are currently used to analyze the presence and abundance of non-canonical DNA nucleotides in different biological systems. Focusing particularly on the newly discovered and less studied DNA modifications that are enzymatically produced and are likely to play specific roles in various biological processes, the volume explores chromatography- and mass spectrometry-based techniques for the detection and quantification of DNA modifications, antibody-based approaches to study their spatial distribution in different cells and tissues, and methods to analyze their genomic distribution with the help of bioinformatics tools that interrogate the corresponding datasets. 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 comprehensive, DNA Modifications: Methods and Protocols serves as an ideal guide to research scientists and PhD students in this rapidly developing discipline, and, thus, will ultimately contribute to deciphering the roles of non-canonical DNA nucleotides in different biological systems.