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.

This book describes the development of genetic resources in amaranths, with a major focus on genomics, reverse, and forward genetics tools and strategies that have been developed for crop improvement. Amaranth is an ancient crop native to the New World. Interest in amaranths is being renewed, due to their adaptability, stress tolerance, and nutritional value. There are about 65 species in the genus, including Amaranthus caudatus L., A. cruentus L., and A. hypochondriacus L., which are primarily grown as protein-rich grains or pseudocereals. The genus also includes major noxious weeds (e.g., A. palmeri). The amaranths are within the Caryophyllales order and thus many species (e.g., A. tricolor) produce red (betacyanin) or yellow (betaxanthin) betalain pigments, which are chemically distinct from the anthocyanins responsible for red pigmentation in other plants. A. hypochondriacus, which shows disomic inheritance (2n = 32; n= 466 Mb), has been sequenced and annotated with 23,059 protein-coding genes. Additional members of the genus are now also been sequenced including weedy amaranths, other grain amaranths, and their putative progenitors.

This detailed volume explores rice molecular biology, genetic engineering, and genome editing technologies. Dividing into three parts, the book covers subjects such as genetic engineering and tissue culture of rice, including efficient methods for rice transformation and regeneration, genome editing, targeted integration, and gene stacking in rice, including multiple methods utilizing CRISPR systems for targeted gene knock-out or genome modification via base editing, and diverse methods describing bioinformatic, molecular, and cellular analyses in rice. 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, Rice Genome Engineering and Gene Editing: Methods and Protocols serves as a valuable resource for researchers worldwide striving to further their efforts on advancing research and producing genetically improved rice varieties.

The aim of molecular diagnostics is preferentially to detect a developing disease before any symptoms appear. There has been a significant increase, fueled by technologies from the human genome project, in the availability of nucleic acid sequence information for all living organisms including bacteria and viruses. When combined with a different type of instrumentation applied, the resulting diagnostics is specific and sensitive. Nucleic acid-based medical diagnosis detects specific DNAs or RNAs from the infecting organism or virus and a specific gene or the expression of a gene associated with a disease. Nucleic acid approaches also stimulate a basic science by opening lines of inquiry that will lead to greater understanding of the molecules at the center of life. One can follow Richard Feynman's famous statement "What I cannot create, I do not understand."

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.

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 thirteenth volume of a continuing series.

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.

This book explores recent advances in the microbial production of xylitol and its applications in food and medical sector. Xylitol is an important biomolecule from lignocellulose biorefinery which is produced from the xylose by chemical reactions or microbial fermentation methods. Currently, the demand of xylitol at commercial scale is being met through chemical methods. However, recent breakthroughs made in plant cell wall destruction, genetic engineering to develop the designer microorganisms, fermentation methods and media formulations and downstream processing have led the ways for sustainable production of xylitol at commercial scale in lignocellulose biorefineries. Microbial production of xylitol is preferred over the chemical processes as it is environmentally friendly, higher process efficiency with the desired product yield, and product recovery with minimum impurities. This book is a unique compilation of 11 book chapters written by experts in their respective fields. These chapters present critical insights and discuss the current progress and future progress in this area into fermentative xylitol production. Chapter 9 is licensed under the terms of the Creative Commons Attribution 4.0 International License. For further details see license information in the chapter.

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. "

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.

This book highlights the technicalities of plant breeding in a seed-business environment and explains the crucial aspects of the value chain. It educates the readers on how to initiate, participate, sustain national and international agreements for material transfer, how consortia work to facilitate germplasm accessibility, and how to set visionary goals to develop a superior plant varieties. The book covers the aspects such as how to conduct disease screening trials at hot spots, preparing an operational budget, and how to accelerate product advancement. Plant breeding is broadly defined as manipulation of plant genotypes to create phenotypes that are beneficial to mankind. It helps to achieve food security and sustainability by developing high yielding, climate-resilient, nutritious varieties of crops and hence is able to address unprecedented challenges like rising global population, diminishing genetic biodiversity, and uncertainties of the weather . This book is an extraordinary source of information starting from goal-genesis to market-oriented product-profiling and help readers to accelerate/enhance? their work/professional performance more effectively. This book will be very useful to practicing plant breeders at various levels in the public and private sectors. It is a must-have book for potential plant breeders who enter plant breeding profession just after the completion of their formal plant breeding education.

Microarray technology is a major experimental tool for functional genomic explorations, and will continue to be a major tool throughout this decade and beyond. The recent explosion of this technology threatens to overwhelm the scientific community with massive quantities of data. Because microarray data analysis is an emerging field, very few analytical models currently exist. Methods of Microarray Data Analysis II is the second book in this pioneering series dedicated to this exciting new field. In a single reference, readers can learn about the most up-to-date methods, ranging from data normalization, feature selection, and discriminative analysis to machine learning techniques.

Currently, there are no standard procedures for the design and analysis of microarray experiments. Methods of Microarray Data Analysis II focuses on a single data set, using a different method of analysis in each chapter. Real examples expose the strengths and weaknesses of each method for a given situation, aimed at helping readers choose appropriate protocols and utilize them for their own data set. In addition, web links are provided to the programs and tools discussed in several chapters. This book is an excellent reference not only for academic and industrial researchers, but also for core bioinformatics/genomics courses in undergraduate and graduate programs.

Evolutionary Psychology: The Basics is a jargon-free and accessible introduction to evolutionary psychology, which examines behaviour, thoughts, and emotions in relation to evolutionary theory. Reader and Workman outline how evolutionary thinking can enhance the core areas of psychology: social, developmental, biological, cognitive, and individual differences/abnormal psychology. Covering topics such as genetics and natural selection, mate choice, culture, morality, mental health, and childhood, among others, the book integrates psychology into the biological sciences and explains the different approaches in the field by evaluating current and past evolutionary research and theory. Key studies and theories are explored in an accessible way, with the work of key evolutionary and behavioural scientists from Darwin to Dawkins examined and explained. Including a glossary and further reading, this is the essential introduction to evolutionary psychology for students of psychology and related areas, and academics and researchers, as well as anyone interested in learning more about this fascinating 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.

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, which is the first volume of Biomedical Translational Research, summarizes emerging technologies in healthcare. The book reviews the advancements in biomedical sciences in genomics, immunology, stem cell, tissue engineering, nanotechnology, computational and structural biology, biomedical engineering, and telemedicine biology. The book highlights the applications of artificial intelligence in the diagnosis of infectious diseases and examines the role of system biology approaches for understanding human complexity, variability, and its influence on health and diseases. It presents the applications of flow cytometry in monitoring the progression and treatment of disease. It covers emerging technologies in cancer research, including CRISPR-Cas9, NGS, and nanotechnology. This book is a useful source of information for clinical researchers, basic scientists, biomedical engineers, and computational biologists.

The co-evaluation of plants and microbes has led to an elaborate system of genes involved in recognitions, attack and defence. This volume explores the genes and the regulation of their expression. Topics covered range from considerations of population genetics to the identification of defence-related genes and their regulation. The book provides a concise review of the latest developments in this rapidly developing field of agronomic importance.

Depite the rapid expansion of the field of biophysics, there are very few books that comprehensively treat specific topics in this area. Recently, the field of single molecule biophysics has developed very quickly, and a few books specifically treating single molecule methods are beginning to appear. However, the promise of single molecule biophysics is to contribute to the understanding of specific fields of biology using new methods. This book would focus on the specific topic of the biophysics of DNA-protein interactions, and would include the use of new approaches, including both bulk methods as well as single molecule methods. This would make the book attractive to anyone working in the general area of DNA-protein interactions, which is of course a much wider market than just single molecule biophysicists or even biophysicists. The subject of the book will be the biophysics of DNA-protein interactions, and will include new methods and results that describe the physical mechanism by which proteins interact with DNA. For example, there has been much recent work on the mechanism by which proteins search for specific binding sites on DNA. A few chapters will be devoted to experiments and theory that shed light on this important problem. We will also cover proteins that alter DNA properties to facilitate interactions important for transcription or replication. Another section of the book will cover the biophysical mechanism by which motor proteins interact with DNA. Finally, we will cover larger protein-DNA complexes, such as replication forks, recombination complexes, DNA repair interactions, and their chromatin context.

GW bodies are novel cytoplasmic foci that were discovered and named by Dr. Chan's group in 2002. These bodies are now known to be active cytoplasmic foci involved with the new gene regulation process mediated by microRNA that leads to translational repression and mRNA degradation. The detailed biological functions of these cytoplasmic structures are still being uncovered and the idea for this book is to provide the history of the discovery and the major work from different laboratories that has led to the characterization and elucidation of the structure and function of these new multiple subcellular structures.

This second volume provides new and updated methods detailing advancements in CRISPR-Cas technical protocols. Chapters guide readers through protocols on prime editing, base editing, multiplex editing, editing in cell-free extract, in silico analysis of gRNA secondary structure and CRISPR-diagnosis. Authoritative and cutting-edge, CRISPR-Cas Methods, Volume 2 aims to serves as a laboratory manual providing scientists with a holistic view of CRISPR-Cas methodologies and its practical application for the editing of crop plants, cell lines, nematode and microorganism. The chapter "CRISPR/Cas9-mediated gene editing in human induced pluripotent stem cells" is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This volume explores a collection of different protocols for the analysis and characterization of DNAzymes and their functions. The topics covered in this book range from bioinformatics and molecular dynamics simulations for the study or modification of nucleic acids to the descriptions of spectroscopic, fluorescence-based, or crystallographic methods to understand the structure and function of DNAzymes. 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, DNAzymes: Methods and Protocols is a valuable resource for scientists and researchers interested in learning more about this evolving field.

This fourth edition provides all new methods on yeast that have not been included in the past three editions. Divided in four parts, chapters guide readers through general applications for genetic manipulation in yeast cells, genome-wide studies, systematically rearrange the yeast chromosomes, and pathway methods. 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, Yeast Protocol, Fourth Edition aims to compliment previous editions while offering new tools for the yeast research community.

This volume provides readers with wide-ranging coverage of CRISPR systems and their applications in various plant species. The chapters in this book discuss topics such as plant DNA repair and genome editing; analysis of CRISPR-induced mutations; multiplexed CRISPR/Cas9 systems; CRISPR-Cas12a (Cpf1) editing systems; and non-agrobacterium based CRISPR delivery systems. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and thorough, Plant Genome Editing with CRISPR Systems: Methods and Protocols is a valuable resource for any researcher interested in learning about and using CRISPR systems in plants.

This volume explains the recent findings on the mutualistic plant-microbe interactions and how they can be utilized for sustainable agriculture practices including land reclamation. The book covers mainly plant growth promoting microorganisms (PGPMs) including both the symbiotic bacteria and fungi and their role in mobilization of nutrients, providing protection to the crops from phytopathogens and abiotic stresses. PGPMs play important roles in survival and health of the plant. These useful microorganisms provide plants with nutrients, protect them from pathogens and help them combat abiotic stresses. It is important that these mutualistic interactions between plant and soil microbes are well understood so as to develop reliable products in the form of biostimulants and biopesticides, as well as managing biotic and abiotic stresses in crops. Apart from enhancing crop productivity plant-microbe interactions can also perform activities such as reclamation of degraded lands, degradation of pollutants and remediation of saline or marginal lands. This book is of interest to teachers, researchers, plant scientists and microbiologists. Also, the book serves as additional reading material for undergraduate and graduate students of agriculture, microbiology, biotechnology, ecology, soil science and environmental sciences.