This volume presents protocols for Brachypodium genomics in numerous areas ranging from marker development, trait evolution, functional genomics, metabolomics, transcriptomics, genomics, and tilling. This book also explores techniques to study the widening genetic base of Brachypodium that will help researchers better understand the model plant using NGS technologies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Brachypodium Genomics: Methods and Protocols is a valuable resource for bench-oriented molecular biologists and computational biologists working towards further evolving this field.

This volume is the result of an explosion of molecular-based research on Cilia, which began with the discovery of the universality of intraflagellar transport (IFT) and ciliary genomics/proteomics. The chapters in this book cover topics such as: high resolution imaging and functional characterization of sensory and primary cilia in mammalian cells and zebrafish, methods to study ciliary-mediated chemoresponse in Paramecium, and methods to study centrosomes and cilia in C. elegans and Drosophila. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and cutting-edge, Cilia: Methods and Protocols is broad and covers motile, sensory, and primary cells. It is a valuable resource to anyone interested in entering the field of ciliary biology using model organisms, including flagellate algae, ciliates, planaria, nematodes, insects, zebrafish, and mammalian cells.

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

This two-volume set takes an in-depth look at stress signaling in plants from a uniquely genomic and proteomic perspective and offers a comprehensive treatise that covers all of the signaling pathways and mechanisms that have been researched so far. Currently, plant diseases, extreme weather caused by climate change, drought and an increase in metals in soil are amongst the major limiting factors of crop production worldwide. They devastate not only the food supply but also the economy of a nation. With global food scarcity in mind, there is an urgent need to develop crop plants with increased stress tolerance so as to meet the global food demands and to preserve the quality of our planet. In order to do this, it is necessary to understand how plants react and adapt to stress from the genomic and proteomic perspective. Plants adapt to stress conditions by activating cascades of molecular mechanisms, which result in alterations in gene expression and synthesis of protective proteins. From the perception of the stimulus to the transduction of the signal, followed by an appropriate cellular response, the plants employ a complex network of primary and secondary messenger molecules. Cells exercise a large number of noticeably distinct signaling pathways to regulate their activity. In order to contend with different environmental adversities, plants have developed a series of mechanisms at the physiological, cellular and molecular levels that respond to stress. Each chapter in this volume provides an in-depth explanation of what we currently know of a particular aspect of stress signaling and where we are heading. Together with the highly successful first volume, Stress Signaling in Plants: Genomics and Proteomics Perspective, Volume 2 covers an important aspect of plant biology for both students and seasoned researchers.

Pattern Formation in the Vertebrate CNS: Hox Gene Function and the Development of the Head; M. Mark, et al. Genetic Mechanisms Responsible for Pattern Formation in the Vertebrate Hindbrain: Regulation of Hoxb1; M. Studer, et al. Pax Genes as Pleiotropic Regulators of Embryonic Development; P. Tremblay, et al. Introduction and the Generation of Regional and Cellular Diversity in the Developing Mammalian Brain; A.S. LaMantia. Genetic Determinants of Neural Cell Fate: Potential Role of Homeobox Genes in Neural Cell Differentiation; M. Gulisano, et al. Multiple Roles for Proneural Genes in Drosophila Neurogenesis; A.P. Jarman, Y.N. Jan. Genetic Analysis of Neuronal Migration in The Nematode Caenorhabditis elegans; G. Garriga. Induction and Differentiation of Motor Neurons; S.L. Pfaff, et al. Neural Cell Differentiation: Neuronal Development in the Rat Sympathoadrenal Lineage; S.J. Birren, et al. Specification of Cell Fate in the Vertebrate Retina; C.P. Austin. Neurotrophins and Trk Receptors in Hippocampal Development; D. Collazo, R. McKay. 8 additional articles. Index.

This book concerns the mathematical modeling and computer simulation of the human stomach. It follows the four modern P's (prevention, prediction, personalization, and precision in medicine) approach in addressing the highly heterogeneous nature of processes underlying gastric motility disorders manifested as gastroparesis, functional dyspepsia, myenteric enteropathy etc. The book comprehensively guides readers through the fundamental theoretical concepts to complex physiological models of the organ. This requires a deep and thorough understanding of driving pathophysiological mechanisms as well as the collaborative effort of specialists working in fundamental and biological science. Such a multidisciplinary partnership is vital because it upholds gnostic capabilities and provides the exchange of thoughts and ideas thus offering broad perspectives into the evolution and management of diseases. The book is a valuable resource for applied mathematicians, computational biologists, bioengineers, physicians, physiologists and researchers working in various fields of biomedicine.

Small molecule microarrays (SMM) were introduced in 1999 and within just a short span of time, have established themselves as a vibrant next generation platform for high-throughput screening. Small Molecule Microarrays: Methods and Protocols consolidates a significant collection of examples, which serve to guide researchers toward ways in which SMM technology may be effectively deployed for multiplexed screening, drug discovery and ligand identification. The volume is organized into three sections covering microarray fabrication, imaging modes, and discovery approaches. The chapters cover a range of small molecule library types, ranging from synthetic combinatorial libraries to peptide and carbohydrate libraries, with lessons and techniques that can be widely applied. Written in the highly successful Methods in Molecular Biology series, format, chapters include introductions of their respective topics, lists of the requisite materials and reagents, step-by-step and readily reproducible laboratory protocols as well as vital tips on troubleshooting and advice on avoiding known pitfalls. Authoritative and cutting-edge, Small Molecule Microarrays: Methods and Protocols provides meticulous insights into the successful applications of SMM, by experts in the field. Building on this collection of knowledge, the volume seeks to inspire a future generation of microarray practitioners to propel this significant technology to even greater heights

This second edition volume expands on the previous edition with an update on the latest developments in the field and new techniques used to study secondary and supersecondary structures (SSS) in proteins. Chapters in this book discuss topics such as sequence and structural features of different SSS elements; software used for the automatic annotation of secondary structure elements in proteins; the new developments in secondary and SSS prediction and the modern approaches for energy landscape calculation; protein misfolding and amyloid structural formation; analysis of 'transformer proteins'; discovery of the structure of the hydrophobic nucleus; and discussions of the main principles of protein structures formation. The contributing authors of the volume are the eminent experts in the field of protein research and bioinformatics. 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 authoritative, Protein Supersecondary Structures: Methods and Protocols, Second Edition is a valuable resource for researchers who are interested in learning more about the relationship between amino acids sequences and protein structures, the evolution of proteins and the dynamics of protein formation.

The rapid expansion of the area of free radical biology in the last 25 years has occurred within a framework of assumptions and preconceived notions that has at times directed the course of this movement. The most dominant of these notions has been the view that free radical production is without exception a bad thing, and that the more efficient our elimination of these toxic substances, the better off we will be. The very important observation by Bernard Babior and colleagues in 1973 that activated phagocytes produce superoxide in order to kill micro organisms, served to illustrate that constructive roles are possible for free radicals. For many in the field, however, this merely underscored the deadly nature of oxygen-derived radicals, both from the microbe's point of view and from the host's as well. (Phagocyte-produced superoxide is responsible in part for the tissue injury manifested as inflammation. See Harris and Granger, Chapter 5, and Leff, Hybertson and Repine, Chapter 6.)
Mother Nature, however, has a penchant for being able to make a silk purse from a sow's ear. If one is dealt a bad hand, one must simply make the best of it. After two decades of focusing on the destructive side of free radicals, the last few years have begun to reveal a new and finer perspective on free radical metabolism - a role in regulation of cellular function (see Schulze-Osthoff and Baeuerle, Chapter 2). Evidence from a number of sources suggests that an increase in the oxidative status of cell encourages that cell to grow and divide. Increasing the expression of mangnese superoxide dismutase can suppress the malignant phenotype of melanon cells (see Oberley and Oberley, Chapter 3). Oxidative stress beyond a certain poitosis (from the Greek, literally "to fall apart"). Is this suicide response an evolutionary fail-safe device to curtail tumorogenesis? Does oxidative stress-induced apoptosis account for the loss of immune cells in AIDS (see Flores and McCor Chapter 4)?
This volume attempts to present the spectrum of roles, both good and bad played by active oxygen species as understood at this point in the evolution of this field of free radical biology.

This volume covers past and present western blot techniques, such as diffusion blotting, slice blotting, blotting of high and low molecular weight proteins, single cell blotting and automated blotting. 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. Thorough and cutting-edge, Western Blotting: Methods and Protocols will serve as an invaluable reference for those interested in further study into this fascinating field.

This richly illustrated book provides an overview of the design and analysis of experiments with a focus on non-clinical experiments in the life sciences, including animal research. It covers the most common aspects of experimental design such as handling multiple treatment factors and improving precision. In addition, it addresses experiments with large numbers of treatment factors and response surface methods for optimizing experimental conditions or biotechnological yields. The book emphasizes the estimation of effect sizes and the principled use of statistical arguments in the broader scientific context. It gradually transitions from classical analysis of variance to modern linear mixed models, and provides detailed information on power analysis and sample size determination, including 'portable power' formulas for making quick approximate calculations. In turn, detailed discussions of several real-life examples illustrate the complexities and aberrations that can arise in practice. Chiefly intended for students, teachers and researchers in the fields of experimental biology and biomedicine, the book is largely self-contained and starts with the necessary background on basic statistical concepts. The underlying ideas and necessary mathematics are gradually introduced in increasingly complex variants of a single example. Hasse diagrams serve as a powerful method for visualizing and comparing experimental designs and deriving appropriate models for their analysis. Manual calculations are provided for early examples, allowing the reader to follow the analyses in detail. More complex calculations rely on the statistical software R, but are easily transferable to other software. Though there are few prerequisites for effectively using the book, previous exposure to basic statistical ideas and the software R would be advisable.

Examining the physical basis of the structure of macromolecules proteins, nucleic acids, and their complexes using calorimetric techniques Many scientists working in biology are unfamiliar with the basics of thermodynamics and its role in determining molecular structures. Yet measuring the heat of structural change a molecule undergoes under various conditions yields information on the energies involved and, thus, on the physical bases of the considered structures. Microcalorimetry of Macromolecules offers protein scientists unique access to this important information. Divided into thirteen chapters, the book introduces readers to the basics of thermodynamics as it applies to calorimetry, the evolution of the calorimetric technique, as well as how calorimetric techniques are used in the thermodynamic studies of macromolecules, detailing instruments for measuring the heat effects of various processes. Also provided is general information on the structure of biological macromolecules, proteins, and nucleic acids, focusing on the key thermodynamic problems relating to their structure. The book covers: * The use of supersensitive calorimetric instruments, including micro and nano-calorimeters for measuring the heat of isothermal reactions (Isothermal Titration Nano-Calorimeter), the heat capacities over a broad temperature range (Scanning Nano-Calorimeter), and pressure effects (Pressure Perturbation Nano-Calorimeter) * Two of the simplest but key structural elements: the and polyproline helices and their complexes, the -helical coiled-coil, and the pyroline coiled-coils * Complicated macromolecular formations, including small globular proteins, multidomain proteins and their complexes, and nucleic acids * Numerous examples of measuring the ground state of protein energetics, as well as changes seen when proteins interact The book also reveals how intertwined structure and thermodynamics are in terms of a macromolecule's organization, mechanism of formation, the stabilization of its three-dimensional structure, and ultimately, its function. The first book to describe microcalorimetric technique in detail, enough for graduate students and research scientists to successfully plumb the structural mysteries of proteins and the double helix, Microcalorimetry of Macromolecules is an essential introduction to using a microcalorimeter in biological studies.

This volume offers detailed step-by-step instructions to allow beginners and experts alike to run appropriate copy number variants (CNV) detection software on a dataset of choice and discern between false positive noise and true positive CNV signals. Chapters guide readers through single nucleotide polymorphism (SNP) chips, optical mapping assembly techniques, and current open-source programs specializing in CNV detection. 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, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Copy Number Variants: Methods and Protocols aims to provide guidance to Bioinformaticians and Molecular Biologists who are interested in identifying copy number variants (CNV) with a wide variety of experimental media

This fourth volume in the series covers such topics as endogenous fuels, electric organs, histidine-related dipeptides, and origins of luciferins. The book will be invaluable to fisheries scientists, aquaculturists, and animal biochemists, physiologists and endocrinologists; it will provide researchers and students with a pertinent information source from theoretical and experimental angles.

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 fundamental physical principles, together with their mathematical formulations, for modelling the propagation of signals in nerve fibres. Above all, it focuses on the complex electro-mechano-thermal process that produces an ensemble of waves composed of several components, besides the action potential. These components include mechanical waves in the biomembrane and axoplasm, together with the temperature change. Pursuing a step-by-step approach, the content moves from physics and mathematics, to describing the physiological effects, and finally to modelling the coupling effects. The assumptions and hypotheses used for modelling, as well as selected helpful concepts from continuum mechanics, are systematically explained, and the modelling is illustrated using the outcomes of numerical simulation. The book is chiefly intended for researchers and graduate students, providing them with a detailed description of how to model the complex physiological processes in nerve fibres.

This book addresses a number of questions from the perspective of complex systems: How can we quantitatively understand the life phenomena? How can we model life systems as complex bio-molecular networks? Are there any methods to clarify the relationships among the structures, dynamics and functions of bio-molecular networks? How can we statistically analyse large-scale bio-molecular networks? Focusing on the modeling and analysis of bio-molecular networks, the book presents various sophisticated mathematical and statistical approaches. The life system can be described using various levels of bio-molecular networks, including gene regulatory networks, and protein-protein interaction networks. It first provides an overview of approaches to reconstruct various bio-molecular networks, and then discusses the modeling and dynamical analysis of simple genetic circuits, coupled genetic circuits, middle-sized and large-scale biological networks, clarifying the relationships between the structures, dynamics and functions of the networks covered. In the context of large-scale bio-molecular networks, it introduces a number of statistical methods for exploring important bioinformatics applications, including the identification of significant bio-molecules for network medicine and genetic engineering. Lastly, the book describes various state-of-art statistical methods for analysing omics data generated by high-throughput sequencing. This book is a valuable resource for readers interested in applying systems biology, dynamical systems or complex networks to explore the truth of nature.

Since its inception, patch-clamp has continued to be widely considered the gold standard method to record ion channel activity. "Patch-Clamp Methods and Protocols, Second Edition," provides a comprehensive collection of new techniques for the development of automated, high-throughput screening systems for pharmacological evaluation, the use of various patch-clamp configurations together with novel molecular biological and imaging methodologies and enhanced stimulation protocols and perfusion systems. Divided into sections on pharmacology, physiology and biophysics, the chapters cover methods to generate more physiologically relevant conditions for drug application and screening technologies, recently developed applications such as optogenetic stimulation, advances in whole-cell recordings in freely-moving animals and novel technologies to create custom microelectrodes designed for reducing the access resistance and improving the rate of molecular diffusion. Patch-clamp is an indispensable technique for conducting pharmacological, physiological and biophysical research aimed at understanding crucial aspects of cellular and network function. 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, "Patch-Clamp Methods and Protocols, Second Edition" will provide a useful technical and methodological guide to diverse audiences of electrophysiologists, from students to experienced investigators.

The formation of placenta can be viewed as a controlled process of inflammation or cancer development in which cell proliferation, invasion, and immune surveillance or evasion are promoted in a time- and space-specific manner. This suggests that the functions of prostasin are mainly active in pathophysiological conditions, more so than those in basic or normal physiological conditions. The uniqueness of the prostasin serine protease is its membrane anchorage via a glycosylphosphatidylinositol moiety. This anchorage exposes the entire prostasin molecule to the outside while still being immobilized on the cell membrane and gives prostasin a better chance to be used as a biomarker or drug target. As presented in placenta development, the equilibrium between growth and differentiation dictates healthy and disease states.This book provides readers with an integrated knowledge on serine protease prostasin, starting with its discovery, protein isolation, cDNA, and gene cloning, to its functions in physiology and pathophysiology, and to its application in the development of therapeutics. This is the first-of-its-kind book that covers the history, present state of knowledge, and future perspectives of the prototypic glycosylphosphatidylinositol-anchored epithelial extracellular serine protease prostasin, which is a key player in the regulation and maintenance of the extracellular fluid homeostasis. The chapters encapsulate all that has been learned about prostasin in the technical sophistication, but more importantly, also highlight a critical analysis on the problems with the current state of research and outline the challenges for the future.

This volume presents the most recent technologies used in the Polycomb Group Proteins (PcG) field. Chapters detail state-of-the-art methods, creating a unique and comprehensive reference source for investigating Polycomb function in the nucleus. 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, Polycomb Group Proteins: Method and Protocols aims to ensure successful results in the further study of this vital field.

This volume guides readers through the field of systems medicine by defining the terminology, and describing how established computational methods form bioinformatics and systems biology can be taken forward to an integrative systems medicine approach. Chapters provide an outlook on the role that systems medicine may or should play in various medical fields, and describe different facets of the systems medicine approach in action. Ultimately it introduces tools, resources and methodologies from bioinformatics and systems biology, and how to apply these in a systems medicine project. Written for the Methods in Molecular Biology series, chapters include introductions to their respective topics, and discuss experimental and computational approaches, methods, and tools that should be considered for a successful systems medicine project. Systems Medicine aims to motivate and provide guidance for collaborations across disciplines to tackle today's challenges related to human health and well-being.

This second edition provides up-to-date chapters and new chapters focusing on the most recent advances in the field of drug safety evaluation. Divided into seven parts, chapters detail specific aspects related to the experimental design of preclinical studies conducted to support the safety of pediatric and combination drugs, necropsy and histopathology evaluation, mass spectrometry imaging, genetic toxicology protocols including the Pig-a mutation assay, safety pharmacology methods such as automatization of patch-clamp procedures, target safety assessment for investigative toxicology, screening assays for developmental toxicology, and methods to characterize novel translational safety biomarkers like microRNAs. 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 to avoid known pitfalls. Authoritative and practical, Drug Safety Evaluation: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

Fungi cause a spectrum of diseases in humans ranging from comparatively innocuous superficial skin diseases caused by dermatophytes to invasive life-threatening infections caused by species such as Candida albicans, or Crytococcus neoformans. Due to the opportunistic nature of most invasive mycoses, fungal pathogenicity has proven difficult to define. However the application of new genomic and other molecular techniques in recent years has revolutionized the field revealing fascinating new insights into the mechanisms of fungal pathogenesis. In this book, a panel of high profile authors critically reviews the most important research to provide a timely overview.

This volume provides state-of-the-art techniques for studying various aspects of cholesterol homeostasis, including its uptake, synthesis and efflux from the cell, as well as its trafficking within the cell. Chapters also cover techniques for studying the regulation of cholesterol homeostasis at both the transcriptional and post-translational levels, as well as studying the membrane topology and structure of cholesterol-related proteins. 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 practical, Cholesterol Homeostasis: Methods and Protocols aims to provide key techniques in tackling the investigation of cholesterol homeostasis.

This thesis reports the latest developments in the direct amination of various C H bonds using an H Zn exchange/electrophilic amination strategy. McDonald and co-workers reveal this approach to be a rapid and powerful method for accessing a variety of functionalized amines. The material outlined in this book shows how McDonald achieved C H zincation using strong, non-nucleophilic zinc bases and subsequent electrophilic amination of the corresponding zinc carbanions with copper as a catalyst and O-benzoylhydroxylamines as the electrophilic nitrogen source. McDonald's findings are of relevance to medicinal chemistry, drug discovery and materials science. Her thesis is a source of inspiration for scientists entering the field and students beginning their PhD in a related area.