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 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.

Epigenetic Technological Applications is a compilation of state-of-the-art technologies involved in epigenetic research. Epigenetics is an exciting new field of biology research, and many technologies are invented and developed specifically for epigenetics study. With chapters covering the latest developments in crystallography, computational modeling, the uses of histones, and more, Epigenetic Technological Applications addresses the question of how these new ideas, procedures, and innovations can be applied to current epigenetics research, and how they can keep pushing discovery forward and beyond the epigenetic realm.

Basics in Human Evolution offers a broad view of evolutionary biology and medicine. The book is written for a non-expert audience, providing accessible and convenient content that will appeal to numerous readers across the interdisciplinary field. From evolutionary theory, to cultural evolution, this book fills gaps in the readers' knowledge from various backgrounds and introduces them to thought leaders in human evolution research.

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.

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.

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.

Mitochondria, the "power plants" of eukaryotic cells, are best known for the generation of adenosine triphosphate (ATP), the universal cellular "energy currency" of the cell, and the synthesis of different essential components. Mitochondrial dysfunction is known to lead to various degenerative disorders, disease, and aging. The Mitochondrion in Aging and Disease works to unravel the processes leading to mitochondrial impairments and of pathways involved in mitochondrial quality control and their impact on health and aging will be addressed.

This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in riboswitch discovery and validation, synthesis and sample prep methods for large RNAs, riboswitch structure and function methods, folding pathways and dynamics, and ligand interactions and thermodynamics.

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.

"Natural Hosts of SIV: Implications in AIDS" thoroughly reviews the possible mechanisms by which African nonhuman primate natural hosts of lentiviruses remain essentially disease-free while other hosts exhibit disease and death. The book ultimately indicates directions for further research and potential translations of this compelling phenomenon into novel approaches to treat and prevent HIV. When Asian non-human primate non-natural hosts are experimentally infected with viruses isolated from African species, disease and death normally results. Meanwhile, these African nonhuman primate natural hosts maintain similar levels of plasma and cellular viremia and exhibit compellingly different, essentially disease-free, states. This work attempts to answer the question of how the natural host remains disease resistant.
Summarizes the past 30 years of research in this field and describes the latest developments in AIDS research using nonhuman primate animal modelsProvides insights into how this large body of scientific work can be translated into novel approaches to treat and prevent HIVHighlights the areas that merit future pursuit, focusing on potential applications for the treatment and prevention of HIV infection

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.

"Progress in Molecular Biology and Translational Science" provides a forum for discussion of new discoveries, approaches, and ideas in molecular biology. It contains contributions from leaders in their fields and abundant references.

Volume 126 features in-depth reviews that focus on the tools required to investigate mechanotransduction. Additional chapters focus on how we can use these tools to answer fundamental questions about the interaction of physical forces with cell biology, morphogenesis, and function of mature structures. Chapters in the volume are authored by a unique combination of cell biologists and engineers, providing a range of perspectives on mechanotransduction.
Provides a unique combination of perspectives from biologists and engineersEngaging to people of many training backgrounds

Learn how nutrition has driven--and continues to drive--human evolution

This pioneering text draws from molecular nutrition, nutritional sciences, dietetics, genetics, genomics, and anthropology to examine how chemical nutrients and genetics shape the human species. It presents a vital portrait of the fundamental role that nutrition has played and continues to play in shaping who and what human beings are, where we evolved from, and where we might be headed as a species.

The author's innovative molecular biological approach moves the field of nutrition well beyond its traditional dietetic and anthropological origins to the front lines of genomic research. Following a presentation of molecular biology concepts that are essential for the study of human nutrition, the author explores such key topics as:

Bioinformatics and the -omics revolution

Recent human evolution

Molecular mechanisms of gene-nutrient interactions

Role of nutrients and genomics in disease

Evolution of micronutrient metabolism, protein structure, and human disease

Nutrients and the human life cycle

Mismatch of contemporary dietary patterns and our genetic makeup

Laboratory tools for nutrigenomics and human evolutionary studies

Figures and illustrations provided throughout the text help readers grasp and visualize complex concepts and processes with ease. For readers interested in pursuing particular topics in greater depth, an extensive list of current references is provided.

This text is ideal for undergraduate and graduate students in human nutrition, dietetics, metabolism, molecular biology, and many other allied health sciences. Nowhere else can readers find such an integratedblend of medical, nutritional, and biochemical disciplines to aid in understanding the role of nutrients in human evolution.

This detailed book provides state-of-art computational approaches to further explore the exciting opportunities presented by single-cell technologies. Chapters each detail a computational toolbox aimed to overcome a specific challenge in single-cell analysis, such as data normalization, rare cell-type identification, and spatial transcriptomics analysis, all with a focus on hands-on implementation of computational methods for analyzing experimental data. 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, Computational Methods for Single-Cell Data Analysis aims to cover a wide range of tasks and serves as a vital handbook for single-cell data analysis.

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 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.

Epigenetic Shaping of Sociosexual Interactions: From Plants to Humans is the first attempt to interpret the higher social functions of organisms. This volume covers an extraordinarily wide range of biological research and provides a novel framework for understanding human-specific brain functions.

"International Review of Celland Molecular Biology" presents comprehensive reviews and current advances in cell and molecular biology. Articles address structure and control of gene expression, nucleocytoplasmic interactions, control of cell development and differentiation, and cell transformation and growth.

The series has a world-wide readership, maintaining a high standard by publishing invited articles on important and timely topics authored by prominent cell and molecular biologists. Impact factor for 2012: 4.973.
Authored by some of the foremost scientists in the field Provides comprehensive reviews and current advancesWide range of perspectives on specific subjectsValuable reference material for advanced undergraduates, graduate students and professional scientists
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Cell Colonies: Fractal Growth and Morphological Change in Bacterial Colony Formation; M. Matsushita, et al. Surfaces and Interfaces: Dynamic Scaling in Surface Growth Phenomena; F. Family. Diffusion Limited Aggregation, Viscous Fingering and Fracture: Ionic Concentration and Electric Field in Fractal Electrodeposition; M. Rosso, et al. Cellular Patterns: 2D Manifolds Arising from Local Interactions; H. Terrones, et al. Dynamical Systems: Order, Pattern Selection, and Noise in Low-Dimensional Systems; M. San Miguel. Self-Replication: Molecular Quasi-Species in Hopfield Replication Landscapes; P. Tarazona. Self-Organization: Effects of Noise on Self-Organized Critical Phenomena; A. Diaz-Guilera. Measurement and Characterization: The Practical Measurement of Fractal Parameters; E.H. Dooijes, Z.R. Struzik. 36 additional articles. Index.

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.