This volume introduces databases containing the results from the recent revolution in sequencing technologies. Chapters in Plant Genomics Databases: Methods and Protocols describe database content, as well as typical use-cases. Some chapters explore databases that primarily present genome sequences focusing on one or a few related species, while others include additional datatypes and/or data from various plant species. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Plant Genomics Databases: Methods and Protocols is a valuable resource for providing clear guidance in accessing an important collection of plant databases that can be used to add biological value to genomic data.

Ever since the birth of molecular biology, the tantalizing possibility of treating disease at its genetic roots has become increasingly feasible. Gene therapy - though still in its infancy - remains one of the hottest areas of research in medicine. Its approach utilizes a gene transfer vehicle ('vector') to deliver therapeutic DNA or RNA to cells of the body in order to rectify the defect that is causing the disease. Successful therapies have been reported in humans in recent years such as cures in boys with severe immune deficiencies. Moreover, gene therapy strategies are being adapted in numerous biomedical laboratories to obtain novel treatments for a variety of diseases and to study basic biological aspects of disease. Correction of disease in animal studies, is steadily gaining ground, highlighting the immense potential of gene therapy in the medical profession.This book will cover topics that are at the forefront of biomedical research such as RNA interference, viral and non-viral gene transfer systems, treatment of hematological diseases and disorders of the central nervous system. Leading experts on the respective vector or disease will contribute the individual chapters and explain cutting-edge technologies. It also gives a broad overview of the most important gene transfer vectors and most extensively studied target diseases. This comprehensive guide is therefore a must-read for anyone in the biotechnology, biomedical or medical industries seeking to further their knowledge in the area of human gene therapy.

Volume 6 of Biomembranes covers transmembrane receptors and channels. A particularly important role for the membrane is that of passing messages between a cell and its environment. Part I of this volume covers receptors for hormones and growth factors. Here, as in so many other areas of cell biology, the application of the methods of molecular biology have led to the recognition of a number of families of receptors. Typically, such receptors contain an extracellular ligand binding domain, a transmembrane domain, and an intracellular catalytic domain whose activation, as a result of ligand binding, leads to generation of second messengers within the cell and stimulation of a range of cytosolic enzymes. An alternative signaling strategy, exploited in particular in the nervous system, is to use ion channels to allow controlled movement of monovalent (Na+, K+) or divalent (Ca2+) cations in or out of the cell, resulting in changes in membrane potential or alterations in the intracellular concentration of Ca2+. Part II of this volume is concerned with these ion channels and with other, often simpler, ion channel systems whose study can throw light on channel mechanism.

Progenitor cells have become important in regenerative medicine therapies, due to their potential to differentiate into many cell types. This capability, and understanding how to regulate the cells, will provide the basis for future cell therapies aimed at correcting tissue and organ dysfunction as a result of disease or injury. In, Progenitor Cells: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to investigate progenitor cells. These include methods and techniques of the manipulation of physical forces that shape progenitor cell behavior, studying progenitor cells in vivo, using non-mammalian and mammalian model systems, and investigating human progenitor cells, including their isolation, characterization and application in cell-based therapies. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Progenitor Cells : Methods and Protocols seeks to aid scientists in the further study progenitor cells and how they are studied across multiple systems.

Volume 5 of Biomembranes covers an important group of membrane proteins, the ATPases. The P-type ATPases couple the hydrolysis of ATP to the movement of ions across a membrane and are characterized by the formation of a phosphoyrlated intermediate. Included are the plasma membrane and muscle sarcoplasmic reticulum Ca2+ -ATPases, the (Na+ -K+) -ATPase, the gastric (H+ -K+) -ATPase, the plasma membrane H+ -ATPase of fungi and plants, the Mg2+ - transport ATPase, the Salmonella typhimurium, and the K+ -ATPase of Escherichia coli, KdpB. The other important classes of ATPase in eukaryotic systems are the vacuolar H+ -ATPases and the F0F1 ATP synthase, and, in bacteria, the anion-translocating ATPases, responsible for resistance to arsenicals and antimonials, and the (Na+ -Mg2+) -ATPase of Acholeplasma. Finally, eukaryotic systems contain a variety of ectonucleotidases important, for example, in hydrolysis of extracellular ATP released as a cotransmitter from cholinergic and adrenergic nerve terminals. Volume 5 of Biomembranes explores structure-function relationships for these mebrane-bound ATPases.

Classical natural product chemistry is transitioning to modern day metabolomics as a result of the advent of comprehensive analytical platforms and sensitive analytical instrumentation. Therefore, it is worthwhile to summarize recent developments with current analytical platforms and highlight how metabolomics is being integrated into this classical field to dereplicate and profile natural product extracts. Metabolomics Tools for Natural Product Discoveries: Methods and Protocols aims to unite diverse and recently developed methodologies and protocols in order to identify bioactive secondary metabolites for the purpose of drug discovery. Some topics covered in this volume include applications for the extraction of selected natural products from less common sources such as bryophytes and hard corals, various biological assays, comprehensive applications and strategies for GC-MS, LC-MS, and NMR, as well as protocols and strategies for the structure elucidation of isolated natural products. 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 Metabolomics Tools for Natural Product Discoveries: Methods and Protocols seeks to serve both professionals and research students with its well-honed methodologies for natural product isolation, biomarker discovery, dereplication, biological assays, and comprehensive metabolomic platforms available for high-throughput analyses.

Along with its companion volume on intraflagellar transport, this book provides researchers with a comprehensive and up-to-date source of methods for the analysis cilia and flagella, focusing primarily on approaches that have been devised or significantly extended since the last volume of Methods in Cell Biology on this topic (volume 47, 1995). Edited by Stephen M. King and Gregory J. Pazour, the newest installment of this highly acclaimed serial will serve as an essential addition to the study of cilia and flagella.

* Covers protocols for cilia and flagella across systems and species * Both classic and state-of-the-art methods readily adaptable across model systems, and designed to last the test of time * Relevant to clinicians interested in respiratory disease, male infertility, and other syndromes, who need to learn biochemical, molecular, and genetic approaches to studying cilia, flagella, and related structures

This fully revised 2e provides the only unified synthesis of available information concerning the mechanisms of higher-order memory formation. It spans the range from learning theory, to human and animal behavioral learning models, to cellular physiology and biochemistry. It is unique in its incorporation of chapters on memory disorders, tying in these clinically important syndromes with the basic science of synaptic plasticity and memory mechanisms. It also covers cutting-edge approaches such as the use of genetically engineered animals in studies of memory and memory diseases. Written in an engaging and easily readable style and extensively illustrated with many new, full-color figures to help explain key concepts, this book demystifies the complexities of memory and deepens the reader s understanding.
More than 25% new content, particularly expanding the scope to include new findings in translational research. Unique in its depth of coverage of molecular and cellular mechanisms Extensive cross-referencing to Comprehensive Learning and Memory Discusses clinically relevant memory disorders in the context of modern molecular research and includes numerous practical examples
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In this volume we will cover technologies and associated methodologies that allow identification, characterization and application of therapeutic peptides.

The section covering identification will cover areas such as display on the surface of filamentous or lytic phage, substrate phage display, ribosome display and the use of peptide library pools.

Often the output from library selection is not a peptide but the sequence of a peptide. We will therefore discuss approaches to produce peptide ligands both synthetically and through recombinant techniques. This section will also include a discussion of how peptides may be produced such that their serum residence time can be extended to allow weekly dosing such as fusions to other larger proteins or through modification with PEG.

The next section covers biophysical tools for characterization of peptide interactions with proteins. These include fluorescence polarization, equilibrium dialysis, radioligand binding assays, regular and array based SPR analysis.

The remaining section outlines methods for preparation and application of peptides as: imaging agents; targeting agents for radionuclei; receptor antagonists, and as tools to mediate cell penetration

Biobanking is considered to be one of the ten ideas changing the world with an estimated value of $45 billion by 2025. Despite the challenges, as the climate for innovation in the biobanking industry continues to flourish around the world, it is certain that amazing discoveries will emerge from this large-scale method of preserving and accessing human samples; biobanking is no longer just a place for collecting and storing samples. This book will cover a wide variety of subjects from across the future biobanking spectrum including scientific strategies, personalized medicine, regenerative medicine and stem cell challenges, disease surveillance, population genetics and innovative methods of biobanking.

The book introduces the bioinformatics tools, databases and strategies for the translational research, focuses on the biomarker discovery based on integrative data analysis and systems biological network reconstruction. With the coming of personal genomics era, the biomedical data will be accumulated fast and then it will become reality for the personalized and accurate diagnosis, prognosis and treatment of complex diseases. The book covers both state of the art of bioinformatics methodologies and the examples for the identification of simple or network biomarkers. In addition, bioinformatics software tools and scripts are provided to the practical application in the study of complex diseases. The present state, the future challenges and perspectives were discussed. The book is written for biologists, biomedical informatics scientists and clinicians, etc. Dr. Bairong Shen is Professor and Director of Center for Systems Biology, Soochow University; he is also Director of Taicang Center for Translational Bioinformatics.

Before the therapeutic potential of cell replacement therapy or the development of therapeutic drugs for stimulating the body 's own regenerative ability to repair cells damaged by disease and injury can be fully realized, control of stem cell fate, immuno-rejection, and limited cell sources must be overcome. In Cellular Programming and Reprogramming: Methods and Protocols, expert researchers cover the most recent technologies and their related mechanisms involved in the programming and reprogramming of cell fate. 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, laboratory protocols, and notes to highlight tips on troubleshooting and avoiding known pitfalls.

Essential and cutting-edge, Cellular Programming and Reprogramming: Methods and Protocols promises to aid scientists attempting to advance stem cell biology in order to better treat devastating human diseases, including cardiovascular disease, neurodegenerative disease, musculoskeletal disease, diabetes, and cancer.

Along with its companion volume on axonemal dynein-mediated motility, this book provides researchers with a comprehensive and up-to-date source of methods for the analysis cilia and flagella, focusing primarily on approaches that have been devised or significantly extended since the last volume of Methods in Cell Biology on this topic (volume 47, 1995). Edited by Stephen M. King and Gregory J. Pazour, the newest installment of this highly acclaimed serial will serve as an essential addition to the study of cilia and flagella.

* Covers protocols for cilia and flagella across systems and species * Both classic and state-of-the-art methods readily adaptable across model systems, and designed to last the test of time * Relevant to clinicians interested in respiratory disease, male infertility, and other syndromes, who need to learn biochemical, molecular, and genetic approaches to studying cilia, flagella, and related structures

This book provides insights into some of the key achievements made in the study of Lotus japonicus (birdsfoot trefoil), as well as a timely overview of topics that are pertinent for future developments in legume genomics. Key topics covered include endosymbiosis, development, hormone regulation, carbon/nitrogen and secondary metabolism, as well as advances made in high-throughput genomic and genetic approaches. Research focusing on model plants has underpinned the recent growth in plant genomics and genetics and provided a basis for investigations of major crop species. In the legume family Fabaceae, groundbreaking genetic and genomic research has established a significant body of knowledge on Lotus japonicus, which was adopted as a model species more than 20 years ago. The diverse nature of legumes means that such research has a wide potential and agricultural impact, for example, on the world's protein production.

Volume 4 of Biomembranes covers endocytosis, exocytosis and related processes. A major role of the plasma membrane is as a permeability barrier, keeping the inside of the cell inside and the outside, outside. Mechanisms must then exist to allow movement of material between the cell and its environment. One mechanism for export from the cell is by exocytosis, a process in which the membranes of secretory vesicles fuse with the plasma membrane releasing the contents of the vesicle into the extracellular medium. The process has been studied in particular depth for the release of neurotransmitters at the synapse. Import into the cell is possible by the process of receptor-mediated endocytosis in which selected plasma membrane proteins are internalizes; when these proteins are receptors for macromolecules, the result is uptake of the macromolecule. Transferring, the low-density lipoprotein, and asialoglycoproteins are all taken up into cells in this way. Phagocytosis, the ingestion of cells and cell fragments by neutrophils and macrophages, also involves receptors - on the phagocytic membrane - of which the best studied are those for the Fc domain of IgG, for the third component of complement, and for the mannose/fructose carbohydrates. Protection of a host against infection can also be achieved by damaging the integrity of the plasma membrane of the invading organism. This is the strategy evolved by the cytotoxic T lymphocytes, which produce a pore-forming toxin, perforin. Volume 4 of Biomembranes explores the structures and mechanisms involved in these biologically and medically important processes.

Integrated bioinformatics solutions have become increasingly valuable in past years, as technological advances have allowed researchers to consider the potential of omics for clinical diagnosis, prognosis, and therapeutic purposes, and as the costs of such techniques have begun to lessen. In Bioinformatics Methods in Clinical Research, experts examine the latest developments impacting clinical omics, and describe in great detail the algorithms that are currently used in publicly available software tools. Chapters discuss statistics, algorithms, automated methods of data retrieval, and experimental consideration in genomics, transcriptomics, proteomics, and metabolomics. Composed in the highly successful Methods in Molecular Biology series format, each chapter contains a brief introduction, provides practical examples illustrating methods, results, and conclusions from data mining strategies wherever possible, and includes a Notes section which shares tips on troubleshooting and avoiding known pitfalls.

Informative and ground-breaking, Bioinformatics Methods in Clinical Research establishes a much-needed bridge between theory and practice, making it an indispensable resource for bioinformatics researchers."

"Metabolic Flux Analysis: Methods and Protocols "opens up the field of metabolic flux analysis to those who want to start a new flux analysis project but are overwhelmed by the complexity of the approach. Metabolic flux analysis emerged from the current limitation for the prediction of metabolic fluxes from a measured inventory of the cell. Divided into convenient thematic parts, topics in this essential volume include the fundamental characteristics of the underlying networks, the application of quantitative metabolite data and thermodynamic principles to constrain the solution space for flux balance analysis (FBA), the experimental toolbox to conduct different types of flux analysis experiments, the processing of data from 13C experiments and three chapters that summarize some recent key findings. 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, "Metabolic Flux Analysis"" Methods and Protocols" presents protocols that cover a range of relevant organisms currently used in the field, providing a solid basis to anybody interested in the field of metabolic flux analysis.

This book describes the molecular biology, pathogenesis, epidemiology, and potential strategies for control of chikungunya virus (CHIKV) infection. It offers insight into the structure and functions of CHIKV proteins as they relate to host response, interaction with the arthropod vector, and vaccination. A detailed account of both the epidemiological outlook and the clinical syndrome of CHIKV infection is provided. The complex host-virus interaction and the signaling pathways that mediate such interactions are also covered. Throughout the book, graphics and charts are used to provide stimulating discussion on important findings in the field of chikungunyalogy. The chapters are written with a global perspective by experts of CHIKV from around the world. This project is especially significant given that CHIKV is a pathogen of worldwide public health concern. Although the presence of CHIKV infection is not global yet, worldwide dissemination is predicted in the future due largely to the lack of effective treatment/therapy, efficient control of transmission, and knowledge about mechanisms of pathogenesis. Additionally, globalization of CHIKV is predicated on its mode of dissemination (mosquito vector) and cross border travel and migration.

This book is devoted to Slime mould Physarum polycephalum, which is a large single cell capable for distributed sensing, concurrent information processing, parallel computation and decentralized actuation. The ease of culturing and experimenting with Physarum makes this slime mould an ideal substrate for real-world implementations of unconventional sensing and computing devices The book is a treatise of theoretical and experimental laboratory studies on sensing and computing properties of slime mould, and on the development of mathematical and logical theories of Physarum behavior. It is shown how to make logical gates and circuits, electronic devices (memristors, diodes, transistors, wires, chemical and tactile sensors) with the slime mould. The book demonstrates how to modify properties of Physarum computing circuits with functional nano-particles and polymers, to interface the slime mould with field-programmable arrays, and to use Physarum as a controller of microbial fuel cells. A unique multi-agent model of slime is shown to serve well as a software slime mould capable for solving problems of computational geometry and graph optimization. The multiagent model is complemented by cellular automata models with parallel accelerations. Presented mathematical models inspired by Physarum include non-quantum implementation of Shor's factorization, structural learning, computation of shortest path tree on dynamic graphs, supply chain network design, p-adic computing and syllogistic reasoning. The book is a unique composition of vibrant and lavishly illustrated essays which will inspire scientists, engineers and artists to exploit natural phenomena in designs of future and emergent computing and sensing devices. It is a 'bible' of experimental computing with spatially extended living substrates, it spanstopics from biology of slime mould, to bio-sensing, to unconventional computing devices and robotics, non-classical logics and music and arts.

Structural genomics is the systematic determination of 3-D structures of proteins representative of the range of protein structure and function found in nature. The goal is to build a body of structural information that will predict the structure and potential function for almost any protein from knowledge of its coding sequence. This is essential information for understanding the functioning of the human proteome, the ensemble of tens of thousands of proteins specified by the human genome. While most structural biologists pursue structures of individual proteins or protein groups, specialists in structural genomics pursue structures of proteins on a genome wide scale. This implies large-scale cloning, expression and purification. One main advantage of this approach is economy of scale.

Compared with data from general application domains, modern biological data has many unique characteristics. Biological data are often characterized as having large volumes, complex structures, high dimensionality, evolving biological concepts, and insufficient data modelling practices. Over the past several years, bioinformatics has become an all-encompassing term for everything relating to both computer science and biology. The goal of this book is to cover data and applications identifying new issues and directions for future research in biomedical domain. The book will become a useful guide learning state-of-the-art development in biomedical data management, data-intensive bioinformatics systems, and other miscellaneous biological database applications. The book addresses various topics in bioinformatics with varying degrees of balance between biomedical data models and their real-world applications.

The discovery of stem and progenitor cells in the adult mammalian CNS challenged the long standing no new neuron doctrine and opened the door to the potential for cell replacement therapy. The process from discovery to clinical applications can be long and tortuous, requiring rigorous steps involving standardized and precise protocols. "Neural Progenitor Cells: Methods and Protocols "is a collection of practical articles describing techniques used to study neural stem and progenitor cells. The volume also highlights the promise of stem cell-based therapeutic applications for CNS disorders. 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, "Neural Progenitor Cells: Methods and Protocols "serves both professionals and novices with its well-honed methodologies. "

This volume provides a collection of protocols aimed toward the study of ethylene signaling in plants. Ethylene Signaling: Methods and Protocols is divided into three sections: ethylene biosynthesis, the signal transduction pathway, and the diverse ethylene responses of dicots and monocots. The chapters in section one discuss techniques for the measurement of activities related to the biosynthetic enzymes ACC synthase and ACC oxidase, the levels of ethylene synthesized by plants, and the treatment of plants with exogenous ethylene. Section two focuses on the analysis of the new membrane-associated proteins involved in the initial perception and transduction of the ethylene signal, such as ethylene receptors, CTR1, and EIN2. The third section covers assays applicable to dicots and monocots, including methods related to the roles of ethylene in germination, growth, abscission, abiotic stress, and defense. Section three also includes information on Arabidopsis mutants and the variety of chemical inhibitors that affect ethylene responses. 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 comprehensive, Ethylene Signaling: Methods and Protocols is a valuable resource for both experienced and beginner researchers with prior experience in the study of ethylene signaling and for those who are just entering this exciting research field.

Ataxia-telangiectasia (A-T) is a rare and severe genetic disorder affecting children. A-T is a multisystem disease characterized by progressive neurodegeneration, immunodeficiency and cancer predisposition. This detailed volume explores the ever expanding field of research into the ATM (ataxia-telangiectasia, mutated) gene and the role played by ATM kinase in DNA damage signaling and diverse cellular processes. What follows is a handy desktop reference for both seasoned A-T researchers and postgraduate students, as it demonstrates the breadth of recent developments in A-T studies. 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. Both classic and cutting-edge techniques are described, including ATM gene mutation detection, assays for radiosensitivity and radioresistant DNA synthesis, new methods to measure ATM kinase activity by imaging microscopy and high content screening as well as proteomics, phosphoproteomics and bioinformatics approaches to decipher ATM-dependent signalling pathways. Additional methods include generation of patient-specific stem cells and approaches to study ATM functions in the nervous system. Comprehensive and practical, ATM Kinase: Methods and Protocols aims to ignite and attract the interest of colleagues from diverse fields to A-T research in an effort to bring their expertise and fresh ideas to resolve many A-T puzzles still waiting to be pieced together and to alleviate the suffering of A-T children and their families.

"Molecular Biology of RGS Proteins," a volume of "Progress in Molecular Biology and Translational Science," will include historical discussion of RGS proteins, the role of RGS proteins in addiction, depression and Parkinson's disease and the biology and functional regulation of RGS9 isoforms. This publication further discusses RGS proteins in cellular signaling, protein control in lymphocyte function, and alternative splicing of RGS transcripts and nuclear RGS proteins, offering the latest in research of RGS proteins.