PlantOmics: The Omics of Plant Science provides a comprehensive account of the latest trends and developments of omics technologies or approaches and their applications in plant science. Thirty chapters written by 90 experts from 15 countries are included in this state-of-the-art book. Each chapter describes one topic/omics such as: omics in model plants, spectroscopy for plants, next generation sequencing, functional genomics, cyto-metagenomics, epigenomics, miRNAomics, proteomics, metabolomics, glycomics, lipidomics, secretomics, phenomics, cytomics, physiomics, signalomics, thiolomics, organelle omics, micro morphomics, microbiomics, cryobionomics, nanotechnology, pharmacogenomics, and computational systems biology for plants. It provides up to date information, technologies, and their applications that can be adopted and applied easily for deeper understanding plant biology and therefore will be helpful in developing the strategy for generating cost-effective superior plants for various purposes. In the last chapter, the editors have proposed several new areas in plant omics that may be explored in order to develop an integrated meta-omics strategy to ensure the world and earth's health and related issues. This book will be a valuable resource to students and researchers in the field of cutting-edge plant omics.

Proteins are the most diverse group of biologically important substances. With the recent technological advances in the genomics area and the efforts in proteomics research, the rate of discovery for new proteins with unknown structure and function has increased. These proteins generated from genomic approaches present enormous opportunities for research and industrial application. Protein Downstream Processing: Design, Development and Application of High and Low-Resolution Methods is a compilation of chapters within the exciting area of protein purification designed to give the laboratory worker the information needed to design and implement a successful purification strategy. It presents reliable and robust protocols in a concise form, emphasizing the critical aspects on practical problems and questions encountered at the lab bench. 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, Protein Downstream Processing: Design, Development and Application of High and Low-Resolution Methods will be an ideal source of scientific information to advanced students, junior researchers, and scientists involved in health sciences, cellular and molecular biology, biochemistry, and biotechnology and other related areas in both academia and industry.

This book focuses on C-type lectin receptors, a newly emerging family of pattern-recognition receptors (PRRs) and a crucial part of the human innate immune system. Above all, the authors highlight these receptors' role in the recognition of pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs) - one of the first steps in responding to foreign and potentially dangerous structures in the human body. The respective chapters chiefly examine various C-type lectin receptors, their corresponding ligands, and signalling. In addition to offering immunologists and clinicians important insights from the latest research, they may also provide novel points of departure for future drug development.

This volume provides the most current methods to study RNA remodeling proteins. Chapters detail methods, ranging from basic to complex, procedures to identify RNA remodeling proteins and their cofactors, physiological RNA targets and biological functions, and complex molecular mechanisms of action using purified components. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA Remodeling Proteins: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

An introduction to underlying principles and experimental procedures using the newest strategies and techniques for obtaining extensive NMR assignments in biopolymers based on NMR data and the primary structure. Includes an extensive and non-mathematical discussion of 2D NMR and Nulcear Overhauser effects; resonance assignments and structure determination in proteins; and resonance assignments and structure determination in nucleic acids. Enables specialists and non-specialists to evaluate the potentialities and limitations of the method.

The Protein Reviews series serves as a publication vehicle for reviews that focus on crucial contemporary and vital aspects of protein structure, function, evolution and genetics. Volume 20, Purinergic Receptors, has ten chapters. The first five chapters deal with various aspects of membrane binding. The first chapter focuses on the phox-homology (PX) domain, which is a phosphoinositide-binding domain conserved in all eukaryotes and present in forty-nine human proteins. The next chapter deals with the modeling of PH domains/phosphoinositides interactions. This is followed by a chapter on BAR domain proteins regulate Rho GTPase signaling. The BAR (Bin-Amphiphysin-Rvs) domain is a membrane lipid binding domain present in a wide variety of proteins, often proteins with a role in Rho-regulated signaling pathways. The fourth article presents AP180 N-terminal homology (ANTH) and Epsin N-terminal homology (ENTH) domains and discusses their physiological functions and involvement in disease. The fifth article reviews the polyphosphoinositide-binding domains and presents insights from peripheral membrane and lipid-transfer proteins. This is followed by a chapter on the physiological functions of phosphoinositide-modifying enzymes and their interacting proteins in Arabidopsis, then by a chapter on the molecular mechanisms of Vaspin action in various tissues such as adipose tissue, skin, bone, blood vessels, and the brain. The eighth chapter deals with exceptionally selective substrate targeting by the metalloprotease anthrax lethal factor followed by an article on Salmonella, E. coli, and Citrobacter type III secretion system effector proteins that alter host innate immunity. The last chapter presents New techniques to study intracellular receptors in living cells, with insights into RIG-I-like receptor signaling. Volume 20 is intended for research scientists, clinicians, physicians and graduate students in the fields of biochemistry, cell biology, molecular biology, immunology and genetics.

Focuses on the aggregation of recombinant proteins in bacterial cells in the form of inclusion bodies and on their use in biotechnological and medical applications The first book devoted specifically to the topic of aggregation in bacteria, Protein Aggregation in Bacteria: Functional and Structural Properties of Inclusion Bodies in Bacterial Cells provides a large overview of protein folding and aggregation, including cell biology and methodological aspects. It summarizes, for the first time in one book, ideas and technical approaches that pave the way for a direct use of inclusion bodies in biotechnological and medical applications. Protein Aggregation in Bacteria covers: * Molecular and cellular mechanisms of protein folding, aggregation, and disaggregation in bacteria * Physiological importance and consequences of aggregation for the bacterial cell * Factors inherent to the protein sequence responsible for aggregation and evolutionary mechanisms to keep proteins soluble * Structural properties of proteins expressed as soluble aggregates and as inclusion bodies within bacterial cells both from a methodological point of view and with regard to their similarity with amyloids * Control of the structural and functional properties of aggregated proteins and use thereof in biotechnology and medicine Protein Aggregation in Bacteria is ideal for researchers in protein science, biochemistry, bioengineering, biophysics, microbiology, medicine, and biotechnology, particularly if they are related with the production of recombinant proteins and pharmaceutical science.

Cell surface molecules are critically important in regulating cell structure and function. Recent advances on the functional role of cell surface molecules, particularly glycoconjugates are presented in this book. Comprising of 22 chapters from the 2011 International Symposium on Biochemical Roles of Eukaryotic Cell Surface Macromolecules, it covers topics on the analysis of glycome, biophysical approaches to study cell surface molecules, glycoconjugate metabolism and its dysregulation, and molecular mechanisms involved in cell-cell and cell-matrix interaction.

Cancer is one of the leading death cause of human population increasingly seen in recent times. Plants have been used for medicinal purposes since immemorial times. Though, several synthetic medicines are useful in treating cancer, they are inefficient and unsafe. However, plants have proved to be useful in cancer cure. Moreover, natural compounds from plants and their derivatives are safe and effective in treatment and management of several cancer types. The anticancer plants such as Catharanthus roseus, Podophyllum peltatum, Taxus brevifolia, Camptotheca acuminate, Andrographis paniculata, Crateva nurvala, Croton tonkinensis, Oplopanax horridus etc., are important source of chemotherapeutic compounds. These plants have proven their significance in the treatment of cancer and various other infectious diseases. Nowadays, several well-known anticancer compounds such as taxol, podophyllotoxins, camptothecin, vinblastine, vincristine, homoharringtonine etc. have been isolated and purified from these medicinal plants. Many of them are used effectively to combat cancer and other related diseases. The herbal medicine and their products are the most suitable and safe to be used as an alternative medicine. Based on their traditional uses and experimental evidences, the anticancer products or compounds are isolated or extracted from the medicinally important plants. Many of these anticancer plants have become endangered due to ruthless harvesting in nature. Hence, there is a need to conserve these species and to propagate them in large scale using plant tissue culture. Alternatively, plant cell tissue and organ culture biotechnology can be adopted to produce these anticancer compounds without cultivation. The proper knowledge and exploration of these isolated molecules or products could provide an alternative source to reduce cancer risk, anti-tumorigenic properties, and suppression of carcinogen activities. Anticancer plants: Volume 1, Properties and Application is a very timely effort in this direction. Discussing the various types of anticancer plants as a source of curative agent, their pharmacological and neutraceutical properties, cryo-preservations and recent trends to understand the basic cause and consequences involved in the diseases diagnosis. We acknowledge the publisher, Springer for their continuous inspiration and valuable suggestions to improvise the content of this book. We further extend our heartfelt gratitude to all our book contributors for their support, and assistance to complete this assignment. I am sure that these books will benefit the scientific communities including academics, pharmaceuticals, nutraceuticals and medical practitioners.

This book explores the remarkable information correspondences and probability structures of proteins. Correspondences are pervasive in biochemistry and bioinformatics: proteins share homologies, folding patterns, and mechanisms. Probability structures are just as paramount: folded state graphics reflect Angstrom-scale maps of electron density. The author explores protein sequences (primary structures), both individually and in sets (systems) with the help of probability and information tools. This perspective will enhance the reader's knowledge of how an important class of molecules is designed and put to task in natural systems, and how we can approach class members in hands-on ways.

Photoswitching Proteins: Methods and Protocols, focuses on proven applications of photoswitching proteins in cell and neurobiology. Optical approaches have been mostly embraced by the neurosciences to allow fast, high-resolution characterization and manipulation of single cells in complex neuronal tissue. These tools, including photoswitching of proteins, are now successfully used in almost all fields of biological research. 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 key tips on troubleshooting and avoiding known pitfalls.Comprehensive and practical, Photoswitching Proteins: Methods and Protocols highlights many of the possibilities for research based on light-inducible, high-resolution manipulation of biological systems.

This book is the first to be entirely devoted to the challenging art of handling membrane proteins out of their natural environment, a key process in biological and pharmaceutical research, but one plagued with difficulties and pitfalls. Written by one of the foremost experts in the field, Membrane Proteins in Aqueous Solutions is accessible to any member of a membrane biology laboratory. After presenting the structure, functions, dynamics, synthesis, natural environment and lipid interactions of membrane proteins, the author discusses the principles of extracting them with detergents, the mechanisms of detergent-induced destabilization, countermeasures, and recent progress in developing detergents with weaker denaturing properties. Non-conventional alternatives to detergents, including bicelles, nanodiscs, amphipathic peptides, fluorinated surfactants and amphipols, are described, and their relative advantages and drawbacks are compared. The synthesis and solution properties of the various types of amphipols are presented, as well as the formation and properties of membrane protein/amphipol complexes and the transfer of amphipol-trapped proteins to detergents, nanodiscs, lipidic mesophases, or living cells. The final chapters of the book deal with applications: membrane protein in vitro folding and cell-free expression, solution studies, NMR, crystallography, electron microscopy, mass spectrometry, amphipol-mediated immobilization of membrane proteins, and biomedical applications. Important features of the book include introductory sections describing foundations as well as the state-of-the-art for each of the biophysical techniques discussed, and topical tables which organize a widely dispersed literature. Boxes and annexes throughout the book explain technical aspects, and twelve detailed experimental protocols, ranging from in vitro folding of membrane proteins to single-particle electron cryomicroscopy, have been contributed by and commented on by experienced users. Membrane Proteins in Aqueous Solutions offers a concise, accessible introduction to membrane protein biochemistry and biophysics, as well as comprehensive coverage of the properties and uses of conventional and non-conventional surfactants. It will be useful both in basic and applied research laboratories and as a teaching aid for students, instructors, researchers, and professionals within the field.

The basic principle of electron crystallography is to calculate a 3D density map by combining the amplitudes obtained from electron diffraction patterns with the experimental phases calculated from images of two-dimensional crystals of membrane or soluble proteins. This technology is very well developed and has produced a number of atomic models of membrane proteins in a lipid environment. Focused on comprehensive experimental protocols, Electron Crystallography of Soluble and Membrane Proteins: Methods and Protocols covers the entire range of techniques used in electron crystallography, including protein sample preparation, 2D crystallization, and screening in negative stain over electron cryo-microscopy (cryo-EM) and data processing, as well as modeling of conformational changes. Additional chapters provide perspective on past, present, and future challenges as well as complementary methods. Written for the popular Methods in Molecular Biology (TM) series, the work contains the kind of detailed descriptions and implementation advice necessary to ensure successful results. Comprehensive and cutting-edge, Electron Crystallography of Soluble and Membrane Proteins: Methods and Protocols serves laboratories new to the methods as well as state-of-the-art facilities pursuing this exciting area of protein science.

Covering a wide-ranging facet of a "gold-standard" targeted mass spectrometry (MS) method for the consistent detection and accurate quantification of preselected proteins in complex biological matrices, Selected Reaction Monitoring Mass Spectrometry (SRM-MS) in Proteomics: A Comprehensive View describes: The knowledge-based development of highly efficient SRM methodology including assay workflow, selection of proteins, peptides, transitions and its validation, and quality assessment Available bioinformatic tools - for both pre-acquisition method development and post-MS acquisition data analysis and data repositories Various relative and absolute quantification techniques SRM-MS' widespread applications in biomarker development and in clinical studies, as well as in the analysis of various posttranslational modifications (PTMs) Current challenges and contemporary trends to overcome those difficulties In addition, it features the historical development of modern-day mass spectrometry with its vivid applications and also covers basic MS instrumentation, ionization techniques, and various proteomics approaches. Comprehensive discussion, extensive references at the end of each chapter, and the list of review articles in the bibliography offer invaluable resources for advanced readings. Researchers from the undergraduate to postgraduate level and beyond in both academic or industry settings studying and working on mass spectrometry and/or proteomics will benefit from this book.

This book discusses the decoding of the lytic mechanism of an -helical pore-forming toxin, YaxAB, composed of two different subunits. Pore-forming toxins (PFTs) are among the most common bacterial toxins. They are produced by a variety of pathogens, which infect a wide range of organisms including plants, insects and humans. Yet the maturation of these particles and the structural changes required for pore formation are still poorly understood for many PFT families. Using a diverse panel of biochemical and structural techniques, including X-ray crystallography and cryo-electron microscopy, Dr. Brauning and colleagues have succeeded in identifying the mechanistic contributions of the two toxin components and elucidating the lytic state of the pore complex. The results of this thesis on the YaxAB system are applicable to orthologues from agriculturally relevant insect pathogens, and offer valuable structural and mechanistic insights to inform future bioengineering efforts.

This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.

This book includes a series of reviews on general aspects of biomarker use in the study of psychiatric and neurodegenerative diseases and the development of medications involved in their treatment. It describes the pros and cons of the various approaches and covers the successes and failures in this research field. It is only by a thorough understanding of the shortcomings that progress can be made. The overall goal is to facilitate the understanding and treatment of these disorders, by providing a viable mechanism of catching up with other areas of modern medicine, such as diabetes and heart disease. Finally, it is anticipated that the development and application of valid biomarker tests and the leveraging of novel drug targets will help the fields of psychiatry on neurodegenerative disorders move into the area of personalized medicine where the right patients can receive the right medication at the right time for the best possible outcome.

This volume presents detailed protocols for novel strategies and approaches to improve functional understanding of protein N- and C-terminal biology. Protein Terminal Profiling: Methods and Protocols addresses topics such as protease specificity profiling, N-terminal acetylation, assays to probe protease activity in cellular systems, protein N- and C-termini on a proteome-wide scale, and biochemical approaches to explain and examine extracellular protease activities. 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 thorough, Protein Terminal Profiling: Methods and Protocols is a valuable resource for researchers that focus on biochemistry and cell biology, and those who share a broad interest in protein functionality and protein modifications.

In the decade since publication of the first edition this book, the field has seen several major developments. These developments have both accelerated the pace of structure determination and made crystallography accessible to a broader range of investigators. Volume I is dedicated to crystallization and ways to increase the odds of obtaining crystals in macromolecules. Volume 2 covers both computational methods for characterizing crystals and solving structures.

In this present volume, different approaches are detailed to produce membrane proteins, purify them, study their function, determine their structure, and model them in membrane. Since every membrane protein behaves mostly in a unique way /fashion, knowledge of guidelines and tricks may help to increase chances to express, purify and characterize a peculiar membrane protein. Production of correctly folded protein remains a challenge. Moreover, getting a functional and stable protein requires to optimize membrane mimicking environments that can be detergent or artificial membranes. In some cases, the finding of the correct ligand which will stabilize the desired conformation is needed. In other cases, stabilization can be obtained using specific antibodies. This volume also presents different techniques to analyze the functional status of membrane proteins. Written in the highly successful Methods in Molecular Biology series format, chapters in Membrane Protein Structure and Function Characterization: Methods and Protocols provide different techniques to analyze the functional and structural status of membrane proteins. 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, Membrane Protein Structure and Function Characterization: Methods and Protocols aims to ensure successful results in the further study of this vital field.

The use of the chemical modification of proteins has evolved over the past 80 years, benefiting from advances in analytical, physical, and organic chemistry. Over the past 30 years, the use of chemical reagents to modify proteins has been crucial in determining the function and structure of purified proteins. This groundbreaking work is part of the foundation of emerging disciplines of proteomics, chemical biology, structure biology, and chemical proteomics. Chemical Reagents for Protein Modification, Fourth Edition provides a comprehensive review of reagents used for the chemical modification of proteins, representing a major revision of the work presented in previous editions. The completely updated Fourth Edition is substantially larger and includes five new chapters: Alkylating Agents Acylating Agents Nitration and Nitrosylation Oxidation Modification of Proteins with Reducing Agents There is greatly increased coverage of the chemical modification of cysteine, which is critical for bioconjugate synthesis. The chapter on reduction also provides information necessary for bioconjugate synthesis as well as for the processing of inclusion bodies. The book places emphasis on conditions that affect the specificity of the chemical modification of proteins, such as solvent and temperature. The format has been markedly revised, presenting information based on the chemical nature of the modifying material and on the amino acid residue modified. This new version has increased significance to biopharmaceuticals. Much of the information is in tabular form, which enables the rapid location of cited material.

Protein Structure Prediction, Third Edition expands on previous editions by focusing on software and web servers. With new chapters that provide instructions on how to use a computational method with examples of prediction by the method. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Protein Structure Prediction, Third Edition provides diverse methods detailing the expansion of the computational protein structure prediction field.

Protein tyrosine phosphatases remove phosphates from the phosphotyrosine residues of target proteins and reverse the action of various protein tyrosine kinases. This essential interplay between the opposing actions of protein tyrosine phosphatases and protein tyrosine kinases forms the basis of signaling networks that underlie the cellular workings of human physiology. Initially passed-off as housekeeping genes; these proteins were only acknowledged to maintain a steady background of phosphotyrosine levels in the cell. However, recent progress in studying their role in embryonic development and human disease has established their importance as regulators of signal regulation. Convincing evidence shows the role of mutations in these proteins to cause and/or intensify the severity of various diseases including metabolic and neurological disorders and also cancer. Protein tyrosine phosphatases have slowly, yet convincingly become crucial targets for therapeutic intervention of various human pathophysiologies. This book describes these signaling enzymes using the molecular details of their structure and mechanistic function. Various subtypes of cysteine-based Class I, II, III and the Haloacid dehalogenase related Class IV protein tyrosine phosphatases have been illustrated and explained. The superfamily of proteins is also described vis-a-vis its complimentary protein phosphoserine/phosphoserine phosphatases. Membrane bound receptor forms and the cytosolic non-receptor protein tyrosine phosphatases have been described for their biological function. This book serves as a reference for any reader looking to understand the sequence features, structural elements, molecular mechanism and cellular function of this superfamily of signaling enzymes.

This new edition provides updated and novel protocols of neuroproteomics methods that encompass both global-scale as well as targeted and specialized topics, which are timely additions for the molecular and phenotypic analysis of the central nervous system and CNS-related disorders. The detailed contents of this book include the exploration of several exciting areas of advanced methods used for neuroproteomics research including relative and absolute protein quantitation by mass spectrometry, characterization of post-translational modifications, as well as bioinformatics and computational approaches. Written for the highly successful Methods in Molecular Biology series, methodology chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Updated and accessible, Neuroproteomics: Methods and Protocols, Second Edition serves researchers and clinical scientists involved in the area of biomarker research and protein biochemistry, as well as molecular biologists and biochemists who have been involved in proteomics research already or even for those new to the field.

Recent research suggests that adult growth hormone (GH) deficiency, whether of pathological or physiological origin, is associated with a dis tinct syndrome that includes alterations in body composition, endocrine metabolic function, immune competence, and physical and psychosocial well-being. Not surprisingly, substantial investigative effort is currently focused on validating the above hypothesis and on determining whether restoration of a normal GH-IGF-I axis in various states of adult GH deficiency is clinically useful, safe, and cost-beneficial. This book contains the proceedings from the Symposium on GHRH, GH, and IGF-I: Basic and Clinical Advances, held December 9 to 12, 1993, in San Diego, California, and sponsored by Serono Symposia USA, Inc. The conference was meant to highlight selected novel and exciting clinical research developments related to possible therapeutic uses of recombinant human GH and IGF-I, GHRH, GH releasing peptides, and related GH secretagogues. This meeting occurred only one year after a similar Serono symposium that was somewhat more oriented to novel basic science discoveries, thus attesting to the current scientific and clinical interest in this area."