With the completion of sequencing projects and the advancement of a- lytical tools for protein identification, proteomics-the study of the expressed part of the genome-has become a major region of the burgeoning field of functional genomics. High-resolution 2-D gels can reveal virtually all p- teins present in a cell or tissue at any given time, including posttranslationally modified proteins. Changes in the expression and structure of most cellular proteins caused by differentiation or external stimuli can be displayed and eventually identified using 2-D protein gels. 2-D Proteome Analysis Protocols covers all aspects of the use of 2-D protein electrophoresis for the analysis of biological problems. The contri- tors include many of the leaders in the fields of biochemistry and analytical chemistry who were instrumental in the development of high-resolution 2-D gels, immobilized pH gradients, computer analysis, and mass spectromet- based protein identification methodologies. This book is intended as a benchtop manual and guide both for novices to 2-D gels and for those aficionados who wish to try the newer techniques. Any group using protein biochemistry-especially in the fields of molecular biology, biochemistry, microbiology, and cell biology-should find this book eminently useful. 2-D Proteome Analysis Protocols takes the researcher through the c- plete process of working with 2-D protein gels from making the protein - tract to finally identifying the proteins of interest. It includes protocols for generating 2-D protein extracts from most of the standard model organisms, including bacteria, yeast, nematode, Drosophila, plants, mouse, and human.

Non-vesicular intracellular cholesterol transport is an important mechanism for maintaining membrane cholesterol homeostasis. Recent reports of studies directed at soluble cholesterol transport proteins indicate that aberrant expression of the START proteins may contribute to disease states associated with disorders in cholesterol homeostasis. This is an exciting new direction in the field and the purpose of this book will be to highlight the current research directed at potential roles for the START family in diabetes, cancer, and atherogenesis. This book also provides a personal and historical perspective of the discovery-to-publication journey that the authors had for their particular START domain family member. The goal will be to provide perspectives to graduate students, post-doctoral fellows, and endocrinology fellows on the research discovery process.

In an ever-increasing domain of activity Amino Acids Peptides and Proteins provides an annual compilation of the world's research effort into this important area of biological chemistry. Volume 29 provides a review of literature published during 1996. Comprising a comprehensive review of significant developments at this biology/chemistry interface each volume opens with an overview of amino acids and their applications. Work on peptides is reviewed over several chapters ranging from current trends in their synthesis and conformational and structural analysis to peptidomimetics and the discovery of peptide-related molecules in nature. The application of advanced techniques in structural elucidation is incorporated into all chapters whilst periodic chapters on metal complexes of amino acids, peptides and beta-lactams extend the scope of coverage. Efficient searching of specialist topics is facilitated by the sub-division of chapters into discrete subject areas allowing annual trends to be monitored. All researchers in the pharmaceutical and allied industries and at the biology/chemistry interface in academia will find this an indispensable reference source.

The breadth of modern biology is characterized by a comprehension of phenomena at many levels of organization. Such levels of understanding range from the organismal to the molecular. It is when all these levels can be discussed together that a sense of true achievement begins to be felt. The topical area of fatty acid transport and metabolism was the focus of the Third International Conference on Lipid-Binding Proteins held at the University of Minnesota in May 1997. This volume contains a sampling of the proceedings of this meeting.

This book provides an overview of the biology and biochemistry of peroxisomes, and discusses the contribution of these organelles to peroxisomal and neurodegenerative diseases. It begins with a detailed introduction to the biogenesis and metabolic functions of peroxisomes, and highlights their role in oxidative stress and in lipid metabolism such as fatty acid oxidation. The following chapters focus on the molecular and clinical aspects of peroxisomal disorders caused by defects in peroxisomal function. In particular, the biological aspects of peroxisomal biogenesis disorders such as Zellweger syndrome and Heimler syndrome are discussed. This includes their underlying genetic causes as well as the biochemical and metabolic defects associated with the disorders. In addition, several chapters cover recent observations suggesting an association between peroxisomal dysfunction and neurodegenerative diseases such as Alzheimer's, Multiple Sclerosis and other degenerative cerebellar pathologies. The final section of the book discusses important cell and animal models for studying the role of peroxisomes in human diseases and presents current therapeutic strategies for their treatment. This book deals with a highly topical subject that is at the heart of current research, and represents a valuable contribution for all students and researchers who want to understand the complex biology of peroxisomes and their role in human diseases.

This volume brings together cutting-edge laboratory protocols to characterize the novel fluorescent proteins (FPs) and approaches based on fluorescent proteins that aim to answer some of the key cell biological questions. The book covers topics ranging from the database of fluorescent proteins to their characterization and adaptation to a wide range of biological systems. 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 and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Fluorescent Proteins: Methods and Protocols serves as an ideal guide for students and academicians enthusiastic about the recent progress in the practical application of fluorescent protein technology.

This highly authoritative volume highlights the remarkable superfamily of molecular motors called myosins, which are involved in such diverse cellular functions as muscle contraction, intracellular transport, cell migration and cell division. In a timely compilation of chapters written by leading research groups that have made key discoveries in the field, the current understanding of the molecular mechanisms and biological functions of these intriguing proteins is explored.

This volume provides a state-of-the-art update on Fc Receptors (FcRs). It is divided into five parts. Part I, Old and New FcRs, deals with the long-sought-after FcR and the recently discovered FCRL family and TRIM21. Part II, FcR Signaling, presents a computational model of Fc RI signaling, novel calcium channels, and the lipid phosphatase SHIP1. Part III, FcR Biology, addresses major physiological functions of FcRs, their glycosylation, how they induce and regulate both adaptive immune responses and inflammation, especially in vivo, FcR humanized mice, and the multifaceted properties of FcRn. Part IV, FcRs and Disease, discusses FcR polymorphism, FcRs in rheumatoid arthritis and whether their FcRs make macaques good models for studying HIV infection. In Part V, FcRs and Therapeutic Antibodies, the roles of various FcRs, including Fc RIIB and Fc RI, in the immunotherapy of cancer and autoimmune diseases using monoclonal antibodies and IVIg are highlighted. All 18 chapters were written by respected experts in their fields, offering an invaluable reference source for scientists and clinicians interested in FcRs and how to better master antibodies for therapeutic purposes.

This book is devoted to the fascinating superfamily of plant ATP-binding cassette (ABC) transporters and their variety of transported substrates. It highlights their exciting biological functions, covering aspects ranging from cellular detoxification, through development, to symbiosis and defense. Moreover, it also includes a number of chapters that center on ABC transporters from non-Arabidopsis species.

ABC proteins are ubiquitous, membrane-intrinsic transporters that catalyze the primary (ATP-dependent) movement of their substrates through biological membranes. Initially identified as an essential aspect of a vacuolar detoxification process, genetic work in the last decade has revealed an unexpectedly diverse variety of ABC transporter substrates, which include not only xenobiotic conjugates, but also heavy metals, lipids, terpenoids, lignols, alkaloids and organic acids.

The discovery that members of the ABCB and ABCG family are involved in the movement of phytohormones has further sparked their exploration and provided a new understanding of the whole family. Accordingly, the trafficking, regulation and structure-function of ABCB-type auxin transporters are especially emphasized in this book.

Colorectal cancer has for more than two decades served as the paradigm for the multi-step concept of cancer initiation and progression. Perhaps more than any other organ site, cancer of the colon is extensively characterized at the molecular level. We are now entering a time when molecular classification, rather than histologic classification, of cancer subtypes is driving the development of clinical trials with emerging targeted therapies. The book will focus on the progression from the identification of mutations that drive colorectal cancer initiation and progression to the search for novel therapies to treat the disease.

Plant Proteomics highlights rapid progress in this field, with emphasis on recent work in model plant species, sub-cellular organelles, and specific aspects of the plant life cycle such as signaling, reproduction and stress physiology. Several chapters present a detailed look at diverse integrated approaches, including advanced proteomic techniques combined with functional genomics, bioinformatics, metabolomics and molecular cell biology, making this book a valuable resource for a broad spectrum of readers.

This detailed volume explores newly-developed methods in PIWI-interacting RNAs (piRNAs) research, methods currently applied to other ncRNAs involved in nuclear regulation which can be used to study piRNAs, and piRNA methods applied in non-classical organisms. It also includes several bioinformatic and biophysical methods related to piRNA studies, consistent with the increasing importance of high-throughput sequencing and computational methods. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, piRNA: Methods and Protocols serves as an ideal guide for researchers seeking to elucidate the numerous mysteries of this area of multicellular biology.

This volume provides an overview on the influence of Extracellular Matrix (ECM) on tumor progression. It covers topics such as signaling induced by structural ECM proteins including collagen and fibronectin, the control of ECM deposition and the turnover in tumors. Also discussed are the migration of cells through basement membranes and the function of proteoglycans including lumican and veriscan in tumor progression. Biomaterial-based in-vitro models as well as C. elegans models of the tumor microenvironment are used to show how these models can lead to a greater understanding of the disease mechanisms that promote cancer progression. The book addresses researchers working on cancer biology or ECM, and oncologists alike.

The mucins (mucus glycoproteins) have long been a complex corner of glycoprotein biology. While dramatic advances in the separation, structural an- ysis, biosynthesis, and degradation have marked the progress in general glycop- tein understanding, the mucins have lagged behind. The reasons for this lack of progress have always been clear and are only now being resolved. The mucins are very large molecules; they are difficult to separate from other molecules present in mucosal secretions or membranes; they are often degraded owing to natural protective functions or to isolation methodology and their peptide and oligos- charide structures are varied and complex. Understanding these molecules has demanded progress in several major areas. Isolation techniques that protect the intact mucins and allow dissociation from other adsorbed but discrete molecules needed to be developed and accepted by all researchers in the field. Improved methods for the study of very large molecules with regard to their aggregation and polymerization were also needed. Structural analysis of the peptide domains and the multitude of oligosaccharide chains was required for smaller sample sizes, for multiple samples, and in shorter time. In view of these problems it is perhaps not surprising that the mucins have remained a dilemma, of obvious biological importance and interest, but very difficult to analyze.

Transmissible spongiform encephalopathies (TSE), known as prion diseases, have been recognized for nearly 300 years in animals and almost 100 years in humans. Modern studies, including the protein-misfolding cyclic amplification (PMCA), have greatly advanced our understanding of the pathogenesis of prion diseases and facilitated the identification of new prion diseases in animals and humans. In the second edition of Prions and Diseases, more than 60 leading researchers and clinicians worldwide provide an up-to-date discussion of these unique infectious pathogens and their associated diseases. The book provides up-to-date knowledge about the etiology, pathogenesis, classification, histopathological, and clinical aspects of the full range of animal and human prion diseases. As a result, the book contains by far the most authoritative views about the past, present, and future of prions and prion diseases. The new second edition covers such important emerging topics such as inherited human prion disease, stem-cell models in prion research, human prion disease surveillance, and gene therapy strategies.

This volume explores the latest methods used to study various aspects of TET proteins and their biology. Chapters in this book are divided into five parts. Part One describes technologies aimed at detecting and quantifying DNA methylation turnover using massively parallel sequencing, ELISA, and mass spectrometry approaches. Part Two looks at data analyses protocols for distinguishing acting versus passive DNA demethylation and estimation of 5mC and 5hmC levels. Part Three deals with a new topic that takes advantage of modified CRISPR/Cas9 genome editing systems to target DNA demethylation activity to genomic loci of interest. Part Four discusses protocols that detail how to purify TET proteins and unravel their protein interactions, and Part Five looks at the assessment of TET protein function and activity in vivo and in vitro. 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, TET Proteins and DNA Demethylation: Methods and Protocols is a valuable resource that aims to help research scientists at all levels working in the fields of DNA demethylation dynamics. Chapters 3, 7 and 17 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This book offers an authoritative review of biopharmaceuticals and their clinical relevance. Biopharmaceuticals have been showing high therapeutic potential by means of biological and biosimilar medicines, particularly for the treatment of cancer, chronic diseases (e.g. diabetes, Crohn's disease, psoriasis and rheumatoid arthritis), neurodegenerative disorders (e.g. multiple sclerosis), and they have also been contributing to the progress of innovative therapies such as assisted reproductive medicine. Since the eighties, several biopharmaceuticals have been approved and, due to patents expiration, many biosimilars are also marketed. In this book, readers will find the most relevant updated information about the main clinical applications of pharmaceutical biotechnology. The authors provide expert analysis about the industrial challenges of recombinant proteins and the different classes of biopharmaceuticals, including monoclonal antibodies, vaccines, growth factors and stem cells. Topics such as bioprinting technologies in tissue engineering, gene therapy and personalized medicine are also covered in this book. Professionals, students and researchers interested in this field will find this work an important account.

This book examines detailed experimental and computational approaches for the analysis of many aspects vital to the understanding of membrane protein structure and function. Readers will receive guidance on the selection and use of methods for over-expression and purification, tools to characterize membrane proteins within different phospholipid bilayers, direction on functional studies, and approaches to determine the structures of membrane proteins. Detailed experimental steps for specific membrane proteins with critical notes allow the protocols to be modified to different systems. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of practical information and implementation advice that leads to excellent, reproducible results. Authoritative and up-to-date, Structure and Function Studies of Membrane Proteins serves as an ideal guide for biologists, biochemists, and biophysicists striving to further understand these essential proteins and their many biological roles.

Throughout the more than 20 years that have followed the beginnings of capillary electrophoresis (CE), its application to the analysis of proteins and peptides has continued to be reliable, versatile, and productive. Over time, CE has matured to become a superb complement to HLPC, and in many cases has also evolved as an automated and quantitative replacement for conventional slab gel electrophoresis methods such as SDS-PAGE and isoelectric focusing. Within Capillary Electrophoresis of Proteins and Peptides, we have assembled contributions from researchers who are applying state-of-the-art CE for protein and peptide analysis, including topics that we believe are of great potential both in the present and for the future. In comparison to traditional separation methods, CE represents a miniaturized analysis technique (especially in its microchip-based format) that is highly dependent upon the basic fundamentals of effective sample recovery and high sensitivity detection. With these issues in mind, Chapters 1-4 describe recently developed approaches for both capillary coatings and analyte detection via laser-induced fluorescence. Since the discipline of biotechnology has established itself as a primary platform for the application of CE to the analysis of proteins and peptides, Chapters 5-7 demonstrate a variety of examples of the specific techniques that have been applied for the development of biopharmaceuticals and their commercialization. The methods covered here include also the analysis of oligosaccharides from glycoproteins.

The importance of polyamines for all living cells has been recognized since spermine was discovered in human semen more than 300 years ago. Polyamine research intensified when analytical methods were developed for their determination, particularly in tissues and biological fluids. Discovering their close correlation with cancer, and that polyamine concentrations change during the cell cycle, gave reason for further research in this topic. Polyamines in Health and Nutrition concentrates on the direction of polyamine research which has the capacity to influence and benefit our health and which can explain some of the discrepancies and failures of earlier research. It is important to recognize the dietary contribution to the polyamine body pool and to investigate how the polyamine content of the diet can be changed, with the ultimate aim of using this information to improve our health.

The development of new methodologies has played a key role in the advancement of all areas of research. Specifically, the initial advances in our understanding of lipoprotein structure and metabolism were made possible by the development of ultracentrifugation and electrophoretic techniques. More recently, the advent of molecular biological techniques opened possibilities that were unthinkable just a few decades ago. The use of the analytical ult- centrifuge to study plasma lipoproteins began in the 1940s with the work of Mutzenbecher, McFarlene, Pedersen, Gofman, Lindgren, and Elliot. Another crucial step, during the 1950s, was the development of this tool as a prepa- tive technique by Havel, Eder, and Bragdon, among others. This technolo- cal progress allowed investigators to "dig" deeper into the structure of these complex macromolecules made of lipids and proteins, and permitted inves- gators to continue unraveling the physical and chemical characteristics of the proteins associated with lipoprotein particles (apolipoproteins) and the enzymes involved in their processing. This information led to both a better understanding of the biological functions of the lipoprotein fractions and their constituents, and creation of a more comprehensive overall scheme for plasma lipoprotein metabolism. Several gaps in this puzzle were filled through the work of Goldstein and Brown, who elucidated the structure and role of the low-density lipoprotein - ceptor. This was the first identified among a profusion of receptors that are key for the cellular catabolism of these particles.

"This volume explores numerous techniques used to study the ubiquitin proteasome system. The chapters in this book are organized into five parts and cover topics such as determining the mechanisms of action for E2s, E3s, and DUB enzymes; the latest advances to study the formation of poly-ubiquitin chains as well as their linkage types; the binding partners of proteins in the UPS; methods for structure determination by x-ray crystallography, cryo electron microscopy and SAXS; screening assays to select for degrons or modulators of E3s and DUBs; proteomics approaches in the ubiquitin field and methods to study 26S proteasome function. 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 authoritative, The Ubiquitin Proteasome System: Methods and Protocols is a valuable resource for both experienced and novice scientists who are interested in expanding their knowledge in this field.

Upon completion of the human genome project over 800 G protein-coupled receptor 1 (GPCR) genes, subdivided into five categories, were identified. These receptors sense a diverse array of stimuli, including peptides, ions, lipid analogues, light and odour, in a discriminating fashion. Subsequently, they transduce a signal from the ligand-receptor complex into numerous cellular responses. The importance of GPCRs is further reflected in the fact that they constitute the most common target for therapeutic drugs across a 2 wide range of human disorders. Phylogenetic analysis of GPCRs produced the GRAFS classification system, which subdivides GPCRs into five discrete families: glutamate, rhodopsin, adhesion, frizzled/taste2 and secretin receptors. The adhesion-GPCR family 2 can be further subdivided into eight groups. The field of adhesion-GPCR biology has indeed become large enough to require a volume dedicated solely to this field. The contributors to this book have made a courageous effort to address the key concepts of adhesion-GPCR biology, including the evolution and biochemistry of adhesion-GPCRs; there are extensive discussions on the functional nature of these receptors during development, the immune response and tumourgenesis. Finally, there are chapters dedicated to adhesion-GPCR signalling, an area of intense investigation.

"Bioinformatics of Human Proteomics" discusses the development of methods, techniques and applications in the field of protein bioinformatics, an important direction in bioinformatics. It collects contributions from expert researchers in order to provide a practical guide to this complex field of study. The book covers the protein interaction network, drug discovery and development, the relationship between translational medicine and bioinformatics, and advances in proteomic methods, while also demonstrating important bioinformatics tools and methods available today for protein analysis, interpretation and predication. It is intended for experts or senior researchers in the fields of clinical research-related biostatistics, bioinformatics, computational biology, medicine, statistics, system biology, molecular diagnostics, biomarkers, or drug discovery and development. Dr.Xiangdong Wang works as a distinguished professor of Respiratory Medicine at Fudan University, Shanghai, China. He serves as Director of Biomedical Research Center, Fudan University Zhongshan Hospital and adjunct professor of Clinical Bioinformatics at Lund University, Sweden. His main research is focused on the role of clinical bioinformatics in the development of disease-specific biomarkers and dynamic network biomarkers, the molecular mechanism of organ dysfunction and potential therapies.

A prerequisite for elucidating the structure and function of any protein is the prior purification of that protein. This necessity has led to the development of many purification schemes and chromatographic methods for the isolation of native proteins from complex sources. In Protein Chromatography: Methods and Protocols, leading researchers present clear protocol-style chapters that are suitable for newcomers and experts alike. The book opens with vital topics in protein biochemistry, addressing such areas as protein stability and storage, avoiding proteolysis during chromatography, protein quantitation methods including immuno-qPCR, and the contrasting challenges that microfluidics and scale-up production pose to the investigator, and then it segues into key methods involving the generation and purification of recombinant proteins through recombinant antibody production and the tagging of proteins, amongst other means, as well as many variations on classic techniques such as ion-exchange and immunoaffinity chromatography. Written in the highly successful Methods in Molecular Biology (TM) series format, protocols chapters include introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Protein Chromatography: Methods and Protocols will greatly aid scientists in establishing these essential techniques in their own laboratories and furthering our understanding of the many imperative functions of proteins.