The second edition of Adhesion Protein Protocols combines traditional techniques with cutting-edge and novel techniques that can be adapted easily to different molecules and cell types. The topics discussed include novel techniques for studying cell-cell adhesion, neutrophil chemotaxis, in vitro assays used to study leukocyte migration through monolayers of cultured endothelial cells, and novel techniques to purify pseudopodia from migratory cells. The protocols discussed in this volume are suitable for both novice and expert scientists, who will gain further insight into the complex and incompletely understood processes involved in cellular adhesion.
Adhesion molecules are of fundamental importance in the regulation of immunity, inflammation, tissue remodeling, and embryonic development. They comprise different families of homologous proteins, such as selectins, integrins, cadherins, and immunoglobins. In addition, beyond these groups, other str- tures with adhesive properties, such as proteoglycans, occludin, and CD44, have been characterized recently. An understanding of the type and characteristics of adhesive molecules expressed by the different cell types and the possibility of manipulating their activity promises considerable clinical potential. Antibodies, small peptidic and nonpeptidic molecules, have recently been used to inhibit thrombosis by blocking platelet aggregation or inflammation through inhibition of leukocyte infiltration and adhesion. Inhibitors of adhesive molecules are used in expe- mental systems for the study of tumor growth and dissemination. Among major goals in the field are the identification of new members of the known adhesive protein families and of independent new adhesive structures. After structural characterization, even more demanding is the study of the biological activity of the new proteins, and the development of simple, rapid tests for the screening of possible inhibitors. In this regard, the production of such reagents as fragments and antibodies would help define the structure–function relati- ship of individual proteins. Data available in the literature show the complexity of the adhesive process and how different molecular epitopes might contribute to the adhesive properties of a single structure. Finally, a new area of investi- tion is the characterization of the intracellular signaling cascade triggered by the engagement of transmembrane adhesive proteins.
This volume details the importance of multiple experimental techniques and computational methods needed to obtain the comprehensive picture of protein complex structure, dynamics and assembly afforded by the emerging field of integrative structural biology. Chapters guide readers through the broad spectrum of approaches required for a complete representation of protein complexes, including expression and purification, experimental characterization of structure and assembly, and computational methods for identifying protein complexes and modelling their assembly. 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, Protein Complex Assembly: Methods and Protocols aims to ensure successful results in the further study of this vital field.
This volume provides the most cutting edge technologies related to the study of integrin activation and the characterization of their vast interactomes. Chapters detail protocols on experimental approached to quantify focal adhesion parameters, integrin activation, and the lateral interaction of integrins with transmembrane binding partners. 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, The Integrin Interactome: Methods and Protocols aims to give the reader a multi-scale journey from single bonds inside protein structures to the function of these crucial adhesion receptors at a whole organism level in physiology and pathology.
Computers have become an essential component of modern biology. They help to manage the vast and increasing amount of biological data and continue to play an integral role in the discovery of new biological relationships. This in silico approach to biology has helped to reshape the modern biological sciences. With the biological revolution now among us, it is imperative that each scientist develop and hone today’s bioinformatics skills, if only at a rudimentary level. Bioinformatics Methods and Protocols was conceived as part of the Methods in Molecular Biology series to meet this challenge and to provide the experienced user with useful tips and an up-to-date overview of current developments. It builds upon the foundation that was provided in the two-volume set published in 1994 entitled Computer Analysis of Sequence Data. We divided Bioinformatics Methods and Protocols into five parts, including a thorough survey of the basic sequence analysis software packages that are available at most institutions, as well as the design and implemen- tion of an essential introductory Bioinformatics course. In addition, we included sections describing specialized noncommercial software, databases, and other resources available as part of the World Wide Web and a stimul- ing discussion of some of the computational challenges biologists now face and likely future solutions.
In this new volume, renowned authors contribute fascinating, cutting-edge insights into microarray data analysis. Information on an array of topics is included in this innovative book including in-depth insights into presentations of genomic signal processing. Also detailed is the use of tiling arrays for large genomes analysis. The protocols follow the successful Methods in Molecular BiologyTM series format, offering step-by-step instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding pitfalls.
As researchers continue to make enormous progress in mapping disease genes, exciting, novel, and complex analyses have emerged. In this book, scientists from around the world, who are leaders in this field, contribute their vast experience and expertise to produce a comprehensive and fascinating text for researchers and clinicians alike. They provide cutting-edge analysis of the most up-to-date and preeminent information available.
Developmental biology is one of the most exciting and fast-growing fields today. In part, this is so because the subject matter deals with the innately fascinating biological events—changes in form, structure, and function of the org- ism. The other reason for much of the excitement in developmental biology is that the field has truly become the unifying melting pot of biology, and provides a framework that integrates anatomy, physiology, genetics, biochemistry, and cellular and mole- lar biology, as well as evolutionary biology. No longer is the study of embryonic development merely “embryology.” In fact, development biology has produced - portant paradigms for both basic and clinical biomedical sciences alike. Although modern developmental biology has its roots in “experimental emb- ology” and the even more classical “chemical embryology,” the recent explosive and remarkable advances in developmental biology are critically linked to the advent of the “cellular and molecular biology revolution.” The impressive arsenal of expe- mental and analytical tools derived from cell and molecular biology, which promise to continue to expand, together with the exponentially developing sophistication in fu- tional imaging and information technologies, guarantee that the study of the devel- ing embryo will contribute one of the most captivating areas of biological research in the next millennium.
Glycobiology involves studies of complex carbohydrates and posttrans- tional modifications of proteins, and has become an important interdiscip- nary field encompassing chemistry, biochemistry, biology, physiology, and pathology. Although initial research was directed toward elucidation of the different carbohydrate structures and the enzymes synthesizing them, the field has now moved toward identifying the functions of carbohydrates. The pro- cols described in Glycobiology Protocols form a solid basis for investigations of glycan functions in health and disease. The cloning of many of the genes participating in glycosylation processes has helped to enhance our knowledge of how glycosylation is controlled, but has also added another dimension of complexity to the great heterogeneous variety of the structures of the oligos- charides of glycoproteins, proteoglycans, and glycolipids. A family of similar enzyme proteins exists for each glycosylation step. Glycosyltransferases are extremely specific for both the nucleotide sugar donor and the acceptor s- strate, but many other factors control sugar transfer, including the locali- tion and topology of enzymes, cofactors, possible chaperone proteins, and the availability of sugar acceptor substrates. The analysis of the intracellular organization of glycosylation and of the factors controlling the activities of the participating enzymes in the cell are important areas that need more research efforts. Another challenge for future research is to understand the glycodynamics of a cell, that is, how the cell responds to stimuli leading to biological and pathological changes in terms of alterations in glycosylation, and how this affects the biology of the cell.
The purpose of Calpain Methods and Protocols is quite straightf- ward: it is to present the actual experimental methods used in many different laboratories for the study of calpain. It will provide the vital experimental detail, and the discussion of possible pitfalls, for which the standard journals no longer provide space. This will make it as easy as possible for investi- tors interested in calpain to adopt established methods without repeating old mistakes, and to adapt and apply these methods in novel approaches to the many outstanding calpain questions. These questions range from purely biochemical problems of protein structure and enzyme regulation at the molecular level, through large areas of cell biology, to applied and clinical aspects of calpain function in human d- ease. Within this panoply of topics, a wide range of investigators will find many fascinating and as yet unanswered questions about calpain. Calpain Methods and Protocols will provide instant access to many essential te- niques, while saving them the time and effort involved in developing a new method. In addition to questions relating to the normal physiological roles of the calpains, there is considerable evidence that inappropriate calpain activity may have pathological effects in many tissues, for example, following ischemia. This provides a major stimulus for the development of specific calpain inhi- tors for therapeutic purposes, and for the development of methods to evaluate such inhibitors.
