"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.

Starting from a comprehensive quantum mechanical description, this book introduces the optical (IR, Raman, UV/Vis, CD, fluorescence and laser spectroscopy) and magnetic resonance (1D and 2D-NMR, ESR) techniques. The book offers a timely review of the increasing interest in using spin-label ESR as an alternative structural technique for NMR or X-ray diffraction. Future aspects are treated as well, but only as an illustration of the progress of ESR in this field.

Proteomics is a multifaceted, interdisciplinary field which studies the complexity and dynamics of proteins in biological systems. It combines powerful separation and analytical technology with advanced informatics to understand the function of proteins in the cell and in the body. This book provides a clear conceptual description of each facet of proteomics, describes recent advances in technology and thinking in each area, and provides details of how these have been applied to a variety of biological problems. It is written by expert practitioners in the field, from industry, research institutions, and the clinic. It provides junior and experienced researchers with an invaluable proteomic reference, and gives fascinating glimpses of the future of this dynamic field.

Omics is an emerging and exciting area in the field of science and medicine. Numerous promising developments have been elucidated using omics (including genomics, transcriptomics, epigenomics, proteomics, metabolomics, interactomics, cytomics and bioinformatics) in cancer research. The development of high-throughput technologies that permit the solution of deciphering cancer from higher dimensionality will provide a knowledge base which changes the face of cancer understanding and therapeutics. This is the first book to provide such a comprehensive coverage of a rapidly evolving area written by leading experts in the field of omics. It complies and details cutting-edge cancer research that covers the broad advances in the field and its application from cancer-associated gene discovery to drug target validation. It also highlights the potential of using integration approach for cancer research. This unique and timely book provides a thorough overview of developing omics, which will appeal to anyone involved in cancer research. It will be a useful reference book for graduate students of different subjects (medicine, biology, engineering, etc) and senior scientists interested in the fascinating area of advanced technologies in cancer research. Readership: This is a precious book for all types of readers - cancer researchers, oncologists, pathologists, biologists, clinical chemists, pharmacologists, pharmaceutical specialists, biostatisticians, and bioinformaticists who want to expand their knowledge in cancer research.

The last 15 years in development of biology were marked with accumulation of unprecedentedly huge arrays of experimental data. The information was amassed with exclusively high rates due to the advent of highly efficient experimental technologies that provided for high throughput genomic sequencing; of functional genomics technologies allowing investigation of expression dynamics of large groups of genes using expression DNA chips; of proteomics methods giving the possibility to analyze protein compositions of cells, tissues, and organs, assess the dynamics of the cell proteome, and reconstruct the networks of protein-protein interactions; and of metabolomics, in particular, high resolution mass spectrometry study of cell metabolites, and distribution of metabolic fluxes in the cells with a concurrent investigation of the dynamics of thousands metabolites in an individual cell. Analysis, comprehension, and use of the tremendous volumes of experimental data reflecting the intricate processes underlying the functioning of molecular genetic systems are unfeasible in principle without the systems approach and involvement of the state-of-the-art information and computer technologies and efficient mathematical methods for data analysis and simulation of biological systems and processes. The need in solving these problems initiated the birth of a new science- postgenomic bioinformatics or systems biology in silico.

Gabriel Waksman Institute of Structural Molecular Biology, Birkbeck and University College London, Malet Street, London WC1E 7HX, United Kingdom Address for correspondence: Professor Gabriel Waksman Institute of Structural Molecular Biology Birkbeck and University College London Malet Street London WC1E 7H United Kingdom Email: g. waksman@bbk. ac. uk and g. waksman@ucl. ac. uk Phone: (+44) (0) 207 631 6833 Fax: (+44) (0) 207 631 6833 URL: http://people. cryst. bbk. ac. uk/?ubcg54a Gabriel Waksman is Professor of Structural Molecular Biology at the Institute of Structural Molecular Biology at UCL/Birkbeck, of which he is also the director. Before joining the faculty of UCL and Birkbeck, he was the Roy and Diana Vagelos Professor of Biochemistry and Molecular Biophysics at the Washington University School of Medicine in St Louis (USA). The rapidly evolving ?eld of protein science has now come to realize the ubiquity and importance of protein-protein interactions. It had been known for some time that proteins may interact with each other to form functional complexes, but it was thought to be the property of only a handful of key proteins. However, with the advent of hi- throughput proteomics to monitor protein-protein interactions at an organism level, we can now safely state that protein-protein interactions are the norm and not the exception.

The American Peptide Society (APS) provides a forum for advancing and promoting knowledge of the chemistry and biology of peptides. The approximately one thousand members of the Society come from North America and from more than thirty other countries throughout the world. Establishment of the APS was a result of the rapid worldwide growth that has occurred in peptide-related research, and of the increasing interaction of peptide scientists with virtually all fields of science. Peptides for Youth: The Proceedings of the the 20th American Peptide Symposium will highlight many of the recent developments in peptide science, with a particular emphasis on how these advances are being applied to basic problems in biology and medicine. The 20th American Peptide Symposium will take place June 26 - 30, 2007 in Montreal, Canada.

Whole new areas of immunological research are emerging from the analysis of experimental data, going beyond statistics and parameter estimation into what an applied mathematician would recognise as modelling of dynamical systems. Stochastic methods are increasingly important, because stochastic models are closer to the Brownian reality of the cellular and sub-cellular world.

This volume presents a review of the latest numerical techniques used to identify ligand binding and protein complexation sites. It should be noted that there are many other theoretical studies devoted to predicting the activity of specific proteins and that useful protein data can be found in numerous databases. The aim of advanced computational techniques is to identify the active sites in specific proteins and moreover to suggest a generalized mechanism by which such protein-ligand (or protein-protein) interactions can be effected. Developing such tools is not an easy task - it requires extensive expertise in the area of molecular biology as well as a firm grasp of numerical modeling methods. Thus, it is often viewed as a prime candidate for interdisciplinary research.

Microbial infection is increasingly seen as a problem as we begin to run out of antibiotics. Understanding how microbes cause disease is essential. In recent years it has begun to emerge that bacteria, fungi, protozoa and viruses can use their cell stress proteins to cause infection. This volume brings together the world's leading experts in the study of the microbial and human cell stress proteins that are involved in enabling microorganisms to infect humans and cause serious disease.

Physics, mathematics and chemistry all play a vital role in understanding the true nature and functioning of biological membranes, key elements of living processes. Besides simple spectroscopic observations and electrical measurements of membranes we address in this book the phenomena of coexistence and independent existence of different membrane components using various theoretical approaches. This treatment will be helpful for readers who want to understand biological processes by applying both simple observations and fundamental scientific analysis. It provides a deep understanding of the causes and effects of processes inside membranes, and will thus eventually open new doors for high-level pharmaceutical approaches towards fighting membrane- and cell-related diseases.

High-fidelity chromosomal DNA replication underpins all life on the planet. In humans, there are clear links between chromosome replication defects and genome instability, genetic disease and cancer, making a detailed understanding of the molecular mechanisms of genome duplication vital for future advances in diagnosis and treatment. Building on recent exciting advances in protein structure determination, the book will take the reader on a guided journey through the intricate molecular machinery of eukaryotic chromosome replication and provide an invaluable source of information, ideas and inspiration for all those with an interest in chromosome replication, whether from a basic science, translational biology and medical research perspective.

21st Century Kinematics focuses on algebraic problems in the analysis and synthesis of mechanisms and robots, compliant mechanisms, cable-driven systems and protein kinematics. The specialist contributors provide the background for a series of presentations at the 2012 NSF Workshop. The text shows how the analysis and design of innovative mechanical systems yield increasingly complex systems of polynomials, characteristic of those systems. In doing so, it takes advantage of increasingly sophisticated computational tools developed for numerical algebraic geometry and demonstrates the now routine derivation of polynomial systems dwarfing the landmark problems of even the recent past. The 21st Century Kinematics workshop echoes the NSF-supported 1963 Yale Mechanisms Teachers Conference that taught a generation of university educators the fundamental principles of kinematic theory. As such these proceedings will provide admirable supporting theory for a graduate course in modern kinematics and should be of considerable interest to researchers in mechanical design, robotics or protein kinematics or who have a broader interest in algebraic geometry and its applications.

In multicellular organisms, communication between cells involves secretion of proteins that bind to receptors on neighboring cells. While this has been well documented, another mode of intercellular communication has recently become the subject of increasing interest: the release of exosomes. In cancer, tumor exosomes are involved in various aspects of pathogenesis, including proliferation, immunosuppression, and metastasis. Given the ability of exosomes to export unneeded endogenous molecules from cells, these structures hold great potential as anticancer therapeutic agents. They are also being studied as prognostic markers for cancer.

Mitochondria and chloroplasts are eukaryotic organelles that evolved from bacterial ancestors and harbor their own genomes. The gene products of these genomes work in concert with those of the nuclear genome to ensure proper organelle metabolism and biogenesis. This book explores the forces that have shaped the evolution of organelle genomes and the expression of the genes encoded by them. Some striking examples of trends in organelle evolution explored here are the reduction in genome size and gene coding content observed in most lineages, the complete loss of organelle DNA in certain lineages, and the unusual modes of gene expression that have emerged, such as the extensive and essential mRNA editing that occurs in plant mitochondria and chloroplasts. This book places particular emphasis on the current techniques used to study the evolution of organelle genomes and gene expression.

The entire range of the developmental processes in plants is regulated by a shift in the hormonal concentration, tissue sensitivity and their interaction with the factors operating around them. Out of the recognized hormones, attention has largely been focused on five - Auxins, Gibberellins, Cytokinin, Abscisic acid and Ethylene. However, the information about the most recent group of phytohormone (Brassinosteroids) has been incorporated in this book. This volume includes a selection of newly written, integrated, illustrated reviews describing our knowledge of Brassinosteroids and aims to describe them at the present time. Various chapters incorporate both theoretical and practical aspects and may serve as baseline information for future researches through which significant developments are possible. This book will be useful to the students, teachers and researchers, both in universities and research institutes, especially in relation to biological and agricultural sciences.

This thesis presents the first report of the comprehensive and quantitative analysis of the effects of tumor-derived mutations on the tetrameric structure of tumor suppressor protein p53, which plays a central role in maintaining genomic integrity. Inactivation of p53 via mutation of its gene is a key step in tumorigenesis. Biophysical analyses revealed that the stability of the mutant peptides varied widely. Formation of a tetrameric structure is to be critical for protein-protein interactions, DNA binding, and the post-translational modification of p53. A small destabilization of the tetrameric structure therefore could result in dysfunction of tumor suppressor activity. This work suggests that the threshold for loss of tumor suppressor activity, in terms of the disruption of p53's tetrameric structure, could be extremely low. Furthermore, functional control of p53 via tetramer formation was demonstrated, based on the structure-function analysis of mutant p53. The results disclosed that relatively small changes in tetramer formation, induced by the stabilization or inhibition of homo-tetramerization, could control p53 function.

This volume documents this unique family of cell surface proteins. Despite masquerading as intractable and difficult to clone and characterize, ENOX proteins have and continue to offer remarkable opportunities for research, commercial development and outside confirmation of therapeutic, diagnostic and new paradigms to help explain complex biological processes.

Plants have evolved with a complex array of signaling molecules to facilitate their growth and development and their interactions with the environment. A vast number of different peptide molecules form an important but until recently often overlooked component amongst these signaling molecules. Plant peptide signals are involved in regulating meristem growth and organogenesis, modulating plant growth and homeostatic responses. They also have important roles as signals of imminent danger or pathogen attack. This volume focuses on the roles of various peptide signaling molecules in development, defence and homeostasis. As it is likely that further plant peptide signaling molecules remain to be discovered, the last section takes a practical look at methods to identify new peptides and characterise their functions.

Cell-cell adhesion is fundamental for the development and homeostasis of animal tissues and organs. Adherens junctions (AJs) are the best understood cell-cell adhesion complexes. In this volume, a group of internationally recognized experts reviews AJ biology over a wide range of organization; from atoms to molecules, to protein complexes, molecular networks, cells, tissues, and overall animal development. AJs have also been an integral part of animal evolution, and play central roles in cancer development, pathogen infection and other diseases. This book addresses major questions encompassing AJ biology. * How did AJs evolve? * How do cadherins and catenins interact to assemble AJs and mediate adhesion? * How do AJs interface with other cellular machinery to couple adhesion with the whole cell? * How do AJs affect cell behaviour and multicellular development? * How can abnormal AJ activity lead to disease?

Methods in protein sequence analysis constitute important fields in rapid progress. We have experienced a continuous increase in analytical sensitivity coupled with decreases in time necessary for purification and analysis. Several generations of sequencers, liquid/solid/gas-phase, have passed by and returned in other shapes during just over two decades. Similarly, the introduction of HPLC permitted an enormous leap forward in this as in other fields of biochemistry, and we now start to see new major advances in purification/analysis through capillary electrophoresis. Furthermore, progress in the field of mass spectrometry has matched that in chemical analysis and we witness continuous development, now emphasizing ion spray and other mass spectrometric approaches. In short, protein analysis has progressed in line with other developments in modern science and constitutes an indispensable, integral part of present-day molecular biology. Even the available molecular tools, in the form of proteases with different specificities, have increased in number, although we still have far to go to reach an array of "restriction proteases" like the sets of nucleases available to the molecular geneticist. Of course, conferences have been devoted to protein sequence analysis, in particular the MPSA (Methods in Protein Sequence Analysis) series, of which the 8th conference took place in Kiruna, Sweden, July 1-6 1990. Again, we witnessed much progress, saw new instruments, and experienced further interpretational insights into protein mechanisms and functions.

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.

The book contains chapters written by leaders in the research on the structure and function of respiratory complex I. It will provide a concise and authoritative summary of the current knowledge on complex I of respiratory chains. This enzyme is central to energy metabolism and is implicated in many human neurodegenerative diseases, as well as in aging. Until recently it was poorly understood on a structural level, and this book will provide a timely reference resource. Such a book was not published previously. The last time a minireview series on complex I were published was in 2001, and since then complex I field changed quite dramatically.

Six decades after the serendipitous discovery of chlorpromazine as an antipsychotic and four decades after the launch of clozapine, the first atypical or second generation antipsychotic, psychopharmacology has arrived at an important crossroad. It is clear that pharmacological research and pharmaceutical development must now focus on complementary or even alternative mechanisms of action to address unmet medical needs, i.e. poorly treated domains of schizophrenia, improved acceptance by patients, better adherence to medication, safety in psychoses in demented patients, and avoiding cardiac and metabolic adverse effects. The first completely novel mechanisms evolving from our insights into the pathophysiology of psychotic disorders, especially the role of glutamatergic mechanisms in schizophrenia, are now under development, and further principles are on the horizon. This situation, in many respects similar to that when the initial second-generation antipsychotics became available, can be rewarding for all. Preclinical and clinical researchers now have the opportunity to confirm their hypotheses and the pharmaceutical industry may be able to develop really novel classes of therapeutics. When we were approached by the publishers of the Handbook of Experimental Pharmacology to prepare a new volume on antipsychotics, our intention was to capture both, the accumulated preclinical and clinical knowledge about current antipsychotics as well as prospects for new and potentially more specific antischizophrenia principles. These efforts should be based on the pathophysiology of the diseases and the affected neurotransmitter systems. Since preclinical research on antipsychotic compounds is only reliable when intimately linked through translational aspects to clinical results, we decided to include clinical science as well. It turned out that that this endeavor could not be covered by a single volume. We thank the editorial board and the publishers for supporting our decision to prepare two volumes: Current Antipsychotics and Novel Antischizophrenia Treatments. These topics cannot really be separated from one another and should be seen as a composite entity despite the somewhat arbitrary separation of contributions into two volumes. The continuing challenges of developing improved and safer antipsychotic medications remain of concern and are discussed in the first volume. The new opportunities for the field to develop and license adjunctive treatments for the negative symptoms and cognitive deficits that are treated inadequately by existing compounds have been incentivized recently and provide the focus for the second volume. We hope these collective contributions will facilitate the development of improved treatments for the full range of symptomatology seen in the group of schizophrenias and other major psychotic disorders. Gerhard Gross, Ludwigshafen, Germany Mark A. Geyer, La Jolla, CA This volume will try to put current therapy - achievements, shortcomings, remaining medical needs - and emerging new targets into the context of increasing knowledge regarding the genetic and neurodevelopmental contributions to the pathophysiology of schizophrenia. Some of the chapters will also deal with respective experimental and clinical methodology, biomarkers, and translational aspects of drug development. Non-schizophrenia indications will be covered to some extent, but not exhaustively.