Epithelial mucins are large complex cell surface and secreted glycoproteins produced by mucosal epithelial cells. In, Mucins: Methods and Protocols expert researchers in the field detail many of the methods which are now commonly used to study Mucins. These include methods and techniques for the best approaches to analysing each specific area of mucin biochemistry, physiology and biophysics before providing individual detailed experimental protocols together with troubleshooting and interpretation tips. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Mucins: Methods and Protocols is designed to be a useful resource for those entering the mucin field and to facilitate those already studying mucins to broaden their experimental approaches to understanding mucosal biology.

This volume collects new information on the genomics of saprophytic soil Pseudomonas, as well as functions related to genomic islands. It explores life styles in different settings and sheds further insights on the wide metabolic potential of this microbe for the removal of pollutants and production of added-value products. This volume also explores how Pseudomonas responds and reacts to environmental signals, including detection of cell density.

An accurate description of current scientific developments in the field of bioinformatics and computational implementation is presented by research of the BioSapiens Network of Excellence. Bioinformatics is essential for annotating the structure and function of genes, proteins and the analysis of complete genomes and to molecular biology and biochemistry.

Included is an overview of bioinformatics, the full spectrum of genome annotation approaches including; genome analysis and gene prediction, gene regulation analysis and expression, genome variation and QTL analysis, large scale protein annotation of function and structure, annotation and prediction of protein interactions, and the organization and annotation of molecular networks and biochemical pathways. Also covered is a technical framework to organize and represent genome data using the DAS technology and work in the annotation of two large genomic sets: HIV/HCV viral genomes and splicing alternatives potentially encoded in 1% of the human genome.

Humans have been "manually" extracting patterns from data for centuries, but the increasing volume of data in modern times has called for more automatic approaches. Early methods of identifying patterns in data include Bayes' theorem (1700s) and Regression analysis (1800s). The proliferation, ubiquity and incre- ing power of computer technology has increased data collection and storage. As data sets have grown in size and complexity, direct hands-on data analysis has - creasingly been augmented with indirect, automatic data processing. Data mining has been developed as the tool for extracting hidden patterns from data, by using computing power and applying new techniques and methodologies for knowledge discovery. This has been aided by other discoveries in computer science, such as Neural networks, Clustering, Genetic algorithms (1950s), Decision trees (1960s) and Support vector machines (1980s). Data mining commonlyinvolves four classes of tasks: * Classi cation: Arranges the data into prede ned groups. For example, an e-mail program might attempt to classify an e-mail as legitimate or spam. Common algorithmsinclude Nearest neighbor,Naive Bayes classi er and Neural network. * Clustering: Is like classi cation but the groups are not prede ned, so the algorithm will try to group similar items together. * Regression: Attempts to nd a function which models the data with the least error. A common method is to use Genetic Programming. * Association rule learning: Searches for relationships between variables. For example, a supermarket might gather data of what each customer buys.

Trying to address the entire field of presynaptic modulation of neurotransmitter release is a rather daunting undertaking, one that is well beyond the scope of this book. In addition, studies of release modulation, particularly from a biochemical standpoint, have been the subjects of several extensive reviews, meetings, and books (Langer, 1978; Chesselet, 1984; Wessler, 1989; Kalsner and Westfall, 1990), which provide an essential introduction to this subject. What we have focused on, however, are several specific aspects of release modulation that perhaps have not been as extensively discussed. First, we felt that it was important to focus on modulation in the central nervous system; much of the work that has been done in the past has emphasized the peripheral nervous system (e. g. , the autonomic nervous system and the neuromuscular junction), in part because such preparations are more amenable to study. However, it is becoming clear that modulation of release is, if anything, more important in the central nervous system than in the periphery, and that virtually every transmitter system that has been studied shows some type of release modulation. The other way in which we have restricted the scope of this volume has been to try to emphasize studies in which functional (primarily electrophysiological) measures of transmitter release have been used rather than direct biochemical measures of release, and to explore the ways in which release modulation affects the normal physiological function at synapses.

This book outlines three emergent disciplines, which are now poised to engineer a paradigm shift from hypothesis- to data-driven research: theoretical immunology, immunoinformatics, and Artificial Immune Systems. It details how these disciplines will enable new understanding to emerge from the analysis of complex datasets. Coverage shows how these three are set to transform immunological science and the future of health care.

As studies using microarray technology have evolved, so have the data analysis methods used to analyze these experiments. The CAMDA (Critical Assessment of Microarray Data Analysis) conference was the first to establish a forum for a cross section of researchers to look at a common data set and apply innovative analytical techniques to microarray data. Methods of Microarray Analysis V includes selected papers from CAMDA'04, and focuses on data sets relating to a significant global health issue, malaria. Previous books focused on classification (V. I), pattern recognition (V. II), quality control issues (V. III), and associating array data with a survival endpoint, lung cancer, (V. IV). The contributions come from research fields including statistics, biology, computer science and mathematics. Part of the book is devoted to review papers, which provide a more general look at various analytical approaches. It also presents some background readings for the advanced topics discussed in the CAMDA papers.

The many books that have been published on bioinformatics tend toward either of two extremes: those that feature computational details with a great deal of mathematics, for computational scientists and mathematicians; and those that treat bioinformatics as a giant black box, for biologists. This is the first book using comprehensive numerical illustration of mathematical techniques and computational algorithms used in bioinformatics that converts molecular data into organized biological knowledge.

This book brings together contributions from internationally renowned experts in the biochip field. The authors present not only their latest research work, but also discuss current trends in biochip technology. Specific topics range from microarray technology and its applications to lab-on-a-chip technology.

The biological interactions of living organisms, and protein-protein interactions in particular, are astonishingly diverse. This comprehensive book provides a broad, thorough and multidisciplinary coverage of its field. It integrates different approaches from bioinformatics, biochemistry, computational analysis and systems biology to offer the reader a comprehensive global view of the diverse data on protein-protein interactions and protein interaction networks.

Actin is an extremely abundant protein that comprises a dynamic polymeric network present in all eukaryotic cells, known as the actin cytoskeleton. The structure and function of the actin cytoskeleton, which is modulated by a plethora of actin-binding proteins, performs a diverse range of cellular roles. Well-documented functions for actin include: providing the molecular tracks for cytoplasmic streaming and organelle movements; formation of tethers that guide the cell plate to the division site during cytokinesis; creation of honeycomb-like arrays that enmesh and immobilize plastids in unique subcellular patterns; supporting the vesicle traffic and cytoplasmic organization essential for the directional secretory mechanism that underpins tip growth of certain cells; and coordinating the elaborate cytoplasmic responses to extra- and intracellular signals. The previous two decades have witnessed an immense accumulation of data relating to the cellular, biochemical, and molecular aspects of all these fundamental cellular processes. This prompted the editors to put together a diverse collection of topics, contributed by established international experts, related to the plant actin cytoskeleton. Because the actin cytoskeleton impinges on a multitude of processes critical for plant growth and development, as well as for responses to the environment, the book will be invaluable to any researcher, from the advanced undergraduate to the senior investigator, who is interested in these areas of plant cell biology.

This monograph addresses, in a systematic and pedagogical manner, the mathematical methods and the algorithms required to deal with the molecularly based problems of bioinformatics. Prominent attention is given to pair-wise and multiple sequence alignment algorithms, stochastic models of mutations, modulus structure theory and protein configuration analysis. Strong links to the molecular structures of proteins, DNA and other biomolecules and their analyses are developed.

Life is produced by the interplay of water and biomolecules. This book deals with the physicochemical aspects of such life phenomena produced by water and biomolecules, and addresses topics including "Protein Dynamics and Functions", "Protein and DNA Folding", and "Protein Amyloidosis". All sections have been written by internationally recognized front-line researchers. The idea for this book was born at the 5th International Symposium "Water and Biomolecules", held in Nara city, Japan, in 2008.

The initial identification of the Adenomatous polyposis eoli (Ape) gene as the site of mutations in familial adenomatous polyposis (FAP) was described in 1 1992. ,2 A causal relationship between Ape mutations and intestinal tract tumours was confirmed three years later with the establishment ofthe Min mouse model) These mice are heterozygous forApe and develop numerous intestinal tumours that mimic FAP. Subsequently, Ape has emerged as the most commonly mutated gene in colorectal cancerwith reports varying between 50-80% ofsporadic tumours car- rying such mutations. The search for how mutations in Ape initiate and/or support progression oftumours in the intestinal tract has revealed that the Ape protein is a multifunctionalparticipant in a diverse array ofcellular functions. By collecting and assembling the chapters inthisbook, we aimed toprovide an overview of the diverse functions performed by the Ape protein. As summarised in a short final chapter by Trainer,heterozygosityofApe leads to a number ofextracolonic manifestations that further support this emerging picture ofthe Ape protein as an active contributor to many different cellular functions. The first recognised function of Ape was its role in Wnt signalling. o This function is one of the driving forces for how mutations in Ape ensure that cells remain proliferative. Many of the molecular details of this pathway have been discovered and are described in the first chapter by Kennell and Cadigan.

The membranes surrounding cells and organelles constitute their interface with the local environment. The functions of membrane proteins include cell/cell and cell/extracellular matrix recognition, the reception and transduction of extracellular signals, and the tra- port of proteins, solutes and water molecules. Abnormal membrane protein expression has profound biological effects and may, for example, underlie phenotypic and functional differences between normal and tumour cells. Moreover the accessibility, particularly of plasma proteins traversing the plasma membrane of cells, makes them of particular ut- ity to the therapeutic intervention in disease. Indeed, it is estimated that of all currently licensed pharmaceuticals, approximately 70% target proteins resident in the plasma m- brane. In theory, unbiased technologies such as proteomics have the power to de?ne patterns of membrane protein expression characteristic of distinct states of cellular development, differentiation or disease, and thereby identify novel markers of, or targets for intervention in, disease. However, although about 25% of open reading frames in fully sequenced genomes are estimated to encode integral membrane proteins, global analysis of membrane protein expression has proved problematic. Membrane protein analysis poses unique challenges at the level of extraction, solubilization, and separation in particular, and to a lesser extent of identi?cation and quantitation. These challenges have, however, fostered creativity, in- vation, and technical advances, many of which are brought together in Membrane P- teomics.

This is an in-depth guide to the theory and practice of analyzing raw mass spectrometry (MS) data in proteomics. The volume outlines available bioinformatics programs, algorithms, and databases available for MS data analysis. General guidelines for data analysis using search engines such as Mascot, Xtandem, and VEMS are provided, with specific attention to identifying poor quality data and optimizing search parameters.

Recent publications have addressed specific aspects of the endothelins, such as their roles in disease or the importance of endothelin receptors. However, in this book the entire field of endothelins is covered. This includes the pathways of endothelin production and their regulation, the local and systemic actions of endothelins, receptors for the endothelins and the signalling pathways employed, and the involvement of endothelins in a range of diseases. Attention is also paid to the development through chemistry, pharmacology and toxicology of endothelin antagonists and endothelin-converting enzyme inhibitors, with mention of all the important members of these drug classes. This leads to well-rounded discussions of the potential therapeutic benefit of endothelin inhibitors.

Echinostomes are medically- and veterinary-important parasitic flatworms that invade humans, domestic animals and wildlife and also parasitize in their larval stages numerous invertebrate and cold-blooded vertebrate hosts. The interest in echinostomes in parasitology and general biology comes from several areas: (1) Human infections; (2) Experimental models; (3) Animal infections; (4) Systematics. The application of novel techniques is moving the echinostomes to the frontline of parasitology in fields such as systematics, immunobiology in vertebrate and invertebrate organisms and proteomics among others. The Biology of Echinostomes demonstrates the application of new techniques to a group of trematodes that may serve to obtain information of great value in parasitology and general biology. The book includes basic topics, such as biology and systematics, as well as more novel topics, such as immunobiology, proteomics, and genomics of echinostomes. The authors of each chapter emphasize their content with: (i) the most novel information obtained; (ii) analysis of this information in a more general context (i.e. general parasitology); and (iii) future perspectives in view of the information presented. The subjects are analyzed from a modern point of view, considering aspects such as applications of novel techniques and an analysis of host-parasite interactions.

This book presents state-of-the-art analytical methods from statistics and data mining for the analysis of high-throughput data from genomics and proteomics. It adopts an approach focusing on concepts and applications and presents key analytical techniques for the analysis of genomics and proteomics data by detailing their underlying principles, merits and limitations.

Plasma lipoproteins constitute a unique macromolecular system of lipid-protein complexes responsible for the transport of lipids from their sites of origin to their sites of utilization either as metabolic fuel or as structural components of cell membranes. Although studies on the role of lipoproteins in the mechanism of lipid transport are meritorious in their own right, the ever-increasing interest in chemical and functional properties of this remarkable class of conjugated proteins stems from the impressive evidence of their direct involvement in the genesis and develop ment of atherosclerotic lesions. The initial emphasis on neutral lipids and phospholipids as the most characteristic constituents of operationally defined lipoprotein classes has shifted in recent years to their protein moieties or apolipoproteins. The discovery of a number of apolipoproteins and characterization of familial hypolipoproteinemias as apolipoprotein deficiency disorders indicated that apolipoproteins play an essential role in maintaining the structural stability and integrity of lipoprotein particles. In addition to their role in the formation of lipoproteins, apolipoproteins were shown to perform a variety of functions in metabolic conversion of lipoproteins and their interactions with cellular surfaces. Results from several laboratories have demonstrated that the chemical and metabolic heterogeneity of operationally-defined lipoprotein classes is due to the presence of several discrete lipoprotein particles with similar physical properties but different and characteristic apolipoprotein composition. Thus, the apolipoproteins have emerged not only as essential structural and functional constituents of lipoproteins but also as unique chemical markers for identifying and classifying lipoprotein particles."

Bringing together a wide variety of examples of functional amyloid in a single volume, this book explores the importance of amyloid fibrils in fungi, bacteria, algae, invertebrate, and vertebrate animals for providing environmental protection, structural integrity, and regulating biochemical processes. It highlights many of the extraordinary examples of functional amyloid found to date. It, therefore, provides an exciting perspective for the study of amyloid deposits as important and useful protein structures widespread in nature.

We are proud to present Volume 3 of Biological Magnetic Resonance, a series that has met with praise from the scientific community. This volume covers the new applications of various multiple irradia- tion techniques to the NMR of biomolecules; the chapter of Keller and Wuthrich describes much of the technique and its applications to hemo- proteins. The ESR of some hemoproteins in the single crystal is described by Chien and Dickinson, who also include discussions of techniques and methods for single-crystal ESR of paramagnetically intrinsic and spin- labeled protein crystals. Mims and Peisach describe the latest applications and results in electron spin echo spectroscopy of several metalloproteins. Two ESR spin probe techniques are reviewed. Chasteen describes the methods and applications of vanadyl(JV) to several systems. Ohnishi and Tokutomi describe studies of phase separations in mixed and model mem- branes by the nitroxide spin probe technique. We have been successful in continuing to provide topics that are timely and experimentally informative with a heavy emphasis on biolo- gically relevant applications. We thank our colleagues in the scientific com- munity for their suggestions on future coverage-we will remain receptive to future suggestions and comments on this series. A tentative topic list for forthcoming volumes is given on the following pages.

Following their own brilliant careers in haeme protein research, the outstanding scientists Jonathan and Beatrice Wittenberg continue to provide inspiration to the research community in the study of oxygen-binding proteins. Their research has provided the intellectual stimulus to bring together scientists from all over the world with the common goal of developing fascinating new ideas and performing innovative experiments.

This book is dedicated to Jonathan 's and Bea 's lifetime careers. It further illuminates the facts and ideas which dot the paths they traced in Biochemistry and Physiology, elaborating on how these landmark achievements were made and how the haeme proteins community still refers to them. With the field of haeme protein science such a flourishing area, the contributors to this book predict Jonathan and Bea, having played such a seminal role, will continue to be key figures for quite some time to come.

Molecular modeling has undergone a remarkable transformation in the last 20 years. This book provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included in the book, along with chapters covering a wide range of subjects. Links to downloadable software are also provided.

Molecular motor proteins produce force for movement in an incredibly wide variety of cellular processes. This volume explores the extreme functional and structural diversity of molecular motors and presents methods relevant to each motor family. In addition, it describes techniques directed at motors that fall outside of the three characterized families: dynamin and F1ATPase.