In the past decade, there has been an explosion of progress in understanding the roles of carbohydrates in biological systems. This explosive progress was made with the efforts in determining the roles of carbohydrates in immunology, neurobiology and many other disciplines, examining each unique system and employing new technology. This volume represents the first of three in the Methods in Enzymology series, including Glycomics (vol. 416) and Functional Glycomics (vol. 417), dedicated to disseminating information on methods in determining the biological roles of carbohydrates. These books are designed to provide an introduction of new methods to a large variety of readers who would like to participate in and contribute to the advancement of glycobiology. The methods covered include structural analysis of carbohydrates, biological and chemical synthesis of carbohydrates, expression and determination of ligands for carbohydrate-binding proteins, gene expression profiling including micro array, and generation of gene knockout mice and their phenotype analyses.

The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the series contains much material still relevant today-truly an essential publication for researchers in all fields of life sciences.

This book focuses on an "outside the box" notion by utilizing the powerful applications of next-generation sequencing (NGS) technologies in the interface of chemistry and biology. In personalized medicine, developing small molecules targeting a specific genomic sequence is an attractive goal. N-methylpyrrole (P)-N-methylimidazole (I) polyamides (PIPs) are a class of small molecule that can bind to the DNA minor groove. First, a cost-effective NGS (ion torrent platform)-based Bind-n-Seq was developed to identify the binding specificity of PIP conjugates in a randomized DNA library. Their biological influences rely primarily on selective DNA binding affinity, so it is important to analyze their genome-wide binding preferences. However, it is demanding to enrich specifically the small-molecule-bound DNA without chemical cross-linking or covalent binding in chromatinized genomes. Herein is described a method that was developed using high-throughput sequencing to map the differential binding sites and relative enriched regions of non-cross-linked SAHA-PIPs throughout the complex human genome. SAHA-PIPs binding motifs were identified and the genome-level mapping of SAHA-PIPs-enriched regions provided evidence for the differential activation of the gene network. A method using high-throughput sequencing to map the binding sites and relative enriched regions of alkylating PIP throughout the human genome was also developed. The genome-level mapping of alkylating the PIP-enriched region and the binding sites on the human genome identifies significant genomic targets of breast cancer. It is anticipated that this pioneering low-cost, high through-put investigation at the sequence-specific level will be helpful in understanding the binding specificity of various DNA-binding small molecules, which in turn will be beneficial for the development of small-molecule-based drugs targeting a genome-level sequence.

In this fast moving field the main goal of this volume is to provide up-to-date information on the molecular and functional properties and pharmacology of mammalian TRP channels. Leading experts in the field describe properties of a single TRP protein/channel or portray more general principles of TRP function and important pathological situations linked to mutations of TRP genes or their altered expression. Thereby this volume on Transient Receptor Potential (TRP) Channels provides valuable information for readers with different expectations and backgrounds, for those who are approaching this field of research as well as for those wanting to make a trip to TRPs."

Exploring the 2-D gel mapping field, the chapters in this book are separated into four different categories: Part I talks about 2-D maps reproducibility and maps modeling; Part II describes the image analysis tools that provide spot volume datasets; Part III is about the statistical methods applied to spot volume datasets to identify candidate biomarkers; and Part IV discusses differential analysis from direct image analysis tools. 2-D PAGE Map Analysis: Methods and Protocols provides a unique approach to 2-D gel mapping, in that it helps users avoid drawbacks due to ignorance of the basic theoretical mechanisms underlying the technique, including data handling and proper tools for spot analysis. 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, 2-D PAGE Map Analysis: Methods and Protocols, is a useful resource for any scientist or researcher, with a mathematical background, who is interested in 2-D gel mapping.

Themulticomponentnatureofbiologicalmembranesandtheirintra- andextracel- lar interactions make direct investigations on the membrane structure and processes nearly impossible. Clearly, a better understanding of the membrane properties and the mechanisms determining membrane protein functions is crucial to the imp- mentation of biosensors, bioreactors and novel platforms for medical therapy. For this reason, the interest in model systems suitable for the construction and study of complex lipid/protein membrane architectures has increased steadily over the years. The classical portfolio of model membranes used for biophysical and - terfacial studies of lipid (bi)layers and lipid/protein composites includes Langmuir monolayers assembled at the water/air interface, (uni- and multi-lamellar) vesicles in bulk (liposomal) dispersion, bimolecular lipid membranes (BLMs), and various types of solid-supported membranes. All these have speci?c advantages but also suffer from serious drawbacksthat limit their technical applications. Polymer m- branes comprised of entirely synthetic or hybrid (synthetic polymer/biopolymer) block copolymersappeared to be an attractive alternative to the lipid-based models. Generally, the synthetic block copolymer membranes are thicker and more stable and the versatility of polymer chemistry allows the adoption of relevant properties for a wide range of applications. This volume provides a vast overview of the physico-chemical and synthetic - pectsofarti?cial membranes. Numerousmembranemodelsaredescribed,including their properties(i. e. swelling, drying,lateral mobility,stability, electrical conduct- ity, etc. ), advantages, and drawbacks. The potential applications of these models are discussed and supported by real examples. Chapter 1 summarizesmethodsfor the stabilizationof arti?cial lipid membranes.

This series is world-renowned as the leading compilation of current reviews of this vast field. Internationally acclaimed for more than forty years, The Alkaloids: Chemistry and Biology, founded by the late Professor R.H.F. Manske, continues to provide outstanding coverage of this rapidly expanding field. Each volume provides, through its distinguished authors, up-to-date and detailed coverage of particular classes or sources of alkaloids.
* Up-to-date reviews on a large and very important group of natural products from both a chemical and biological perspective.
* Comprehensive dynamic reviews written by the leading authors in the respective fields.
* Broader coverage than before on the biological aspects.

The Ras superfamily (>150 human members) encompasses Ras GTPases involved in cell proliferation, Rho GTPases involved in regulating the cytoskeleton, Rab GTPases involved in membrane targeting/fusion and a group of GTPases including Sar1, Arf, Arl and dynamin involved in vesicle budding/fission. These GTPases act as molecular switches and their activities are controlled by a large number of regulatory molecules that affect either GTP loading (guanine nucleotide exchange factors or GEFs) or GTP hydrolysis (GTPase activating proteins or GAPs). In their active state, they interact with a continually increasing, functionally complex array of downstream effectors.
Since the last Methods in Enzymology volume on this topic in 2000, the study of Ras Family GTPases has witnessed a plethora of new directions and trends. With regards to the founding member of the Ras superfamily, the study of Ras in oncogenesis has seen the development and application of more advanced model cell culture and animal systems. The discovery of mutationally activated B-Raf in human cancers has injected renewed interest in this classical effector pathway of Ras.
*Includes a database for Ras family proteins and their effectors and regulators
*Complimentary to volume 406 coverage of the Rho family
*Over 150 international contributors

Springer Handbook of Enzymes provides data on enzymes sufficiently well characterized. It offers concise and complete descriptions of some 5,000 enzymes and their application areas. Data sheets are arranged in their EC-Number sequence and the volumes themselves are arranged according to enzyme classes.

This new, second edition reflects considerable progress in enzymology: many enzymes are newly classified or reclassified. Each entry is correlated with references and one or more source organisms. New datafields are created: application and engineering (for the properties of enzymes where the sequence has been changed). The total amount of material contained in the Handbook has more than doubled so that the complete second edition consists of 39 volumes as well as a Synonym Index. In addition, starting in 2009, all newly classified enzymes are treated in Supplement Volumes.

Springer Handbook of Enzymes is an ideal source of information for researchers in biochemistry, biotechnology, organic and analytical chemistry, and food sciences, as well as for medicinal applications.

In this book, seven chapters describe studies aimed at understanding and exploiting the key features of such molecular RNA and DNA devices. In the first section of the book, four chapters are devoted to artificial nucleic acid switches and sensors. These chapters introduce the concept of allosteric ribozymes as molecular switches and sensors; describe nucleic acid enzymes that are switched by oligonucleotides and other nucleic acid enzymes that are switched by proteins; and illustrate how switching elements can be integrated rationally into fluorescently signaling molecular sensors made out of nucleic acids. In the second section of the book, three chapters show that nature has been as crafty a molecular-scale engineer as any modern scientist via evolution of natural nucleic acid switches and sensors. RNAs have been found whose activities are modulated either by proteins or by small-molecule metabolites, and both kinds of system are described. Finally, the notion of exploiting naturally occurring RNA switches for drug development is discussed.

The aim of this volume is to review the state-of-the-art in analytical voltammetry with regard to theory and instrumentation, and show how these relate to the analysis of inorganic, organometallic, organic and biological molecules. Modern voltammetric techniques have practical applications in biological, pharmaceutical and environmental chemistry. The growing importance of voltammetry in the development of modified electrodes and biological electrodes and chemical and biological sensors is also highlighted.

Due to their rare combination of high chemical stability, exceptional optical and electrical properties, high surface-to-volume ratio, and high aspect ratio, carbon nanotubes (CNTs) have made an enormous impact on materials science, molecular biology, biomedicine, and bioanalytical chemistry. Carbon Nanotubes: Methods and Protocols provides reliable, consistent protocols on the application of CNTs in molecular biology-related fields. These are of vital importance, as the commercially available CNTs differ in purity, agglomeration state, as well as length and diameter distribution, all of which have a profound influence on the dispersability and surface properties of the tubes. The volume contains detailed sections on functionalization, toxicity, trafficking, scaffolds, and biosensors, provided by expert researchers from various fields. 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 notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Carbon Nanotubes: Methods and Protocols serves to contribute to the achievement of common standards and helps researchers to avoid discrepancies in future biology-related CNT studies.

This book covers the most recent developments in the analysis of allosteric enzymes and provides a logical introduction to the limits for enzyme function as dictated by the factors that are limits for life. The book presents a complete description of all the mechanisms used for changing enzyme activity. It is extensively illustrated to clarify kinetic and regulatory properties. Eight enzymes are used as model systems after extensive study of their mechanisms. Wherever possible, the human form of the enzyme is used to illustrate the regulatory features.

This detailed book provides technical approaches to tackle a variety of questions related to intracellular lipid transport in order to improve our understanding at different scales of how lipids are accurately displaced between organelles, across long distances or at membrane contact sites, or within cellular membranes. The volume begins with methodologies to measure the movement of varied lipid species between or in organelle membranes, inside eukaryotic cells, including plant cells, or in bacteria, and continues in vitro or in silico approaches aiming to define, more from a biochemical and structural standpoints, how lipid transfer proteins (LTPs) or flippases/scramblases precisely function. 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, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Intracellular Lipid Transport: Methods and Protocols serves as an ideal guide for researchers seeking to shed light on diverse aspects of this critical and often elusive cellular process.

The centromere is a chromosomal region that enables the accurate segregation of chromosomes during mitosis and meiosis. It holds sister chromatids together, and through its centromere DNA-protein complex known as the kinetochore binds spindle microtubules to bring about accurate chromosome movements. Despite this conserved function, centromeres exhibit dramatic difference in structure, size, and complexity. Extensive studies on centromeric DNA revealed its rapid evolution resulting often in significant difference even among closely related species. Such a plasticity of centromeric DNA could be explained by epigenetic c- trol of centromere function, which does not depend absolutely on primary DNA sequence. According to epigenetic centromere concept, which is thoroughly d- cussed by Tanya Panchenko and Ben Black in Chap. 1 of this book, centromere activation or inactivation might be caused by modifications of chromatin. Such acquired chromatin epigenetic modifications are then inherited from one cell di- sion to the next. Concerning centromere-specific chromatin modification, it is now evident that all centromeres contain a centromere specific histone H3 variant, CenH3, which replaces histone H3 in centromeric nucleosomes and provides a structural basis that epigenetically defines centromere and differentiates it from the surrounding chromatin. Recent insights into the CenH3 presented in this chapter add important mechanistic understanding of how centromere identity is initially established and subsequently maintained in every cell cycle.

Contents

E.I. Christensen and R. Nielsen: Role of Megalin and Cubilin in Renal Physiology and Pathophysiology

G. Zifarelli and M. Pusch: CLC Chloride Channels and Transporters: A Biophysical and Physiological Perspective

S.F.J. van de Graaf, R.J.M. Bindels and J.G.J. Hoenderop: Physiology of Epithelial Ca2 and Mg2+ Transport

The aim of this series is to provide authoritative reviews in the rapidly expanding area of bioinorganic chemistry. The series will present "state of the art" reviews covering the whole field of bioinorganic chemistry.
The present volume is the fourth in the series and covers the topics: lithium in biology, the structure and function of ceroplasmin, rhenium complexes in nuclear medicine, the anti-HIV activity of macrocyclic polyamines and their metal complexes for dinuclear phosphoesterase enzymes.

Biochemistry laboratory manual for undergraduates - an inquiry based approach by Gerczei and Pattison is the first textbook on the market that uses a highly relevant model, antibiotic resistance, to teach seminal topics of biochemistry and molecular biology while incorporating the blossoming field of bioinformatics. The novelty of this manual is the incorporation of a student-driven real real-life research project into the undergraduate curriculum. Since students test their own mutant design, even the most experienced students remain engaged with the process, while the less experienced ones get their first taste of biochemistry research. Inclusion of a research project does not entail a limitation: this manual includes all classic biochemistry techniques such as HPLC or enzyme kinetics and is complete with numerous problem sets relating to each topic.

Volume 72 addresses the role of peptide backbone solvation in the energetics of protein folding. Particular attention is focused on modeling and computation. This volume will be of particular interest to biophysicists and structural biologists.
*Challenges the longstanding and basic assumptions of structural biology
*Discusses how to solve the problem of protein structure prediction
*Addresses the quantitation of the energetics of folding

Ubiquitin and Protein Degradation, Part B will cover chemical biology, ubiquitin derivatives and ubiquitin-like proteins, deubiquitinating enzymes, proteomics as well as techniques to monitor protein degradation. The chapters are highly methodological and focus on application of techniques.
*Second part of the Ubiquitin and Protein Degration series
*Topics include: E1 Enzymes, E2 Enzymes, E3 Enzymes, Proteasomes, and Isopeptidases

Springer Handbook of Enzymes provides data on enzymes sufficiently well characterized. It offers concise and complete descriptions of some 5,000 enzymes and their application areas. Data sheets are arranged in their EC-Number sequence and the volumes themselves are arranged according to enzyme classes.

This new, second edition reflects considerable progress in enzymology: many enzymes are newly classified or reclassified. Each entry is correlated with references and one or more source organisms. New datafields are created: application and engineering (for the properties of enzymes where the sequence has been changed). The total amount of material contained in the Handbook has more than doubled so that the complete second edition consists of 39 volumes as well as a Synonym Index. In addition, starting in 2009, all newly classified enzymes are treated in Supplement Volumes.

Springer Handbook of Enzymes is an ideal source of information for researchers in biochemistry, biotechnology, organic and analytical chemistry, and food sciences, as well as for medicinal applications.

The book summarizes important aspects of cheminformatics that are relevant for natural product research. It highlights cheminformatics tools that help to match natural products with their respective biological targets or off-targets, and discusses the potential and limitations of this approach.

Disulfide-containing proteins belong to a unique class of proteins for studying the mechanism of protein folding. Their folding mechanism can be analyzed by three distinct techniques: (1) The conventional denaturation-renaturation method (disulfide intact); (2) The disulfide oxidation method (oxidative folding); and (3) The emerging disulfide scrambling method. Each technique provides specific information as to how an unfolded disulfide protein refolds to form the native structure. This book is intended to highlight the knowledge of several important proteins (BPTI, RNase A, beta-Lactalbumin and Lysozyme etc.) that have been characterized in depth by these methodologies. The book will also devote sections to comparing these methodologies and chaperones (PDI and Dsb machineries) that facilitate folding of disulfide proteins. Folding of Disulfide Proteins aims to cover the knowledge of protein folding accumulated from studies of disulfide-containing proteins, including methodologies, folding pathways, and folding mechanism of numerous extensively characterized disulfide proteins. This book will be of interest to those interested in problems related to protein folding, and anyone who is interested in understanding the mechanism of protein misfolding and protein misfolding-related diseases. Folding of Disulfide Proteins aims to cover the knowledge of protein folding accumulated from studies of disulfide-containing proteins, including methodologies, folding pathways, and folding mechanism of numerous extensively characterized disulfide proteins. This book will be of interest to those interested in problems related to protein folding, and anyone who is interested in understanding the mechanism of protein misfolding and protein misfolding-related diseases.

This book gathers 12 outstanding contributions that reflect state-of-the-art industrial applications of fluorescence, ranging from the pharmaceutical and cosmetics industries to explosives detection, aeronautics, instrumentation development, lighting, photovoltaics, water treatment and much more. In the field of fluorescence, the translation of research into important applications has expanded significantly over the past few decades. The 18th volume in the Springer Series on Fluorescence fills an important gap by focusing on selected industrial applications of fluorescence, described in contributions by both industry-based researchers and academics engaged in collaborations with industrial partners.

Since its inception in 1945, this serial has provided critical and integrating articles written by research specialists that integrate industrial, analytical, and technological aspects of biochemistry, organic chemistry, and instrumentation methodology in the study of carbohydrates. The articles provide a definitive interpretation of the current status and future trends in carbohydrate chemistry and biochemistry.
High quality comprehensive reviews covering all aspects of carbohydrate chemistry