This volume focuses on applications of split inteins, and the progress that has been made in the past 5 years on discovery and engineering of fast and more efficient split inteins. The first few chapters in Split Inteins: Methods and Protocols explore new techniques on how to use split inteins for affinity purification of overproduced proteins, and split-intein based technologies to prepare cyclic peptides and proteins. The next few chapters discuss semisynthetic protein trans-splicing using one synthetic intein piece, synthetic intein-extein pieces used to deliver other cargos for chemical modification both of purified proteins and of proteins in living cells, as well as isotopic labeling of proteins for NMR studies, and a discussion on how protein block copolymers can be generated by protein trans-splicing to form protein hydrogels. The last few chapters deal with intein applications in transgenic plants and conditional inteins that can be regulated in artificial ways by small molecules or light, a cassette-based approach to quickly test many intein insertion positions, and a computational approach to predict new intein split sites (the approach also works for other proteins). Written in the highly successful Methods in Molecular Biology series format, chapters include introduction 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, Split Inteins: Methods and Protocols is a valuable resource that will provide guidance toward possibilities of split intein applications, explore proven and detailed protocols adaptable to various research projects, and inspire new method developments.

Amyloid-forming proteins are implicated in over 30 human diseases. The proteins involved in each disease have unrelated sequences and dissimilar native structures, but they all undergo conformational alterations to form fibrillar polymers. The fibrillar assemblies accumulate progressively into disease-specific lesions in vivo. Substantial evidence suggests these lesions are the end state of aberrant protein folding whereas the actual disease-causing culprits likely are soluble, non-fibrillar assemblies preceding the aggregates. The non-fibrillar protein assemblies range from small, low-order oligomers to spherical, annular, and protofibrillar species. Oligomeric species are believed to mediate various pathogenic mechanisms that lead to cellular dysfunction, cytotoxicity, and cell loss, eventuating in disease-specific degeneration and systemic morbidity. The particular pathologies thus are determined by the afflicted cell types, organs, systems, and the proteins involved. Evidence suggests that the oligomeric species may share structural features and possibly common mechanisms of action. In many cases, the structure function interrelationships amongst the various protein assemblies described in vitro are still elusive. Deciphering these intricate structure function correlations will help understanding a complex array of pathogenic mechanisms, some of which may be common across different diseases albeit affecting different cell types and systems."

Multicellular organisms must be able to adapt to cellular events to accommodate prevailing conditions. Sensory-response circuits operate by making use of a phosphorylation control mechanism known as the "two-component system."
Sections include:
Structural Approaches
Reconstitution of Heterogeneous Systems
Intracellular Methods and Assays
Genome-Wide Analyses of Two-Component Systems
Presents detailed protocols
Includes troubleshooting tips

Carbohydrate microarrays emerged as a key technology for the deciphering of the glycospace by providing a multiplex technology where tens to hundreds of carbohydrates/protein interactions can be probed in parallel. Carbohydrate Microarrays: Methods and Protocols aims to give the reader the theoretical and experimental clues necessary for the fabrication and implementation of carbohydrate microarrays. This requires three essential steps: 1) to obtain the carbohydrate probes (monosacharides, oligosacchrides, polysacchairdes, glycoconjugates or glycoclusters), 2) to immobilize these probes, and 3) to implement the protocols for biological/biochemical interaction with the desired target. This volume gives an overview of carbohydrate microarray and carbohydrate chemistry and illustrates different detection techniques and their applications. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Carbohydrate Microarrays: Methods and Protocols compiles a catalogue of protocols on carbohydrate microarrays to span the needs of researchers around the globe.

DNA replication is arguably the most crucial process at work in living cells. It is the mechanism by which organisms pass their genetic information from one generation to the next and life on Earth would be unthinkable without it. Despite the discovery of DNA structure in the 1950s, the mechanism of its replication remains rather elusive. This work makes important contributions to this line of research. In particular, it addresses two key questions in the area of DNA replication: which evolutionary forces drive the positioning of replication origins in the chromosome and how is the spatial organization of replication factories achieved inside the nucleus of a cell?. A cross-disciplinary approach uniting physics and biology is at the heart of this research. Along with experimental support, statistical physics theory produces optimal origin positions and provides a model for replication fork assembly in yeast. Advances made here can potentially further our understanding of disease mechanisms such as the abnormal replication in cancer.

With the rapid development of proteomic technologies in the life sciences and in clinical applications, many bioinformatics methodologies, databases, and software tools have been developed to support comparative proteomics study. In Bioinformatics for Comparative Proteomics, experts in the field highlight the current status, challenges, open problems, and future trends for developing bioinformatics tools and resources for comparative proteomics research in order to deliver a definitive reference providing both the breadth and depth needed on the subject. Structured in three major sections, this detailed volume covers basic bioinformatics frameworks relating to comparative proteomics, bioinformatics databases and tools for proteomics data analysis, and integrated bioinformatics systems and approaches for studying comparative proteomics in the systems biology context. Written for the highly successful Methods in Molecular Biology(TM) series, the contributions in this book provide the meticulous, step-by-step description and implementation advice that is crucial for getting optimal results in the lab. Comprehensive and easy-to-use, Bioinformatics for Comparative Proteomics serves all readers who wish to learn about state-of-the-art bioinformatics databases and tools, novel computational methods and future trends in proteomics data analysis, and comparative proteomics in systems biology.

This is the third of three planned volumes in the Methods in Enzymology series on the topic of stem cells. This volume is a unique anthology of stem cell techniques written by experts from the top laboratories in the world. The contributors not only have hands-on experience in the field but often have developed the original approaches that they share with great attention to detail. The chapters provide a brief review of each field followed by a "cookbook" and handy illustrations. The collection of protocols includes the isolation and maintenance of stem cells from various species using "conventional" and novel methods, such as derivation of ES cells from single blastomeres, differentiation of stem cells into specific tissue types, isolation and maintenance of somatic stem cells, stem cell-specific techniques and approaches to tissue engineering using stem cell derivatives. The reader will find that some of the topics are covered by more than one group of authors and complement each other. Comprehensive step-by-step protocols and informative illustrations can be easily followed by even the least experienced researchers in the field, and allow the setup and troubleshooting of these state-of-the-art technologies in other laboratories.
* Provides complete coverage spanning from derivation/isolation of stem cells, and including differentiation protocols, characterization and maintenance of derivatives and tissue engineering
* Presents the latest most innovative technologies
* Addresses therapeutic relevance including FDA compliance and tissue engineering

This review series covers trends in modern biotechnology, including all aspects of this interdisciplinary technology, requiring knowledge, methods, and expertise from chemistry, biochemistry, microbiology, genetics, chemical engineering and computer science.

This volume includes, in an integrated way, modern computational studies of nucleic acids, ranging from advanced electronic structure quantum chemical calculations through explicit solvent molecular dynamics (MD) simulations up to mesoscopic modelling, with the main focus given to the MD field.It gives an equal emphasis to the leading methods and applications while successes as well as pitfalls of the computational techniques are discussed. The systems and problems studied include: Accurate calculations of base pairing energies; Electronic properties of nucleic acids and electron transfer, through various types of nucleic acid; and, Calculating DNA elasticity. This book is ideally suited to academics and researchers in organic and computational chemistry as well as biochemistry and particularly those interested in the molecular modelling of nucleic acids.Besides the state-of-the art science, the book also provides introductory information to non-specialists to enter this field.

This book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood without dealing with interfacial behaviour. There is an urge to grasp how biologically relevant behaviour is shaped by the structuring of biomolecular interfaces and how interfacial tension affects the molecular events that take place in the cell. This book squarely addresses these needs from a physicist perspective. The book may serve as a monograph for practitioners and, alternatively, as an advanced textbook. Fruitful reading requires a background in physical chemistry and some basics in biophysics. The selected problems at the end of the chapters and the progression in conceptual difficulty make it a suitable textbook for a graduate level course or an elective course for seniors majoring in chemistry, physics, biomedical engineering or related disciplines.

"How did life originate and why were left-handed molecules selected for its architecture?" This question of high public and interdisciplinary scientific interest is the central theme of this book. It is widely known that in processes triggering the origin of life on Earth, the equal occurrence, the parity between left-handed amino acids and their right-handed mirror images, was violated. The balance was inevitably tipped to the left as a result of which life's proteins today exclusively implement the left form of amino acids.

Written in an engaging style, this book describes how the basic building blocks of life, the amino acids, formed. After a comprehensible introduction to stereochemistry, the author addresses the inherent property of amino acids in living organisms, namely the preference for left-handedness. What was the cause for the violation of parity of amino acids in the emergence of life on Earth? All the fascinating models proposed by physicists, chemists and biologist are vividly presented including the scientific conflicts. The author describes the attempt to verify any of those models with the chirality module of the ROSETTA mission, a probe built and launched with the mission to land on a comet and analyse whether there are chiral organic compounds that could have been brought to the Earth by cometary impacts.

A truly interdisciplinary astrobiology book, "Amino Acids and the Asymmetry of Life" will fascinate students, researchers and all readers with backgrounds in natural sciences.

With a foreword by Henri B. Kagan."

Interplay between Metal Ions and Nucleic Acids provides in an authoritative and timely manner in 12 stimulating chapters, written by 24 internationally recognized experts from 8 nations, and supported by nearly 1500 references, about 20 tables, and 125 illustrations, many in color, a most up-to-date view on metal ion-nucleic acid interactions; the characterization of which is covered in solution and in the solid state. The volume concentrates on modern developments encompassing topics in the wide range from G-quadruplexes via DNAzymes, catalysis at the DNA scaffold, and metal-mediated base pairs to peptide nucleic acids (PNAs) being thus of relevance, e.g., for chemistry and nanotechnology but also for molecular biology and (genetic) diagnostics.

From the 39th annual conference of the International Society on Oxygen Transport to Tissue (ISOTT), held in Washington, DC, USA in July 2011, this volume covers aspects of oxygen transport from air to the cells, organs and organisms; instrumentation and methods to sense oxygen and clinical evidence. Oxygen Transport to Tissue XXXIV includes contributions from scientists (physicists, biologists and chemists), engineers, clinicians and mathematicians.

With the development of new quantitative strategies and powerful bioinformatics tools to cope with the analysis of the large amounts of data generated in proteomics experiments, liquid chromatography with tandem mass spectrometry (LC-MS/MS) is making possible the analysis of proteins on a global scale, meaning that proteomics can now start competing with cDNA microarrays for the analysis of whole genomes. In LC-MS/MS in Proteomics: Methods and Applications, experts in the field provide protocols and up-to-date reviews of the applications of LC-MS/MS, with a particular focus on MS-based methods of protein and peptide quantification and the analysis of post-translational modifications. Beginning with overviews of the use of LC-M/MS in protein analysis, the book continues with topics such as protocols for the analysis of post-translational modifications, with particular focus on phosphorylation and glycosylation, popular techniques for quantitative proteomics, such as multiple reaction monitoring, metabolic labelling, and chemical tagging, biomarker discovery in biological fluids, as well as novel applications of LC-MS/MS. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective subjects, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, LC-MS/MS in Proteomics: Methods and Applications presents the techniques and concepts necessary in order to aid proteomic practitioners in the application of LC-MS/MS to essentially any biological problem.

The NATO ARW "Molecular Self-Organization in Micro-, Nano-, and Macro- Dimensions: From Molecules to Water, to Nanoparticles, DNA and Proteins" to commemorate Professor Alexander S. Davydov was held in Kiev, Ukraine, on 8-12 June, 2008, at the Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine. Theobjective ofthisNATOARWistounveilandformulatetheprincipalfeatures that govern myriads of the molecular self-organization processes in micro-, nano-, and macro-dimensions from the following key representatives such as liquid - ter and aqueous solutions, and molecular liquids, nanodots, nanoparticles including gold, solitons, biomolecules such as DNA and proteins, biopolymers and bios- sors, catalysis, molecular modeling, molecular devices, and thin ?lms, and to offer another, more advanced directions in computational, experimental, and technolo- cal areas of nano- and bioscience towards engineering novel and powerful molecular self-organized assemblies with tailored properties. Nanoscience is indeed one of the most important research and development fr- tiers in modern science. Simplistically, nanoscience is the science of small particles of materials of a size of nanometre. Molecular nanoscience and nanotechnology have brought to us the unprecedented experimental control of the structure of matter with novel extraordinary properties that open new horizons and new opportunities, and new ways to make things, particularly in our everyday life, to heal our bodies, and to care of the environment. Unfortunately, they have also brought unwelcome advances in weaponry and opened yet more ways to foul up the world on an en- mous scale.

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 second of three in the Methods in Enzymology series, including Glycobiology (vol. 415) 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 ability of polypeptides to form alternatively folded, polymeric structures such as amyloids and related aggregates is being increasingly recognized as a major new frontier in protein research. This new volume of Methods in Enzymology along with Part C (volume 413) on Amyloid, Prions and other Protein Aggregates continue in the tradition of the first volume (309) in containing detailed protocols and methodological insights, provided by leaders in the field, into the latest methods for investigating the structures, mechanisms of formation, and biological activities of this important class of protein assemblies.
* Presents detailed protocols
* Includes troubleshooting tips
* Provides coverage on structural biology, computational methods, and biology

Population genomics is a recently emerged discipline, which aims at understanding how evolutionary processes influence genetic variation across genomes. Today, in the era of cheaper next-generation sequencing, it is no longer as daunting to obtain whole genome data for any species of interest and population genomics is now conceivable in a wide range of fields, from medicine and pharmacology to ecology and evolutionary biology. However, because of the lack of reference genome and of enough "a priori" data on the polymorphism, population genomics analyses of populations will still involve higher constraints for researchers working on non-model organisms, as regards the choice of the genotyping/sequencing technique or that of the analysis methods. Therefore, "Data Production and Analysis in Population Genomics" purposely puts emphasis on protocols and methods that are applicable to species where genomic resources are still scarce. It is divided into three convenient sections, each one tackling one of the main challenges facing scientists setting up a population genomics study. The first section helps devising a sampling and/or experimental design suitable to address the biological question of interest. The second section addresses how to implement the best genotyping or sequencing method to obtain the required data given the time and cost constraints as well as the other genetic resources already available, Finally, the last section is about making the most of the (generally huge) dataset produced by using appropriate analysis methods in order to reach a biologically relevant conclusion. Written in the 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 protocols, advice on methodology and implementation, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, "Data Production and Analysis in Population Genomics" serves a wide readership by providing guidelines to help choose and implement the best experimental or analytical strategy for a given purpose.

This book review series presents current trends in modern biotechnology. The aim is to cover all aspects of this interdisciplinary technology where knowledge, methods and expertise are required from chemistry, biochemistry, microbiology, genetics, chemical engineering and computer science. Volumes are organized topically and provide a comprehensive discussion of developments in the respective field over the past 3-5 years. The series also discusses new discoveries and applications. Special volumes are dedicated to selected topics which focus on new biotechnological products and new processes for their synthesis and purification. In general, special volumes are edited by well-known guest editors. The series editor and publisher will however always be pleased to receive suggestions and supplementary information. Manuscripts are accepted in English.