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.

Fluorescent proteins are intimately connected to research in the life sciences. Tagging of gene products with fluorescent proteins has revolutionized all areas of biosciences, ranging from fundamental biochemistry to clinical oncology, to environmental research. The discovery of the Green Fluorescent Protein, its first, seminal application and the ingenious development of a broad palette of fluorescence proteins of other colours, was consequently recognised with the Nobel Prize for Chemistry in 2008.

"Fluorescent Proteins I" is devoted to the basic photophysical and photochemical aspects of fluorescent protein technology. Experienced experts highlight colour tuning, the exploration of switching phenomena and respective methods for their investigation. The book provides a thorough understanding of primary molecular processes allowing the design of fluorescent proteins for specific applications.

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 Glycomics (vol. 416), 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.

Plants play a key role in purifying the biosphere of the toxic effects of industrial activity. This book shows how systematic application of the results of investigations into the metabolism of xenobiotics (foreign, often toxic substances) in plants could make a vastly increased contribution to planetary well-being. Deep physiological knowledge gained from an accumulation of experimental data enables the great differences between the detoxifying abilities of different plants for compounds of different chemical nature to be optimally exploited. Hence planting could be far more systematically adapted to actual environmental needs than is actually the case at present.

The book could form the basis of specialist courses in universities and polytechnics devoted to environmental management, and advanced courses in plant physiology and biochemistry, for botany and integrative biology students. Fundamental plant physiology and biochemistry from the molecular level to whole plants and ecosystems are interwoven in a powerful and natural way, making this a unique contribution to the field.

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.