Gene function annotation has been a central question in molecular biology. The importance of computational function prediction is increasing because more and more large scale biological data, including genome sequences, protein structures, protein-protein interaction data, microarray expression data, and mass spectrometry data, are awaiting biological interpretation. Traditionally when a genome is sequenced, function annotation of genes is done by homology search methods, such as BLAST or FASTA. However, since these methods are developed before the genomics era, conventional use of them is not necessarily most suitable for analyzing a large scale data. Therefore we observe emerging development of computational gene function prediction methods, which are targeted to analyze large scale data, and also those which use such omics data as additional source of function prediction. In this book, we overview this emerging exciting field. The authors have been selected from 1) those who develop novel purely computational methods 2) those who develop function prediction methods which use omics data 3) those who maintain and update data base of function annotation of particular model organisms (E. coli), which are frequently referred

This book covers the recent innovations relating to various bioactive natural products (such as alkaloids, glycosides, flavonoids, anthraquinones, steroids, polysaccharides, tannins and polyphenolic compounds, volatile oils, fixed oils, fats and waxes, proteins and peptides, vitamins, marine products, camptothecin, piperines, carvacrol, gedunin, GABA, ginsenosides) and their applications in the pharmaceutical fields related to academic, research and industry.

The lipid-rich and otherwise challenging nature of many key tissues complicates many aspects of current research, and applications of the unique nature of lipoproteins and their biological effects has engendered unique and vital methodologies. In Lipoproteins and Cardiovascular Disease: Methods and Protocols, experts in the field present a compendium of advanced and classical molecular biology methods targeted towards lipoprotein, atherosclerosis, and vascular biology research, bringing together in a single volume an updated set of protocols and strategies for methods now driving the most recent advances, along with classical methods that are still widely used. Among the many topics covered in this cutting-edge work, the book delves into crucial techniques such as quantitative real-time PCR, microarrays, RT-PCR laser capture microdissection, and tissue-specific gene overexpression, knockout, and knockdown methodologies, including AAV as a liver-directed gene delivery vehicle. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and valuable notes which highlight tips on troubleshooting and avoiding known pitfalls. Comprehensive and easy to use, Lipoproteins and Cardiovascular Disease: Methods and Protocols serves both novices and experts alike as a complete guide for any researcher with an interest in lipoproteins and their significant biological effects.

Plant taxonomy is an ancient discipline facing new challenges with the current availability of a vast array of molecular approaches which allow reliable genealogy-based classifications. Although the primary focus of plant taxonomy is on the delimitation of species, molecular approaches also provide a better understanding of evolutionary processes, a particularly important issue for some taxonomic complex groups."Molecular Plant Taxonomy: Methods and Protocols"describes laboratory protocols based on the use of nucleic acids and chromosomes for plant taxonomy, as well as guidelines for phylogenetic analysis of molecular data. Experts in the field also contribute review and application chapters that will encourage the reader to develop an integrative taxonomy approach, combining nucleic acid and cytogenetic data together with other crucial information (taxonomy, morphology, anatomy, ecology, reproductive biology, biogeography, paleobotany), which will help not only to best circumvent species delimitation but also to resolve the evolutionary processes in play.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, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, "Molecular Plant Taxonomy: Methods and Protocols"seeks to provide conceptual as well as technical guidelines to plant taxonomists and geneticists."

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.

This book discusses a broad range of basic and advanced topics in the field of protein structure, function, folding, flexibility, and dynamics. Starting with a basic introduction to protein purification, estimation, storage, and its effect on the protein structure, function, and dynamics, it also discusses various experimental and computational structure determination approaches; the importance of molecular interactions and water in protein stability, folding and dynamics; kinetic and thermodynamic parameters associated with protein-ligand binding; single molecule techniques and their applications in studying protein folding and aggregation; protein quality control; the role of amino acid sequence in protein aggregation; muscarinic acetylcholine receptors, antimuscarinic drugs, and their clinical significances. Further, the book explains the current understanding on the therapeutic importance of the enzyme dopamine beta hydroxylase; structural dynamics and motions in molecular motors; role of cathepsins in controlling degradation of extracellular matrix during disease states; and the important structure-function relationship of iron-binding proteins, ferritins. Overall, the book is an important guide and a comprehensive resource for understanding protein structure, function, dynamics, and interaction.

Conceived with the intention of providing an array of strategies and technologies currently in use for glyco-engineering distinct living organisms, this book contains a wide range of methods being developed to control the composition of carbohydrates and the properties of proteins through manipulations on the production host rather than in the protein itself. The first five sections deal with host-specific glyco-engineering and contain chapters that provide protocols for modifications of the glycosylation pathway in bacteria, yeast, insect, plants and mammalian cells, while the last two sections explore alternative approaches to host glyco-engineering and selected protocols for the analysis of the N-glycans and glyco-profiling by mass spectrometry. 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 extensive, Glyco-Engineering: Methods and Protocols offers vast options to help researchers to choose the expression system and approach that best suits their intended protein research or applications.

The critically acclaimed laboratory standard, 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. The series contains much material still relevant today - truly an essential publication for researchers in all fields of life sciences.

This book provides a knowledge-based view to the dynamic capabilities in an organization. The author integrates two existing views on gaining competitive advantage: the Knowledge View which suggests that the capability of organizations to learn faster than competitors is the only source of competitiveness; and the Dynamic Capability View which speculates that a fi rm's competitive advantage rests on it's ability to adapt to changes in the business environment. Using the IT sector in India as a case study, this book provides and tests a new framework-Knowledge-Based Dynamic Capabilities-in the prediction of competitive advantage in organizations.

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 II" highlights the physicochemical and biophysical aspects of fluorescent protein technology beyond imaging. It is tailored to meet the needs of physicists, chemists and biologists who are interested in the fundamental properties of fluorescent proteins, while also focussing on specific applications. The implementations described are cutting-edge studies and exemplify how the physical and chemical properties of fluorescent proteins can stimulate novel findings in life sciences.

This is the first of three volumes in the "Ion Channels & Transporters in Tumor Biology" collection, which discusses the function of ion transport proteins in cellular and systemic homeostasis. The authors highlight the role of the so-called transportome, which is defined by the entirety of ion transporters and ion channels. Thereby, readers will get a better understanding of the impact dysregulated ion transport has on the whole spectrum of cancer types. Cancers display deficiencies in several, sometimes interdependent members of the transportome. Clinicians will be interested in the fact that controlled expression of ion transport proteins dramatically impacts the life span of cancer patients, as shown in recent studies. These observations offer a promising outlook for biomedical scientists, as members of the transportome could be the tumor markers of tomorrow - both for diagnostic and therapeutic purposes. As part of a three-volume collection, this book will fascinate members of the active research community, as well as clinicians from the cancer field.

Ribonucleases are a ubiquitous and functionally diverse group of enzymes that have a common ability to cleave RNA. Either through scission of internal phosphodiesters, or removal of nucleotides from RNA 5' or 3' ends, ribonucleases perform essential roles in gene expression and regulation, genome replication and maintenance, host defense, stress response, and viral strategies of infection. Ribonucleases have also served as highly informative models to understand virtually every aspect of biomolecular structure and function. The fifteen chapters in this volume are written by recognized researchers in the field, and provide in-depth analyses of the major ribonuclease families. Particular focus is given to the relation of ribonuclease structure and mechanism to biological function, as well as ribonuclease dysfunction in certain disease states. Other topics include the evolutionary genetics and functional diversification of ribonucleases, engineered ribonucleases as anti-cancer agents, the mechanisms of action of artificial ribonucleases, and ribonucleases as models to understand protein folding and stability. This volume should serve as an essential reference for a broad range of researchers and educators with interests in RNA metabolism, enzymology, and gene regulation.

The goal of the characterization and discovery of G protein-coupled receptors, arguably the most important class of signaling molecules in humans and other vertebrates, has spawned numerous vital methodologies. In "Methods for the Discovery and Characterization of G Protein-Coupled Receptors," experts in the field present the very latest on the methods and technology used to characterize and discover novel mechanisms of GPCRs which, in many cases, can be used directly to design experiments for the reader s particular GPCR of interest and their specific avenue of investigation. Divided into four convenient sections, this detailed volume covers GPCRs in the genome, trafficking of GPCRs, GPCRs on the membrane, as well as the regulation of these key receptors. Chapters also feature an important section called Future Directions which gives the reader an insight into advances soon to be realized in each area. Written for the popular "Neuromethods" series, this book contains the kind of detailed description and implementation advice that is crucial for getting optimal results.

Authoritative and cutting-edge, "Methods for the Discovery and Characterization of G Protein-Coupled Receptors" serves as an ideal guide for scientists determined to further our knowledge of crucially important set of receptors.

DNA and RNA fractions have been isolated from the whole blood, serum, plasma, the surface of blood cells, urine, saliva and spinal fluid from both healthy individuals and clinical patients. Recent developments are presented concerning the isolation, quantification and analysis of these molecules and their use in the identification of specific nucleic acid fragments related to a variety of clinical disorders thereby permitting their early diagnosis and prognosis.

Recent concerns over the possible hazards of electrical and magnetic fields in the home and workplace are comprehensively addressed within this book. The chapters contain detailed research on the biological effects of electric and magnetic fields, and evidence for and against any interaction of electromagnetic fields (EMFs) and the biological systems.
The two volumes cover:
* The relative risk of exposure to EMFs
* Putative behavioral and neural effects of EMFs
* EMF effects on cells

Presenting a new way to examine water quality criteria, this volume provides concise, critical reviews of timely advances in the field of xenobiotics. The text explores the research findings and procedures of The University of California-Davis Methodology for Deriving Aquatic Life Pesticide Water Quality Criteria.

Medicinal chemistry is both science and art. The science of medicinal chemistry offers mankind one of its best hopes for improving the quality of life. The art of medicinal chemistry continues to challenge its practitioners with the need for both intuition and experience to discover new drugs. Hence sharing the experience of drug research is uniquely beneficial to the field of medicinal chemistry. Drug research requires interdisciplinary team-work at the interface between chemistry, biology and medicine. Therefore, the topic-related series Topics in Medicinal Chemistry covers all relevant aspects of drug research, e.g. pathobiochemistry of diseases, identification and validation of (emerging) drug targets, structural biology, drugability of targets, drug design approaches, chemogenomics, synthetic chemistry including combinatorial methods, bioorganic chemistry, natural compounds, high-throughput screening, pharmacological in vitro and in vivo investigations, drug-receptor interactions on the molecular level, structure-activity relationships, drug absorption, distribution, metabolism, elimination, toxicology and pharmacogenomics. In general, special volumes are edited by well known guest editors.

Now in its third edition and supplemented with more online material, this book aims to make the "new" information-based (rather than gene-based) bioinformatics intelligible both to the "bio" people and the "info" people. Books on bioinformatics have traditionally served gene-hunters, and biologists who wish to construct family trees showing tidy lines of descent. While dealing extensively with the exciting topics of gene discovery and database-searching, such books have hardly considered genomes as information channels through which multiple forms and levels of information have passed through the generations. This "new bioinformatics" contrasts with the "old" gene-based bioinformatics that so preoccupies previous texts. Forms of information that we are familiar with (mental, textual) are related to forms with which we are less familiar (hereditary). The book extends a line of evolutionary thought that leads from the nineteenth century (Darwin, Butler, Romanes, Bateson), through the twentieth (Goldschmidt, White), and into the twenty first (the final works of the late Stephen Jay Gould). Long an area of controversy, diverging views may now be reconciled.

The series Topics in Heterocyclic Chemistry presents critical reviews on present and future trends in the research of heterocyclic compounds. Overall the scope is to cover topics dealing with all areas within heterocyclic chemistry, both experimental and theoretical, of interest to the general heterocyclic chemistry community. The series consists of topic related volumes edited by renowned editors with contributions of experts in the field. All chapters from Topics in Heterocyclic Chemistry are published Online First with an individual DOI. In references, Topics in Heterocyclic Chemistry is abbreviated as Top Heterocycl Chem and cited as a journal.

First published in 1943, Vitamins and Hormones is the longest-running serial published by Academic Press. In the early days of the Serial, the subjects of vitamins and hormones were quite distinct. Now, new discoveries have proved that several of the vitamins function as hormones and many of the substances inferred by the title of the Serial function in signal transduction processes. Accordingly, the Editor-in-Chief has expanded the scope of the serial to reflect this newer understanding of function-structure relationships in cellular communication. The Editorial Board now reflects expertise in the field of hormone action, vitamin action, X-ray crystal structure, physiology, and enzyme mechanisms.
Under the capable and qualified editorial leadership of Dr. Gerald Litwack, Vitamins and Hormones continues to publish cutting-edge reviews of interest to endocrinologists, biochemists, nutritionists, pharmacologists, cell biologists, and molecular biologists.
The 56th volume of Vitamins and Hormones is a cumulative index of volumes 30 through 55.

Medicinal chemistry is both science and art. The science of medicinal chemistry offers mankind one of its best hopes for improving the quality of life. The art of medicinal chemistry continues to challenge its practitioners with the need for both intuition and experience to discover new drugs. Hence sharing the experience of drug research is uniquely beneficial to the field of medicinal chemistry. Drug research requires interdisciplinary team-work at the interface between chemistry, biology and medicine. Therefore, the topic-related series Topics in Medicinal Chemistry covers all relevant aspects of drug research, e.g. pathobiochemistry of diseases, identification and validation of (emerging) drug targets, structural biology, drugability of targets, drug design approaches, chemogenomics, synthetic chemistry including combinatorial methods, bioorganic chemistry, natural compounds, high-throughput screening, pharmacological in vitro and in vivo investigations, drug-receptor interactions on the molecular level, structure-activity relationships, drug absorption, distribution, metabolism, elimination, toxicology and pharmacogenomics. In general, special volumes are edited by well known guest editors.

New genes and diversity leading to adaptation and evolution are generated in special areas of genomes. One such area in all eukaryotic genomes and in those prokaryotes with linear chromosomes is the region near the ends of the chromosomes. These telomere-associated sequences or subtelomeres, have different properties than the rest of the genome and are one of the most exciting frontiers left in genomics.

This book provides a broad introduction to the field of subtelomeres with detailed information from various fields and systems, covering yeasts and fungi, pathogens and parasites, plants, insects, humans and primates and bacteria with linear chromosomes. Advances in the field as well as continuing challenges are discussed throughout. The mosaic nature of this collection and the everchanging perspectives reflect the nature of subtelomeres themselves.

Unlike the core of most genomes, which are conserved and stable over time, subtelomeres are dynamic and polymorphic, so much so that generally no two individuals look alike in these regions. The dynamic nature of the region and the ability to change the copy number, generate diversity and try novel combinations make it the evolutionary tinker s toolbox. In many organisms the genes found in the region are involved in dealing with the environment. In yeasts, different gene families involved in sugar metabolism as well as clumping together are found in subtelomeres and differences in the region may be the reason why some strains are good for baking, others for brewing and why some are pathogenic. In fungal plant and animal pathogens, many of the genes involved in virulence are found here. In humans and primates there are a number of gene families that vary between ends, for example the diverse olfactory receptor genes. Even in bacterial linear chromosomes the region contains genes involved in adapting to their environments. Perhaps the ultimate use of these regions is in parasites where they rapidly adapt and escape from host immune systems through dynamic changes to the proteins exposed to the host s defenses. Such dynamic, polymorphic structures are also found in plants and insects though it is not always clear what the function might be; in some cases they take on the role of end maintenance. The dynamic, polymorphic nature of subtelomeres, where many ends share segmental duplications, is an exciting area for study but also presents a difficult challenge from the technical perspective."

The account in this inaugural volume of the series covers the period 1900 to 1960, but also outlines the principal developments in earlier centuries from which biochemistry emerged. Findings are considered in the light of present knowledge, rather than in a rigid historical framework.

The aim of this book is to return to the biomimicry and medicinal potential that inspired many of the early supramolecular chemists and to set it in the context of current advances in the field.

Following an overview of supramolecular chemistry, the first section considers the efforts made to synthesize artificial systems that mimic biological entities. The second section addresses the application of supramolecular principles to molecular diagnostics with a particular emphasis on the receptor-relayreporter motif. Many of the examples chosen have clinical importance. The third section takes the clinical diagnostic theme further and demonstrates the therapeutic applications of supramolecular chemistry through photodynamic therapy, drug delivery, and the potential for synthetic peptides to form antibiotic tubes. The short epilogue considers the potential for supramolecular solutions to be found for further challenges in biomimetic and therapeutic chemistry.