This up-to-date volume includes protocols that illustrate the broad use of chromatin immunoprecipitation (ChIP) and ChIP-related methods in a variety of biological research areas. The collection also includes protocols designed to improve the performance of ChIP for specific applications. 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, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Chromatin Immunoprecipitation: Methods and Protocols features techniques, including bioinformatic analysis of ChIP data, will be of interest to a very broad research community in the fields of biochemistry, molecular biology, microbiology, and biomedicine.

Nature, by dint of its constitution, harbors many unassuming mysteries broadly manifested by its constituent cohorts. If physics is the pivot that holds nature and chemistry provides reasons for its existence, then the rest is just manifestation. Nanoscience and technology harbor the congruence of these two core subjects, whereby many phenomenon may be studied in the same perspective. That nature operates at nanoscale-obeying the principles of thermodynamics and supramolecular chemistry-is a well understood fact manifested in a variety of life processes: bones are restored after a fracture; clots potentially leading to cerebral strokes can be dissolved. The regeneration of new structures in our system follows a bottom-up approach. Be it a microbe (benign or pathogenic), plant (lower or higher), plant parts/organs, food beneficiaries, animal (lower), higher animal processing wastes, these all are found to deliver nanomaterials under amenable processing conditions. Identically, the molecules also seem to obey the thermodynamic principles once they get dissociated/ionized and the energy captured in the form of bonding helps in the synthesis of a myriad of nanomaterials. This edited volume explores the various green sources of nanomaterial synthesis and evaluates their industrial and biomedical applications with a scope of scaling up. It provides useful information to researchers involved in the green synthesis of nanomaterials in fields ranging from medicine to integrated agricultural management.

This book comprehensively reviews the state-of-the-art strategies developed for protein-protein interaction (PPI) inhibitors, and highlights the success stories in new drug discovery and development. Consisting of two parts with twelve chapters, it demonstrates the design strategies and case studies of small molecule PPI inhibitors. The first part discusses various discovery strategies for small molecule PPI inhibitors, such as high throughput screening, hot spot-based design, computational approaches, and fragment-based design. The second part presents recent advances in small molecule inhibitors, focusing on clinical candidates and new PPI targets. This book has broad appeal and is of significant interest to the pharmaceutical science and medicinal chemistry communities.

Bioremediation refers to the clean-up of pollution in soil, groundwater, surface water, and air using typically microbiological processes. It uses naturally occurring bacteria and fungi or plants to degrade, transform or detoxify hazardous substances to human health or the environment. For bioremediation to be effective, microorganisms must enzymatically attack the pollutants and convert them to harmless products. As bioremediation can be effective only where environmental conditions permit microbial growth and action, its application often involves the management of ecological factors to allow microbial growth and degradation to continue at a faster rate. Like other technologies, bioremediation has its limitations. Some contaminants, such as chlorinated organic or high aromatic hydrocarbons, are resistant to microbial attack. They are degraded either gradually or not at all, hence, it is not easy to envisage the rates of clean-up for bioremediation implementation. Bioremediation represents a field of great expansion due to the important development of new technologies. Among them, several decades on metagenomics expansion has led to the detection of autochthonous microbiota that plays a key role during transformation. Transcriptomic guides us to know the expression of key genes and proteomics allow the characterization of proteins that conduct specific reactions. In this book we show specific technologies applied in bioremediation of main interest for research in the field, with special attention on fungi, which have been poorly studied microorganisms. Finally, new approaches in the field, such as CRISPR-CAS9, are also discussed. Lastly, it introduces management strategies, such as bioremediation application for managing affected environment and bioremediation approaches. Examples of successful bioremediation applications are illustrated in radionuclide entrapment and retardation, soil stabilization and remediation of polycyclic aromatic hydrocarbons, phenols, plastics or fluorinated compounds. Other emerging bioremediation methods include electro bioremediation, microbe-availed phytoremediation, genetic recombinant technologies in enhancing plants in accumulation of inorganic metals, and metalloids as well as degradation of organic pollutants, protein-metabolic engineering to increase bioremediation efficiency, including nanotechnology applications are also discussed.

Carbohydrate Chemistry provides review coverage of all publications relevant to the chemistry of monosaccharides and oligosaccharides in a given year. The amount of research in this field appearing in the organic chemical literature is increasing because of the enhanced importance of the subject, especially in areas of medicinal chemistry and biology. In no part of the field is this more apparent than in the synthesis of oligosaccharides required by scientists working in glycobiology. Clycomedicinal chemistry and its reliance on carbohydrate synthesis is now very well established, for example, by the preparation of specific carbohydrate- based antigens, especially cancer-specific oligosaccharides and glycoconjugates. Coverage of topics such as nucleosides, amino-sugars, alditols and cyclitols also covers much research of relevance to biological and medicinal chemistry. Each volume of the series brings together references to all published work in given areas of the subject and serves as a comprehensive database for the active research chemist Specialist Periodical Reports provide systematic and detailed review coverage in major areas of chemical research. Compiled by teams of leading authorities in the relevant subject areas, the series creates a unique service for the active research chemist, with regular, in-depth accounts of progress in particular fields of chemistry. Subject coverage within different volumes of a given title is similar and publication is on an annual or biennial basis.

The aim of this book is to show how supramolecular complexity of cell organization can dramatically alter the functions of individual macromolecules within a cell. The emergence of new functions which appear as a consequence of supramolecular complexity, is explained in terms of physical chemistry.
The book is interdisciplinary, at the border between cell biochemistry, physics and physical chemistry. This interdisciplinarity does not result in the use of physical techniques but from the use of physical concepts to study biological problems.
In the domain of complexity studies, most works are purely theoretical or based on computer simulation. The present book is partly theoretical, partly experimental and theory is always based on experimental results. Moreover, the book encompasses in a unified manner the dynamic aspects of many different biological fields ranging from dynamics to pattern emergence in a young embryo.
The volume puts emphasis on dynamic physical studies of biological events. It also develops, in a unified perspective, this new interdisciplinary approach of various important problems of cell biology and chemistry, ranging from enzyme dynamics to pattern formation during embryo development, thus paving the way to what may become a central issue of future biology.

Hormones, Regulators and Hippocampus, Volume 118 in the Vitamins and Hormones serial highlights new advances in the field, with this new volume presenting interesting chapters, including Thyroid hormone regulation of adult hippocampal neurogenesis - putative molecular and cellular mechanisms, Synergistic gene regulation by thyroid hormone and glucocorticoid in the hippocampus, Oxytocin and vasopressin in the hippocampus, Steroid hormones and hippocampal neurogenesis in the adult mammalian brain, Steroidogenic enzymes in the hippocampus: transcriptional regulation aspects, Ectonucleotidases in the hippocampus: spatial distribution and expression after ovariectomy and estradiol replacement, and much more.

This book offers a comprehensive overview of the microbiological fundamentals and biotechnological applications of methanotrophs: aerobic proteobacteria that can utilize methane as their sole carbon and energy source. It highlights methanotrophs' pivotal role in the global carbon cycle, in which they remove methane generated geothermally and by methanogens. Readers will learn how methanotrophs have been employed as biocatalysts for mitigating methane gas and remediating halogenated hydrocarbons in soil and underground water. Recently, methane has also attracted considerable attention as a potential next-generation carbon feedstock for industrial biotechnology, because of its abundance and low price. Methanotrophs can be used as biocatalysts for the production of fuels, chemicals and biomaterials including methanobactin from methane under environmentally benign production conditions. Sharing these and other cutting-edge insights, the book offers a fascinating read for all scientists and students of microbiology and biotechnology.

This book introduces characteristic features of the protein structure prediction (PSP) problem. It focuses on systematic selection and improvement of the most appropriate metaheuristic algorithm to solve the problem based on a fitness landscape analysis, rather than on the nature of the problem, which was the focus of methodologies in the past. Protein structure prediction is concerned with the question of how to determine the three-dimensional structure of a protein from its primary sequence. Recently a number of successful metaheuristic algorithms have been developed to determine the native structure, which plays an important role in medicine, drug design, and disease prediction. This interdisciplinary book consolidates the concepts most relevant to protein structure prediction (PSP) through global non-convex optimization. It is intended for graduate students from fields such as computer science, engineering, bioinformatics and as a reference for researchers and practitioners.

This volume contains refereed manuscripts prepared from presentations made at the 27th annual meeting of the International Society on Oxygen Transport to Tissue (ISOTT). The meeting was held in Hanover, NH, USA, at Dartmouth Medical School.

Rice is a vitally important staple food for almost half of the world's population. As the global population increases, the demands for rice are expected to remain high. Since the rice industry will remain sustainable for a long time, the production of rice by-products will remain high. Substantial evidence suggests that rice by-products such as rice husk, rice straw, broken rice, rice germ, rice bran, and brewers' rice may possess beneficial effects against oxidative stress and metabolic disorders. These beneficial effects have been linked to the phytochemicals present in rice by-products such as vitamin E, dietary fiber, -oryzanol, -aminobutyric acid (GABA), and phytosterols. Despite this evidence, the literature pertaining to rice by-products and its derived components has not well been compiled. To this end, Rice By-products: Phytochemicals and Food Products Application provides full coverage of issues pertaining to rice by-products, namely rice demands and rice by-products production, phytonutrients and antioxidant properties of rice by-products, potential health benefits, application in food products, and future prospects. By summarizing all the information in a lucid and comprehensive manner, authors provide a cohesive representation of the literature on the molecular mechanisms involved in the pharmacological effects of the bioactive components that present in rice by-products, as well as plausible means for the prevention of metabolic disorders for readers and allied stakeholders.

This book presents various examples of how advanced fluorescence and spectroscopic analytical methods can be used in combination with computer data processing to address different biochemical questions. The main focus is on evolutionary biochemistry and the description of biochemical and metabolic issues; specifically, the use of pulse amplitude modulated fluorescence (PAM) for the functional analysis of the cellular state, as well as results obtained by means of the derivative spectroscopy method characterizing structural reorganization of a cell under the influence of external factors, are discussed. The topics presented here will be of interest to biologists, geneticists, biophysicists and biochemists, as well as experts in analytical chemistry, pharmaceutical chemistry and radio chemistry and radio activation studies with protonen and alpha-particles. It also offers a valuable resource for advanced undergraduate and graduate students in biological, physical and chemical disciplines whose work involves derivative spectrophotometry and PAM-fluorescence.

This volume provides protocol references covering recent developments in the aptamer field. Within the last decade, aptamers have become more and more popular, and their sophisticated biophysical properties together with their ability to be easily modified and, thus, adapted to various regimens makes them a very promising class of compounds. Divided into three sections, the book covers selection, a series of analytical methods to assess biophysical properties of aptamer-target interactions, as well as various applications of aptamers. 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. Practical and easy to follow, Nucleic Acid Aptamers: Selection, Characterization, and Application provides a state-of-the-art summary of recent developments in the aptamer field and will be a helpful resource for scientists in the life sciences working with aptamers as tools to elucidate biological systems.

Recent advances in protein structural biology, coupled with new developments in human genetics, have opened the door to understanding the molecular basis of many metabolic, physiological, and developmental processes in human biology. Medical pathologies, and their chemical therapies, are increasingly being described at the molecular level. For single-gene diseases, and some multi-gene conditions, identification of highly correlated genes immediately leads to identification of covalent structures of the actual chemical agents of the disease, namely the protein gene products. Once the primary sequence of a protein is ascertained, structural biologists work to determine its three-dimensional, biologically active structure, or to predict its probable fold and/or function by comparison to the data base of known protein structures. Similarly, three-dimensional structures of proteins produced by microbiological pathogens are the subject of intense study, for example, the proteins necessary for maturation of the human HIV virus. Once the three-dimensional structure of a protein is known or predicted, its function, as well as potential binding sites for drugs that inhibit its function, become tractable questions. The medical ramifications of the burgeoning results of protein structural biology, from gene replacement therapy to "rational" drug design, are well recognized by researchers in biomedical areas, and by a significant proportion of the general population. The purpose of this book is to introduce biomedical scientists to important areas of protein structural biology, and to provide an insightful orientation to the primary literature that shapes the field in each subject.
The chapters in this volume cover aspects of protein structural biology which have led to the recognition of fundamental relationships between protein structure and function.

Leading researchers are specially invited to provide a complete understanding of the key topics in these archetypal multidisciplinary fields. In a form immediately useful to scientists, this periodical aims to filter, highlight and review the latest developments in these rapidly advancing fields.

This volume is a compilation of laboratory protocols and methodology required for the study of molecular chaperones and the cellular stress response. Chapters detail stress response in Hsf1, Hsf2 and Hsf4 knockout mice, mapping HSP interaction networks, the LUminescence-based Mammalian IntERactome (LUMIER), Hsp70 biology, protein folding activity of Hsp90, cytotoxicity of HSP inhibitors, computational approaches for modeling allosteric Hsp90 interactions, HSPs in immunity and vaccine development , and biologies of Hsp70 and Hsp90. Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Chaperones: Methods and Protocols aims to ensure successful results in the further study of this vital field.

The papers assembled in this volume were originally presented at the joint meeting of the Phytochemical Society of North America and the Mid-Atlantic Plant Molecular Biology Society, in August 2000. The symposium from which these chapters were prepared was entitled ""Regulation of Phytochemicals by Molecular Techniques"" and was organised by James Saunders and Ben Matthews. This joint meeting was timely because of recent landmark advances in molecular biology and genomics as well as the renewed interest in phytochemistry as a rich source of nutraceuticals, drugs, and alternatives to synthetic agriculture pesticides. Progress in genome sequencing in plants such as Arabidopsis and rice has been remarkable, as have expressed sequence tag (EST) projects in other plants, including maize and soybean. Recently, private and public sector participants of the Human Genome Project announced that a rough draft of the human genome has been constructed. These advances directly influence phytochemical investigations by providing both insight and tools for exploring and manipulating genomes.
The chapters cover a wide range of applications from molecular biology to phytochemistry, and from basic studies on promoters and gene expression to pathway regulation and engineering with transformed plants. A number of noteworthy aspects emerge from this volume: applications of molecular biology to phytochemical practical problems are succeeding; newly emerging molecular tools promise to open new doors to discovery; and remarkable progress has already occurred in phytochemical pathway engineering.

Epidemiology and Carcinogenesis.- Evidence from Animal Studies for the Carcinogenicity of Inhaled Diesel Exhaust.- Interpretation of Carcinogenicity and Effective Dose in Chronic Exposures of Rats to High Diesel Exhaust Concentrations.- Carcinogenicity of Dinitroarenes in Rat Lung.- In Vivo Metabolism and Genotoxic Effects of the Air Pollutant and Marker for Nitro-PAH's, 2-Nitrofluorene.- Chemistry, Detection, and Occurrence.- Nitroarenes: Their Detection, Mutagenicity and Occurrence in the Environment.- The Atmospheric Formation of Nitroarenes and Their Occurrence in Ambient Air.- Metabolism of 1-Nitropyrene Oxides and Effect of Nitrogen Dioxide on Arene Activation.- Molecular Mechanisms.- Mutagenic and Biochemical Consequences of the Reaction of Arylamines with DNA.- Mutagenesis Induced by a Single Acetylaminofluorene Adduct within the Narl Site is Position Dependent.- Unusual Hydrogen Bonding Patterns in 2-Aminofluorene (AF) and 2-Acetylaminofluorene (AAF) Modified DNA.- DNA Adduct Formation during Chronic Administration of an Aromatic Amine.- Aerial Oxidation of Acetylaminofluorene-Derived DNA Adducts.- Mutations and Homologous Recombination Induced by N-Substituted Aryl Compounds in Mammalian Cells.- Comparison of the Mutagenic Potency of DNA Adducts Formed by Reactive Derivatives of Aflatoxin, Benzidine and 1-Nitropyrene in a Plasmid System.- Mutations Induced in the lacI Gene of E. coli by 1-Nitroso-8-Nitropyrene and Furylfuramide: The Influence of Plasmid pKM101 and Excision Repair on the Mutational Spectrum.- DNA Adduct Formation by 1-Nitropyrene 4,5- and 9,10-Oxide.- Nitropolycyclic Aromatic Hydrocarbons and Diesel Exhaust: Potential Role of DNA Binding in Carcinogenicity.- Validation/Application of 32?-Postlabeling Analysis for the Detection of DNA Adducts Resulting from Complex Air Pollution Sources Containing PAHs and Nitrated PAHs.- Analysis of NO2-PAH DNA Adducts by Mass Spectrometry.- Metabolism.- Generation of Reactive Intermediates from 2-Nitrofluorene that Bind Covalently to DNA, RNA and Protein In Vitro and In Vivo in the Rat.- Activation of Carcinogenic N-Arylhydroxamic Acids by Peroxidase/H2O2/Halide Systems: Route to C-Nitroso Aromatics.- Biochemical Studies on the Putative Nitroso Metabolite of Chloramphenicol: A New Model for the Cause of Aplastic Anemia.- Mechanisms of FANFT/ANFT Induced Bladder Cancer.- Mutagenic Arylazides, Arylnitrenes, Arylnitrenium Ions.- Products Obtained by In Vitro Reaction of 4,5-Epoxy4,5-Dihydro-1-Nitropyrene with DNA.- Oxidative Metabolism of Nitrated Polycyclic Aromatic Hydrocarbons in Mammalian Cell Fractions.- Metabolic Activation of 6-Nitrochrysene and 6-Aminochrysene In Vitro and In Vivo.- Summary.- The Possible Role of Nitroarenes in Human Cancer.- Abstracts Presented at the Meeting.- Contributor Index.

Hereditary tyrosinemia type 1 (HT1), the most severe inborn error of the tyrosine degradation pathway, is due to a deficiency in fumarylacetoacetate hydrolase (FAH). The worldwide frequency of HT1 is one per 100,000 births, but some regions have a significantly higher incidence (1:1,800). The FAH defect results in the accumulation of toxic metabolites, mainly in the liver. If left untreated, HT1 is usually fatal before the age of two. HT1 patients develop several chronic complications including cirrhosis with a high risk of hepatocellular carcinoma (HCC) and neuropsychological impairment. Treatment comprises an inhibitor of the pathway, Nitisinone, a strict dietary treatment or liver transplantation. Early treatment is important to avoid HCC. The book includes the latest developments on the molecular basis of HT1, its pathology, screening and diagnosis and management of the disease written by leading scientists, geneticists, hepatologists and clinicians in the field.

This book covers structure, function, and important roles of the SH domains, structure-function relationships, the versatile nature of their action, mechanisms of aggregation, specificity of interactions, impact of mutations on protein functional dysregulation, and cell signaling. Their involvement in various cellular processes such as migration, invasiveness, actin reorganization, shaping spines, determination of the morphology assembly of fibrils, and mechanotransduction makes these molecules attractive drug targets. Substrates, inhibitors and activators of PTKs present a wide variety of therapeutic agents in the context of delivering treatments for numerous pathologies. The new emerging field of stem cell therapies and design of biomaterials for treatments relies on the directed regulation of stem cell growth, differentiation and morphology, as well as the production of biomimetic scaffolds that respond to programmed signals. Advances in deciphering the mechanisms of action of these important molecules will lead to the implementation and success of their vital applications.

This book is a passionate account of the scientific breakthroughs that led to the solution of the first protein structures and to the understanding of their function at atomic resolution. The book is divided into self-standing chapters that each deal with a protein or protein family. The subject is presented in a fluid, non-technical style that will engage student and scientists in biochemistry, biophysics, molecular and structure biology and physiology.

This book sheds new light on the current state of knowledge concerning chromatin organization. Particular emphasis is given to the new imaging potential offered by super-resolution microscopy, which allows DNA imaging with a very high labeling density. From the early work on chromosomes by Walther Flemming in the nineteenth century to recent advances in genomics, the history of chromatin research now spans more than a century. The various milestones, such as the discovery of the double helix structure, the sequencing of the human genome, and the recent description of the genome in 3D space, show that understanding chromatin and chromosome function requires a clear understanding of its structure. Presenting cutting-edge data from super-resolution single molecule microscopy, the book demonstrates that chromatin manifests several levels of folding, from nucleosomes to chromosomes. Chromatin domains emerge as a new fundamental building block of chromatin architecture, with functions possibly related to gene regulation. A detailed description of chromatin folding in the pachytene stage of meiosis serves as a model for exploring this functionality, showing the apparent interplay between structure, function, and epigenetic regulation. Lastly, the book discusses possible new avenues of innovation to describe chromatin's organization and functions. Gathering essential insights on chromatin architecture, the book offers students an introduction to microscopy and its application to chromatin organization, while also providing advanced readers with new ideas for future research.