This series encompasses design, synthesis, application, and analytical methods (including clinical and in vitro) for the study of these critical interactions. As our understanding of the genome and proteome expands, general developments in the field of DNA sequence specific interaction are likely to play an increasingly important role. Accordingly, manuscripts have been solicited from experts covering a diverse range of fields, reflecting the cross-disciplinary and dynamic nature of the series.

Volume 4 describes work on the modification of DNA by AT specific anticancer drugs, DNA alkylation events which involve metabolite generation, DNA sequence recognition by two selective binders, bulged DNA microenvironments as molecular targets, DNA sequence specific binding by short peptides and the analysis of DNA-protein interactions using DNase I footprinting methodology.

Features include:
Expert contributors from the Biomedical world
Emerging areas of drug design and therapeutic applications
Nucleic acid-protein interactions
Color graphics of molecular modeling analyses
New and emerging methodologies
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Updated and revised, this thorough volume is organized such that it begins with techniques related to the study of chromatin structure. Protocols for reconstitution of chromatin on solid supports for analysis, preparation of positioned mononucleosomes, techniques to study premature chromatin condensation and the use of comparative genomic hybridization to assess genomic aberration are included as well. Novel techniques for imaging chromatin using atomic force microscopy and the isolation of specific genomic regions using engineered DNA binding molecules generated by CRISPR are then examined. That section is followed by protocols to analyze DNA and histone modifications, while the third section includes methods to study DNA replication and repair, in the context of chromatin. Last but not least, protocols for studying chromatin and its relation with transcriptional regulation are presented in a fourth section. 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 up-to-date, Chromatin Protocols, Third Edition aims to help researchers in facilitating in-depth molecular analysis of various aspects of chromatin structure and function.

Supramolecular chemistry is the outburst topic of the next generation of science. While the majority of biomedical research efforts to date have centered on utilizing well-known polymeric materials, the recent progress in supramolecular chemistry has introduced a fascinating new field of macromolecular architecture.

Supramolecular Design for Biological Applications focuses on modulating, altering, and mimicking biological functions with a new family of molecular assemblies. The authors provide innovative ideas and concepts for developing novel biomaterials that could be applied in diagnosis, drug carrier operations, and environmental protection. This reference is comprehensive, presenting principles, applications, recent advances, and future directions. Each chapter includes clear and informative illustrations of molecular architectures. The writing is scientific but allows for easy comprehension of the differences in molecular interactions, dimensions, and supramolecular architecture.

Supramolecular Design for Biological Applications will advance the understanding of supramolecular-structured biomaterials and associated issues regarding biological functions. By explaining recent trends and molecular interactions, this book will enable you to initiate new research for nano-scale science and technology in the 21st century.

In today's world, we are witnessing simultaneous breakthroughs in reproductive technologies, genomics, and molecular biology. Advances in molecular genetic technology and understanding of the bovine genome have led to the development of tools that can be used to enhance profitability on cow-calf enterprises. Factors Affecting Calf Crop: Biotechnology of Reproduction provides a detailed compilation of current and forthcoming technology for managing reproduction in cattle.

The book discusses topics such as: approved techniques for controlling the estrous cycle in cattle; managing follicular growth with progesterone, estrogens, and prostaglandins; freezing, thawing, and transfer of cattle embryos; application of embryo transfer to the beef cattle industry; embryo transfer in topically adapted cattle; new factors affecting bull fertility; embryo collection and utilization technology, in vitro fertilization, somatic cell cloning, and genetic technologies; uses of real-time ultrasound; and sexed semen.

Over 25 leading animal scientists have combined their expertise to produce the first single-source reference that covers successful reproductive techniques that will, most likely, be the wave of the future. Expansive in scope, the book addresses current biotechnologies as they impact the production of beef cattle. Written at a level to appeal to the researcher, commercial producer, or student, Factors Affecting Calf Crop: Biotechnology of Reproduction presents you with a wealth of technologies applicable to animal agriculture.

Medical science constantly demands our attention, as patients or relatives, concerned citizens, voters, investors, or simply curious individuals. But for those without training, the language of science is often hard to follow. The A to Z of DNA Science book series defines and illustrates specialized terms in ways that non-specialists can appreciate and enjoy. This volume focuses on the language of genes, genomes, DNA, biotechnology, and heredity, defining, explaining, and illustrating over 200 terms used in books, broadcasting, websites, and newspaper and magazine articles.

Providing an interface between dry-bench bioinformaticians and wet-lab biologists, DNA Methylation Microarrays: Experimental Design and Statistical Analysis presents the statistical methods and tools to analyze high-throughput epigenomic data, in particular, DNA methylation microarray data. Since these microarrays share the same underlying principles as gene expression microarrays, many of the analyses in the text also apply to microarray-based gene expression and histone modification (ChIP-on-chip) studies. After introducing basic statistics, the book describes wet-bench technologies that produce the data for analysis and explains how to preprocess the data to remove systematic artifacts resulting from measurement imperfections. It then explores differential methylation and genomic tiling arrays. Focusing on exploratory data analysis, the next several chapters show how cluster and network analyses can link the functions and roles of unannotated DNA elements with known ones. The book concludes by surveying the open source software (R and Bioconductor), public databases, and other online resources available for microarray research. Requiring only limited knowledge of statistics and programming, this book helps readers gain a solid understanding of the methodological foundations of DNA microarray analysis.

In Situ hybridization allows the visualization of specific DNA/RNA sequences in individual cells in tissue sections, single cells, or chromosome preparations, and is an especially important method for studying DNA and RNA in heterogeneous cell populations. This book delves into in situ hybridization methods through the use of light microscopy used by molecular biologists, pathologists, geneticists, and biochemists. It will also appeal to research scientists who are interested in visualizing methods for nucleic acids and proteins. The book features a two-column layout for protocols/principles, simplifies the techniques and offers many schemes and tables to help the reader choose the best procedure.

Understanding gene expression and how it changes under normal and pathological conditions is essential to our understanding of the fundamentals of cell biology through to the targeted treatment of disease. In Gene Expression Profiling: Methods and Protocols, Second Edition, experts in their particular fields compile detailed protocols for a broad range of techniques, currently available and being further developed, for the analysis of gene expression at the DNA, RNA, and protein levels. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and easy-to-use, Gene Expression Profiling: Methods and Protocols, Second Edition presents a collection of clearly described and illustrated chapters, certain to be helpful to researchers in academia, in hospitals, and in industry who are interested in applying techniques, whether basic or advanced, for the analysis of gene expression.

When a pharmaceutical company decides to build a Quality System, it has to face the fact that there aren't any guideline that define exactly how such a system has to be built. With terms such as quality system, quality assurance, and quality management used interchangeably, even defining the system's objectives is a problem. This book provides a practical guide to building a quality system. Beginning with explanations of key terms and concepts, it covers ISO 9000 and GMP and how to combine them, and includes a matrix showing their similarities and differences. Implementation reviews illustrate how Quality (Management) Systems have been installed successfully in pharmaceutical companies. Also covered are the individual components of a Quality System; auditing, validation, and supplier qualification systems; and Hazard Analysis Critical Control Points (HACCP).

This book covers the principles of cryopreservation as they relate the preservation of viable cells and cell materials being developed for biopharmaceutical applications. Topics include: the principles of freezing and thawing cells, physiochemical phenomena, process and system design options, method selection considerations, preservation procedures, cryoprotectant additives, freeze-drying human live virus vaccines, and transport system selection criteria. Contributions from well-known experts such as Steven S. Lee, Thomas C. Pringle, William H. Siegel, Richard Wisniewski, and Fangdong Yin make this the single most important study available.

From the Preface
Antibody techniques have allowed us to study microorganisms in situ. However, until recently all methodology lacked the sensitivity necessary for environmental work where microorganisms are in most cases present at very low concentrations or where microbial ecosystems contain a myriad of different organisms. Gene probes have been used successfully for a variety of samples, but this method was still not sensitive enough. The next logical step was the application of the recently developed DNA amplification technique known as the polymerase chain reaction, or PCR. Since then, many laboratories around the world have adopted PCR for environmental work.
Samples obtained from soils, water and air are enormously complex because they are unknown mixtures of DNA and other compounds. Thus, procedures for target DNA amplification from the environment require special attention. The PCR has allowed us to go beyond the need for culturing prior to analysis of microbial communities. It has been shown that even microorganisms that can be routinely grown in the laboratory undergo some physiological changes when exposed to the environment. One of these changes (first observed by R. Colwell and colleagues) is known as the viable-but-non-culturable state, and seems to be a common occurrence. Thus, the use of culture techniques paint only part of the picture in terms of microbial behavior under environmental conditions. The ability to amplify nucleic acids by the PCR has brought about a myriad of very ingenious modifications to the technique that can then be used to study complex ecosystems. The manner in which the PCR can be modified is only limited by the need and/or the imagination of the researcher.
The first manual dedicated specifically to the analysis (by PCR) of environmental samples, Environmental Applications of Nucleic Acid Amplification Techniques presents state of the art methodology for the detection of microorganisms in soil, water, air samples, as well as the amplification of nucleic acids from fossil samples. The manual gives step-by-step procedures for the analysis of these samples. Although several publications have addressed the use of Polymerase Chain Reaction technique, very few of them have been directed toward the application of this technique to environmental samples. This book fills this gap in the literature.

This manual encompasses an integrated series of molecular biology laboratory exercises that involve the cloning and analysis of the bioluminescence "(lux)" genes from the marine bacterium "Vibrio fischeri." The manual is divided into discrete units with each demonstrating one or more aspects of the cloning project. The manual is based on one of nature's most fascinating biological phenomenon: the biological production of light. This results in a recurrent theme of interest and makes the project very relevant to interdisciplinary topics such as fish symbiosis, biochemistry, biophysics, etc. Includes instruction in the basic techniques of modern molecular biology: DNA isolation and analysis, DNA restriction, agarose gel electrophoresis, ligations, transformation of recombinant DNA, preparation and screening a genomic library, restriction mapping, Southern blotting, hybridization, DNA sequencing, pulsed field gel electrophoresis. Designed for a one semester course in Molecular Biology. Also appropriate for a molecular biology component of Microbial Genetics, Genetics, Biochemistry, or Advanced Microbiology courses.

From the early days when RNA interference was a strange artifact in worms to the 2006 Noble Prize received by Fire and Mello and the current clinical trials, the field of RNA interference has grown at a breakneck pace. In RNA Interference: From Biology to Clinical Applications, expert contributors provide an overview of the most current science and protocols that span the biological disciplines from detailed nucleic acid chemistry, to pharmacology, to the manipulation of signal transduction pathways. Divided into three distinct sections, this volume delves into the physiology of RNA interference, RNA interference in the laboratory and siRNA delivery, and preclinical and clinical issues associated with the use of RNAi-inducing agents as drugs in order to stimulate new questions and offer the tools necessary to start addressing those questions. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and inspiring, RNA Interference: From Biology to Clinical Applications aims to promote and motivate innovation by reviewing what has been done, providing details of how it has been done, and encouraging speculation on what the future may hold.

The Greek word apoptosis was used first by Hippocrates as a synonym of dislocations of the bones, structural changes related to tissue, by Marcus Aurelius in political and social context as failure and decline. The physician Galen extended the medical meaning of apoptosis to wound healing and inflammation.

Apoptosis, or cell suicide is an integral part of life cycle of plants and animals indicated by the loss of 140-190g (50-70 billion) cells each day in the human adult, amounting to the body weight in one year. The growing interest in apoptosis is indicated by the number of scientific publications since the 1990s which is now more than 140,000 and will exceed 160,000 by the end of 2008.

The unique feature of this book is the use of synhronized and reversibly permeabilized cells allowing to visualize the dynamic nature of chromatin condensation through transitory chromatin and chromosomal forms including changes upon genotoxic treatment, which were not seen earlier. The chromatin condensation process is illustrated from string (DNA) to rope (chromosomes) in more than 160 figures. The interdisciplinary nature of studies summarized in the book facilitate the global view of readers interested in the higher order structure of nucleic acids. The wealth of additional information will attract a wide population of readers. The natural audience engaged in DNA research such as genetics, cell biology, biochemistry, molecular biology will find that it contains essential material.

This volume contains a compilation of techniques and laboratory protocols directly related to RNA nano technology and its applications in nano biotechnology and nano medicine. The chapters in this book cover a wide range of research methods that can be easily comprehended and carried out in a step-by-step manner by graduate students and postdoctoral fellows from diverse scientific disciplines. Some of the covered topics include various biochemical, biophysical and bioinformatics approaches for analyzing RNA structures and properties; methods to analyze the multi-step assembly process of RNA nano architectures; purification of multifunctional RNA nanoparticles by ultracentrifugation and HPLC; real-time detection of RNA nano constructs in vivo; conjugation of imaging, targeting and therapeutic modules to RNA scaffold; and design and characterization of RNA-protein nanostructures. Written in the highly successful Methods of 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 key tips on troubles troubleshooting and avoiding known pitfalls. Cutting-edge and practical, RNA Nanotechnology and Therapeutics: Methods and Protocols propels the field toward new heights by engaging researchers working in the diverse fields of physical, engineering, and life sciences.

DNA Repair and Replication brings together contributions from active researchers. The first part of this book covers most aspects of the DNA damage response, emphasizing the relationship to replication stress. The second part concentrates on the relevance of this to human disease, with particular focus on both the causes and treatments which make use of DNA Damage Repair (DDR) pathways. Key Selling Features: Chapters written by leading researchers Includes description of replication processes, causes of damage, and methods of repair

Recent insight into the transcripts generated from the mammalian genome (i.e. the transcriptome) has revealed that transcription is a far more complex phenomenon than previously thought. In RNA: Methods and Protocols, expert researchers provide the procedures and methods used to describe the structure of messenger RNAs and non-coding RNAs that are transcribed by RNA polymerase II as the immediate gene products in mammalian cells. Focused on the structure of the RNA products of "gene X" and the mapping of proteins associated with these RNAs, the volume presents appropriate information for non-specialists in RNA biology. Written in the highly successful Methods in Molecular Biology (TM) series format, many chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, RNA: Methods and Protocols views the transcriptional landscape with an appreciation for the role that proteins play in the processing and interpretation of genetic information in an attempt to further our crucial knowledge of the many products and sophisticated regulatory networks that result from it.

Epigenetic modifications act on DNA and its packaging proteins, the histones, to regulate genome function. Manifest as the heritable methylation of DNA and as post-translational histone modifications, these molecular flags influence the architecture and integrity of the chromosome, the accessibility of DNA to gene regulatory components and the ability of chromatin to interact within nuclear complexes. While a multicellular individual has only one genome, it has multiple epigenomes reflecting the diversity of cell types and their properties at different times of life; in health and in disease. Relationships are emerging between the underlying DNA sequence and dynamic epigenetic states and their consequences,such as the role of RNA interference and non-coding RNA. These integrated approaches go hand-in-hand with studies describing the genomic locations of epigenetic modifications in different cell types at different times. The excitement and curiosity surrounding epigenomics is driven by a growing community of researchers in a burgeoning field and the development of new technologies built on the backbone of genome sequencing projects. Research has shown that the adaptability and vulnerability of epigenetic states has profound effects on natural variation, the response of the genome to its environment and on health and disease. The aim of this volume is not to describe epigenomes, but rather to explore how understanding epigenomes tells us more about how biological systems work and the challenges and approaches taken to accomplish this. These contributions have attempted to integrate epigenomics into our understanding of genomes in wider context, and to communicate some of the wonders of epigenetics illustrated through examples across the biological spectrum.

This book contains papers, presented at the eighth annual FoodPlas conference held in Orlando, Florida in 1991, on the role of plastics in supermarkets, food processors and food companies, and on the regulations and design for plastics packaging.

Microarray Image and Data Analysis: Theory and Practice is a compilation of the latest and greatest microarray image and data analysis methods from the multidisciplinary international research community. Delivering a detailed discussion of the biological aspects and applications of microarrays, the book: Describes the key stages of image processing, gridding, segmentation, compression, quantification, and normalization Features cutting-edge approaches to clustering, biclustering, and the reconstruction of regulatory networks Covers different types of microarrays such as DNA, protein, tissue, and low- and high-density oligonucleotide arrays Examines the current state of various microarray technologies, including their availability and affordability Explains how data generated by microarray experiments are analyzed to obtain meaningful biological conclusions An essential reference for academia and industry, Microarray Image and Data Analysis: Theory and Practice provides readers with valuable tools and techniques that extend to a wide range of biological studies and microarray platforms.

Genome Stability: DNA Repair and Recombination describes the various mechanisms of repairing DNA damage by recombination, most notably the repair of chromosomal breaks. The text presents a definitive history of the evolution of molecular models of DNA repair, emphasizing current research. The book introduces the central players in recombination. An overview of the four major pathways of homologous recombinational repair is followed by a description of the several mechanisms of nonhomologous end-joining. Designed as a textbook for advanced undergraduate and graduate students with a molecular biology and genetics background, researchers and practitioners, especially in cancer biology, will also appreciate the book as a reference.

This book provides an introduction to the latest gene mapping techniques and their applications in biomedical research and evolutionary biology. It especially highlights the advances made in large-scale genomic sequencing. Results of studies that illustrate how the new approaches have improved our understanding of the genetic basis of complex phenotypes including multifactorial diseases (e.g., cardiovascular disease, type 2 diabetes, and obesity), anatomic characteristics (e.g., the craniofacial complex), and neurological and behavioral phenotypes (e.g., human brain structure and nonhuman primate behavior) are presented. Topics covered include linkage and association methods, gene expression, copy number variation, next-generation sequencing, comparative genomics, population structure, and a discussion of the Human Genome Project. Further included are discussions of the use of statistical genetic and genetic epidemiologic techniques to decipher the genetic architecture of normal and disease-related complex phenotypes using data from both humans and non-human primates.

This volume provides established approaches for identifying, characterizing, and manipulating circRNAs in vitro, in vivo, and in silico. Chapters highlight the breakthroughs and the challenges in this new field of research. 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, Circular RNAs: Methods and Protocols aims to useful and informative for further study into this vital field.

Life's Greatest Secret is the story of the discovery and cracking of the genetic code. This great scientific breakthrough has had far-reaching consequences for how we understand ourselves and our place in the natural world. The code forms the most striking proof of Darwin's hypothesis that all organisms are related, holds tremendous promise for improving human well-being, and has transformed the way we think about life. Matthew Cobb interweaves science, biography and anecdote in a book that mixes remarkable insights, theoretical dead-ends and ingenious experiments with the pace of a thriller. He describes cooperation and competition among some of the twentieth century's most outstanding and eccentric minds, moves between biology, physics and chemistry, and shows the part played by computing and cybernetics. The story spans the globe, from Cambridge MA to Cambridge UK, New York to Paris, London to Moscow. It is both thrilling science and a fascinating story about how science is done.

'Species' are central to understanding the origin and dynamics of biological diversity; explaining why lineages split into multiple distinct species is one of the main goals of evolutionary biology. However the existence of species is often taken for granted, and precisely what is meant by species and whether they really exist as a pattern of nature has rarely been modelled or critically tested. This novel book presents a synthetic overview of the evolutionary biology of species, describing what species are, how they form, the consequences of species boundaries and diversity for evolution, and patterns of species accumulation over time. The central thesis is that species represent more than just a unit of taxonomy; they are a model of how diversity is structured as well as how groups of related organisms evolve. The author adopts an intentionally broad approach, stepping back from the details to consider what species constitute, both theoretically and empirically, and how we detect them, drawing on a wealth of examples from microbes to multicellular organisms.