The second edition of Horizontal Gene Transfer has been organized to provide a concise and up-to-date coverage of the most important discoveries in this fascinating field. Written by the most prominent gene transfer and genome analytical scientists, this book details experimental evidence for the phenomenon of horizontal gene transfer and discusses further evidence provided by the recent completion of genomic sequences from Archea, Bacteria, and Eucarya members. The relevance of horizontal gene transfer to plant and metazoan taxonomy, GM foods, antibiotic resistance, paleontology, and phylogenetic reconstruction is also explored. Horizontal Gene Transfer is essential for microbiologists, geneticists, biochemists, evolutionary biologists, infectious disease specialists, paleontologists, ecologists, and researchers working in plant/animal systematics and agriculture with an interest in gene transfer. This includes scientific researchers from government and industry concerned with the release of genetically modified organisms.
Up-to-the-minute reviews, maps, conclusions, urls to relevant websites and colour figures.
Unique chapters, for example one written by paleontologists presents data for horizontal gene transfer from fingerprints form the fossil record.

What are the genomic signatures of adaptations in DNA? How often does natural selection dictate changes to DNA? How does the ebb and flow in the abundance of individuals over time get marked onto chromosomes to record genetic history? Molecular population genetics seeks to answer such questions by explaining genetic variation and molecular evolution from micro-evolutionary principles. It provides a way to learn about how evolution works and how it shapes species by incorporating molecular details of DNA as the heritable material. It enables us to understand the logic of how mutations originate, change in abundance in populations, and become fixed as DNA sequence divergence between species. With the revolutionary advances in genomic data acquisition, understanding molecular population genetics is now a fundamental requirement for today's life scientists. These concepts apply in analysis of personal genomics, genome-wide association studies, landscape and conservation genetics, forensics, molecular anthropology, and selection scans. This book introduces, in an accessible way, the bare essentials of the theory and practice of molecular population genetics.

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.

Written by an international team of experts, Somatic Genome Variation presents a timely summary of the latest understanding of somatic genome development and variation in plants, animals, and microorganisms. Wide-ranging in coverage, the authors provide an updated view of somatic genomes and genetic theories while also offering interpretations of somatic genome variation. The text provides geneticists, bioinformaticians, biologist, plant scientists, crop scientists, and microbiologists with a valuable overview of this fascinating field of research.

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).

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.

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.

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

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 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.

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.

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 field of materials science and technology has undergone revolutionary advances due to the development of novel analytical tools, functional materials, and multidisciplinary approaches to engineering. Additionally, theoretical predictions combined with increasingly improved models and computational capabilities are making impressive contributions to the progress of materials science and technology. In particular, the materials science of DNA has emerged as a vital area of research and is expected to immensely broaden the horizon of material science and nanotechnology in this century. Materials Science of DNA highlights the most important subjects and perspectives in the field, with the aim of stimulating the interdisciplinary community and bringing this intensively interesting, emerging field of molecular-scale materials science to maturation. The editors have not only been involved in the research of materials science of DNA for the past decade, but also lead the series of International Biotronics Workshops supported by the US Air Force Research Laboratory. Biotechnology and DNA-based biopolymers are not only applicable for genomic sequencing and clinical diagnosis and treatment, but can also have a major impact on nonbiotech applications-such as electronics and photonics- opening up a whole new field for bioengineering. New concepts and insights gained from DNA research are expected to prove genuinely useful in a variety of devices in nano, micro, and macro dimensions in the future. Where silicon has been the building block of inorganic electronics and photonics, DNA holds promise to become the building block for organic electronics and photonics.

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.

The Affymetrix GeneChip (R) system is one of the most widely adapted microarray platforms. However, due to the overwhelming amount of information available, many Affymetrix users tend to stick to the default analysis settings and may end up drawing sub-optimal conclusions. Written by a molecular biologist and a biostatistician with a combined decade of experience in practical expression profiling experiments and data analyses, Gene Expression Studies Using Affymetrix Microarrays tears down the omnipresent language barriers among molecular biology, bioinformatics, and biostatistics by explaining the entire process of a gene expression study from conception to conclusion. Truly Multidisciplinary: Merges Molecular Biology, Bioinformatics, and Biostatistics This authoritative resource covers important technical and statistical pitfalls and problems, helping not only to explain concepts outside the domain of researchers, but to provide additional guidance in their field of expertise. The book also describes technical and statistical methods conceptually with illustrative, full-color examples, enabling those inexperienced with gene expression studies to grasp the basic principles. Gene Expression Studies Using Affymetrix Microarrays provides novices with a detailed, yet focused introductory course and practical user guide. Specialized experts will also find it useful as a translation dictionary to understand other involved disciplines or to get a broader picture of microarray gene expression studies in general. Although focusing on Affymetrix gene expression, this globally relevant guide covers topics that are equally useful for other microarray platforms and other Affymetrix applications.

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.

Advances in sequencing technology have allowed scientists to study the human genome in greater depth and on a larger scale than ever before - as many as hundreds of millions of short reads in the course of a few days. But what are the best ways to deal with this flood of data? Algorithms for Next-Generation Sequencing is an invaluable tool for students and researchers in bioinformatics and computational biology, biologists seeking to process and manage the data generated by next-generation sequencing, and as a textbook or a self-study resource. In addition to offering an in-depth description of the algorithms for processing sequencing data, it also presents useful case studies describing the applications of this technology.

Computational and high-throughput methods, such as genomics, proteomics, and transcriptomics, known collectively as -omics, have been used to study plant biology for well over a decade now. As these technologies mature, plant and crop scientists have started using these methods to improve crop varieties. Omics in Plant Breeding provides a timely introduction to key omicsbased methods and their application in plant breeding. Omics in Plant Breeding is a practical and accessible overview of specific omics-based methods ranging from metabolomics to phenomics. Covering a single methodology within each chapter, this book provides thorough coverage that ensures a strong understanding of each methodology both in its application to, and improvement of, plant breeding. Accessible to advanced students, researchers, and professionals, Omics in Plant Breeding will be an essential entry point into this innovative and exciting field. A valuable overview of high-throughput, genomics-based technologies and their applications to plant breeding Each chapter explores a single methodology, allowing for detailed and thorough coverage Coverage ranges from well-established methodologies, such as genomics and proteomics, to emerging technologies, including phenomics and physionomics Aluizio Borem is a Professor of Plant Breeding at the University of Vicosa in Brazil. Roberto Fritsche-Neto is a Professor of Genetics and Plant Breeding at the University of Sao Paulo in Brazil.

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.

Oligonucleotides represent one of the most significant pharmaceutical breakthroughs in recent years, showing great promise as diagnostic and therapeutic agents for malignant tumors, cardiovascular disease, diabetes, viral infections, and many other degenerative disorders. The Handbook of Analysis of Oligonucleotides and Related Products is an essential reference manual on the practical application of modern and emerging analytical techniques for the analysis of this unique class of compounds. A strong collaboration among thirty leading analytical scientists from around the world, the book provides readers with a comprehensive overview of the most commonly used analytical techniques and their advantages and limitations in assuring the identity, purity, quality, and strength of an oligonucleotide intended for therapeutic use. Topics discussed include: Strategies for enzymatic or chemical degradation of chemically modified oligonucleotides toward mass spectrometric sequencing Purity analysis by chromatographic or electrophoretic methods, including RP-HPLC, AX-HPLC, HILIC, SEC, and CGE Characterization of sequence-related impurities in oligonucleotides by mass spectrometry and chromatography Structure elucidation by spectroscopic methods (IR, NMR, MS) as well as base composition and thermal melt analysis (Tm) Approaches for the accurate determination of molar extinction coefficient of oligonucleotides Accurate determination of assay values Assessment of the overall quality of oligonucleotides, including microbial analysis and determination of residual solvents and heavy metals Strategies for determining the chemical stability of oligonucleotides The use of hybridization techniques for supporting pharmacokinetics and drug metabolism studies in preclinical and clinical development Guidance for the presentation of relevant analytical information towards meeting current regulatory expectations for oligonucleotide therapeutics This resource provides a practical guide for applying state-of-the-art analytical techniques in research, development, and manufacturing settings.

Assembling the work of an international panel of researchers, Mass Spectrometry of Nucleosides and Nucleic Acids summarizes and reviews the latest developments in the field and provides a window on the next generation of analysis. Beginning with an overview of recent developments, the book highlights the most popular ionization methods and illustrates the diversity of strategies employed in the characterization and sequencing of DNA and RNA oligomers, nucleosides, nucleotides, and adducts. It describes studies performed on deoxyinosine and its analogues and provides an introduction to tandem mass spectrometry (MS/MS).

Next, the contributors examine mass spectrometric application in the study of cyclic nucleotides in biochemical signal transduction. They analyze urinary modified nucleosides and explore DNA adducts. They discuss isotope labeling of DNA-mass spectrometry (ILD-MS) and examine various uses of electrospray ionization mass spectrometry (ESI-MS). The book reviews recent progress in the direct MS characterization of noncovalent nucleic acid-protein complexes, explores the interaction and ionization of guanidine-derived compounds with highly acidic biomolecules, and examines quantitative identification of nucleic acids via signature digestion products detected using mass spectrometry.

The book describes a direct-infusion ESI-MS approach that can serve as a screening technique for the presence of modified nucleosides from small RNAs. Lastly, it discusses the LC-MS/MS method for the in vitro replication studies on damage-containing DNA substrates, and concludes with an examination of the influence of metal ions on the structure and reactivity of nucleic acids.

The exciting developments in mass spectrometry technology have fueled incredible advances in our understanding of nucleic acids and their complexes. The contributions presented in this volume capture the range of these advances, helping to inspire new findings and avenues of research.

Evolution is one of the most important processes in life. It not only explains the detailed history of life on earth, but its scope also extends into many aspects of our own contemporary behavior-who we are and how we got to be here, our psychology, our cultures-and greatly impacts modern advancements in medicine and conservation biology. Perhaps its most important claim for science is its ability to provide an overarching framework that integrates the many life sciences into a single unified whole. Yet, evolution-evolutionary biology in particular-has been, and continues to be, regarded with suspicion by many. Understanding how and why evolution works, and what it can tell us, is perhaps the single most important contribution to the public perception of science. This book provides an overview of the basic theory and showcases how widely its consequences reverberate across the life sciences, the social sciences and even the humanities. In this book, Robin Dunbar uses examples drawn from plant life, animals and humans to illustrate these processes. Evolutionary science has important advantages. Most of science deals with the microscopic world that we cannot see and invariably have difficulty understanding, but evolution deals with the macro-world in which we live and move. That invariably makes it much easier for the lay audience to appreciate, understand and enjoy. Evolution: What Everyone Needs to Know (R) takes a broad approach to evolution, dealing both with the core theory itself and its impact on different aspects of the world we live in, from the iconic debates of the nineteenth century, to viruses and superbugs, to human evolution and behavior.

"Genomic Control Process" explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes.

This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual frameworkProvides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literatureIncludes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant typeDemonstrates the causal power of system-level understanding of genomic control process
Conceptually organizes a constellation of complex and diverse biological phenomenaInvestigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual modelsExplores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome"