During the past few decades we have witnessed an era of remarkable growth in the field of molecular biology. In 1950 very little was known of the chemical constitution of biological systems, the manner in which information was trans mitted from one organism to another, or the extent to which the chemical basis of life is unified. The picture today is dramatically different. We have an almost bewildering variety of information detailing many different aspects of life at the molecular level. There great advances have brought with them some breath-taking insights into the molecular mechanisms used by nature for rep licating, distributing and modifying biological information. We have learned a great deal about the chemical and physical nature of the macromolecular nucleic acids and proteins, and the manner in which carbohydrates, lipids and smaller molecules work together to provide the molecular setting of living sys tems. It might be said that these few decades have replaced a near vacuum of information with a very large surplus. It is in the context of this flood of information that this series of monographs on molecular biology has been organized. The idea is to bring together in one place, between the covers of one book, a concise assessment of the state of the subject in a well-defined field. This will enable the reader to get a sense of historical perspectiv(}-what is known about the field today-and a description of the frontiers of research where our knowledge is increasing steadily."

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.

While extremely large datasets describing gene sequences, mRNA transcripts, protein abundance, and metabolite concentrations are increasingly commonplace, these represent only starting 'parts lists' that are usually insufficient to unlock mechanistic insights on their own right. Fortunately, as "Network Biology: Methods and Applications" examines, concepts emerging from the study of biological entities such as networks (e.g. functional interactions linking genes, proteins, metabolites, etc.) suggest that order rather than chaos prevails, with such principles as modular and hierarchical organization, reactive information-driven causal-response behaviours, systems robustness, co-evolution, and self-organization guiding the way. This volume presents detailed, practical descriptions of the experimental and computational approaches currently prevalent in network biology as written by practiced experts in the field. Written in the highly successful "Methods in Molecular Biology " series format, relevant chapters contain introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.

Comprehensive and accessible, "Network Biology: Methods and Applications" provides an ensemble of procedures that will be of great value to a broad assortment of readers, ranging from graduate students to seasoned professionals looking to polish their skill sets."

Our current knowledge of marine organisms and the factors affecting their ecology, distribution and evolution has been revolutionised by the use, in the last 20 years, of molecular population genetics tools. This book is the result of a meeting of world-leading experts, in Rio de Janeiro, where the state of the art of this field was reviewed. Topics covered include the molecular analysis of bio-invasions, the recent developments in marine biotechnology, the factors affecting levels of genetic variation and population structure in marine organisms and their application to conservation biology, fisheries and aquaculture. This is the first book dedicated to the genetic study of marine organisms. It will be very useful to biology students, scientists and anyone working or simply interested in areas such as marine biology, zoology, ecology, and population and molecular genetics.

The field of epigenetics has played a major role at the forefront not only of molecular biology, but also of medical genetics and clinical medicine. Few disciplines have experienced growth comparable to that which we have witnessed for epigenetics in the past decade. The goal of "Epigenetics Protocols, Second Edition "is to highlight select techniques that have been mainstays in the field as well as to cover methods that are especially relevant to extant discoveries in epigenetics. This volume focuses on the two broad areas of epigenetics: DNA methylation and chromatin modifications, and also covers the complex topic of computational methods for epigenetic analyses which is essential to a complete understanding of the vast body of information that is being derived with the use of these newly-developed tools. Written in the highly successful "Methods in Molecular Biology " series format, chapters contain 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 accessible, "Epigenetics Protocols, Second Edition" serves as an ideal guide to advanced students, basic scientists and clinical researchers as well as clinicians and biotechnology investigators who wish to continue exploring this exciting and progressive research field."

This laboratory manual, published in cooperation with the International Society for Transgenic Technology (ISTT), provides almost all current methods that can be applied to the creation and analysis of genetically modified animals. The chapters have been contributed by leading scientists who are actively using the technology in their laboratories. Based on their first-hand experience the authors also provide helpful notes and troubleshooting sections. Topics range from standard techniques, such as pronuclear microinjection of DNA, to more sophisticated and modern methods, such as the derivation and establishment of embryonic stem (ES) cell lines, with defined inhibitors in cell culture medium. In addition, related topics with relevance to the field are addressed, including global web-based resources, legal issues, colony management, shipment of mice and embryos, and the three R s: refinement, reduction and replacement.

Almost daily, new technologies are being presented that move the field of human pluripotent stem cell research towards a future that may yield highly-effective, personalized medical treatments. Three enabling technologies at hand for human PSCs are 1) directed reprogramming of somatic cells, which eliminate many of the ethical issues associated with the derivation and use of human PSCs, increase genetic diversity of the available human PSC lines, and give rise to better" in vitro" human disease models; 2) the discovery that a Rho-associated protein Kinase (ROCK) inhibitor allows for efficient single cell passaging and cryopreservation, increasing the efficiency and reliability of hPSC culture; and 3) defined, animal-component-free media, which lay the groundwork for simplified scale-up for therapeutic applications, differentiation protocols, and toxicology screens. The aforementioned technologies can be found in "Human Pluripotent Stem Cells: Methods and Protocols," a compilation of 33 detailed protocols in six categories of PSC research that cover laboratory essentials and the derivation of new PSC lines, including induced PSC lines, as well as their growth, maintenance, characterization, genetic manipulation, and differentiation. 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 accessible, "Human Pluripotent Stem Cells: Methods and Protocols" serves as an ideal guide to scientists conducting their own pluripotent cell research programs and makes great strides towards furthering human knowledge and, ultimately, improving the human condition.

Homologous recombination is important in various aspects of DNA metabolism, including damage repair, replication, telomere maintenance, and meiosis, and yeast genetics has successfully provided a framework for the mechanism of homologous recombination. Divided into four convenient sections, DNA Recombination: Methods and Protocols covers recent techniques that best utilize the advantages of the yeast system, prescribing to the belief that yeast will keep serving as a great model organism to study homologous recombination. Chapters have also been included for such exceptions as the group of genes involved in recombination that are found solely in higher eukaryotes, such as BRCA2. And looking forward, a necessary step in the direction of understanding the homologous recombination process is to isolate the machine and let it work in a test tube. Understanding the design by studying the appearance and behavior of the machinery as a single molecule will be an important milestone toward understanding the mechanism of action of the machinery. Techniques covering these topics have also been included. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, DNA Recombination: Methods and Protocols serves as an ideal guide to scientists of all backgrounds with its well-honed methodologies and strives to bring the reader to the next level of understanding regarding this vital subject.

The migration of stem cells has been found to be critical during early development for the organization of the embryonic body as well as during adult life with tissue homeostasis and regeneration of organ function. Due to the low frequency of these cells in vivo, problems in identifying and prospectively purifying tissue specific stem cells near homogeneity, and, most importantly, a lack of adequate technologies and protocols to study stem cell migration in vivo, this vital research has been quite difficult until recently. In "Stem Cell Migration: Methods and Protocols," experts in the field compile and highlight the standard and novel techniques that allow the studying of the migration of stem cells in one succinct manual. Including protocols on germ, neuronal, and hematopoietic stem cells, during development and adulthood with a clear emphasis on in vivo technologies, the volume also extends its coverage to in vitro approaches toward several developmentally-conserved signaling pathways. 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.

Practical and convenient, "Stem Cell Migration: Methods and Protocols" provides key, state-of the art information on experimental techniques for studying stem cell migration both at a cellular and molecular level in development, regeneration, and disease.

Transcription factors are the molecules that the cell uses to interpret the genome: they possess sequence-specific DNA-binding activity, and either directly or indirectly influence the transcription of genes. In aggregate, transcription factors control gene expression and genome organization, and play a pivotal role in many aspects of physiology and evolution.

This book provides a reference for major aspects of transcription factor function, encompassing a general catalogue of known transcription factor classes, origins and evolution of specific transcription factor types, methods for studying transcription factor binding sites in vitro, in vivo, and in silico, and mechanisms of interaction with chromatin and RNA polymerase."

Regulation of gene expression, a major determinant of gene activity, occupies a central place in molecular biology. Yeast Genetic Networks: Methods and Protocols covers approaches to the systems biological analysis of small-scale gene networks in yeast. Divided into four convenient sections, this detailed volume discusses the methods used to analyze gene expression quantitatively, presents a collection of mathematical and computational tools to analyze stochasticity, adaptation, sensitivity in signal transmission, and oscillations in gene expression, provides instructional methods on how to utilize the tools of quantitative genetics to identify genes that regulate stochasticity and oscillations in gene expression, and concludes with a section devoted to the analysis of conserved gene expression systems and networks in different fungal species. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain 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 accessible, Yeast Genetic Networks: Methods and Protocols serves as an ideal and valuable resource for both novices and experienced researchers.

A comprehensive treatment of the characterisation techniques used in investigating inorganic and organic molecules that interact with biomolecules is presented to the reader in a clear fashion. The work consists of two parts: (i) synthetic aspects of metallointercalators along with targeting and improving transport and (ii) the various techniques that are used for probing their interactions, such as; DNA-NMR, PGSE-NMR, DNA ESI-MS, Linear and Circular Dichroism, Fluorescence Spectroscopy, Confocal Microscopy, Viscosity, TGA and dialysis, Microarrays, biological analysis. Chapters are devoted to the synthesis and the techniques used to study the interactions of inorganic complexes with biomolecules. Considerably detailed examples are used to help illustrate the application of these techniques. This book is a useful resource for an array of inorganic and organic advanced undergraduate and graduate courses and for researchers in drug discovery.

Mesenchymal Stem Cells have seen an unprecedented level of interest in the last decade, primarily due to their relative ease of isolation, the large numbers of cells present in the adult, and the ability to propagate these cells in culture. In Mesenchymal Stem Cell Assays and Applications, expert researchers from across the globe explore the latest techniques to propagate, characterize, and engineer this special cell type. Chapters outline a set of protocols and assays used by leading investigators in the field, providing standards that can be applied by all researchers to the population of cells used in their experiments. Composed in the highly successful Methods in Molecular Biology (TM) series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls. Ground-breaking and current, Mesenchymal Stem Cell Assays and Applications is a necessary handbook for all researchers working with this ambiguous population of cells.

With its complex and extensively regulated metabolism, the study of the RNA lifecycle demands tools that allow for the localization of RNAs to be observed either in an in situ setting or, preferably, under in vivo conditions. In RNA Detection and Visualization: Methods and Protocols, the best and brightest investigators provide an up-to-date and in-depth description of basic methods and protocols used for detecting and visualizing mRNAs in both fixed and live cells, from bacteria to mammals. For novices and experts alike, this mix of classic in situ hybridization and advanced live imaging techniques, cell fractionation and affinity purification procedures, and bioinformatics tools gives researchers the most complete and extensive array of research aids possible. As a volume 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 expert tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA Detection and Visualization: Methods and Protocols offers well-honed techniques in order to inspire researchers around the world to further our knowledge of the vital biological significance of RNA.

Cell culture based research is important for our understanding of biological processes at the cellular and molecular level. Using this approach, the previous decades have produced a wealth of mechanistic information in all areas of biomedical research. Such in vitro research, however, lacks the complexity of in vivo investigations, where many different cell types interact with each other in a normal, three-dimensional environment, with normal levels of cytokines and growth factors. Furthermore, complex human diseases, such as cancer, diabetes or chronic inflammation, can only be modeled in vivo. Due to its small size, its short reproduction time, and the possibility to introduce specific gene mutations, the mouse has become the favourite mammalian model organism to study in vivo function of genes during development and in disease. This book combines review articles on selected subjects presented at the symposium "Mouse as a Model Organism - From Animals to Cells", held in Rovaniemi, Finland, 2009. Among other topics, high-throughput phenotyping of mouse mutants, mouse phenotypes dependent on nature and nuture, and a spectrum of in vivo, ex vivo and in vitro methods to study cancer in mice are described. This book will give an excellent introduction to scientists interested in the use of mice as a model to understand complex biological questions in the post-genomic era. It will highlight the possibilities, but also discuss the current problems and shortcomings, to give a realistic view of the current state-of-art in this fascinating field of biomedical research.

The book describes the history of Brassica oilseed crops, introduces the Brassica genome, its evolution, diversity, classical genetic studies and breeding. It also delves into molecular genetic linkage and physical maps, progress with genome sequencing initiatives, mutagenesis approaches for trait improvement, proteomics, metabolomics and bioinformatics. The concluding of portion provides detailed methods for whole genome marker assisted breeding, the genetics and genomics of important traits including disease resistance, herbivory, insect and abiotic stress resistance, and discusses the future prospects for Brassica improvement through genomics. This volume provides a state of the moment view of current Brassica genetics, genomics and breeding research which is the foundation for the continued understanding of oilseed Brassica species, their genomes, evolution and further potential as important food and biofuel crops.

The biological and genetic bases of behavioral diversity have long been topics of study within many disciplines, including evolutionary biology, genetics, ethology, sociobiology, and comparative psychology, but only relatively recently have attempts been made to bring these different approaches together. This volume covers a wide range of interdisciplinary research which uses some of the newest and most promising methods and technologies. Presented here is an overview of findings in the ongoing search for the ultimate causes of behavior in several different species, including primates, dogs, rodents, birds, and fish. Divided into five parts, the work describes research on sexual and kin selection, personality and temperament, molecular genetics of personality, color vision and body coloration, and the neurological underpinnings of complex behaviors. Valuable for researchers as well as graduate students in a wide range of fields from neuroscience to ecology, the book is also useful to those seeking to move beyond the boundaries of their own discipline and to expand their knowledge.

As regenerative medicine involves replacing diseased cells, tissues or organs, or repairing tissues in vivo, the manipulation of stem cells underlie its goals. In Stem Cells in Regenerative Medicine: Methods and Protocols, leading experts in the field provide an updated representation of the landscape of stem cell-based therapies in a wide spectrum of tissue systems and ontogenic stages, from the isolation and culture of stem cells to their actual use in vivo. Written in the highly successful Methods in Molecular Biology series format, these chapters include brief introductions to the topic, lists of the necessary materials and reagents, readily reproducible, step-by-step laboratory protocols, and tips for troubleshooting and avoiding known pitfalls.

Comprehensive and easy-to-use, Stem Cells in Regenerative Medicine: Methods and Protocols is certain to contribute greatly to the definition of standardized procedures for the manipulation of somatic and embryonic stem cells in research and clinical applications."

Gene therapy offers many conceptual advantages to treat muscle diseases, especially various forms of muscular dystrophies; however, it faces a number of unique challenges, including the need to deliver a therapeutic vector to all muscles throughout the body. In Muscle Gene Therapy: Methods and Protocols, expert researchers in the field present a collection of techniques aimed at bridging the translational gap in muscle gene therapy between the prevalent rodent models and vitally important larger animal models. Divided into three sections, this volume examines basic protocols for optimizing the muscle gene expression cassette and for evaluating the therapeutic outcomes, new developments in muscle gene therapy technology such as adeno-associated viral vector (AAV), oligonucleotide-mediated exon-skipping, and novel RNA-based strategies, and step-by-step guidance on muscle gene delivery in swine, ovine, canine, and non-human primates. 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, detailed, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Muscle Gene Therapy: Methods and Protocols serves as an invaluable resource for graduate students, post-doctoral fellows, and principle investigators pursuing the crucial advancement of muscle disease gene therapy in the hope of someday curing these debilitating disorders.

The question of why an individual would actively kill itself has long been an evolutionary mystery. Pierre M. Durand's ambitious book answers this question through close inspection of life and death in the earliest cellular life. As Durand shows us, cell death is a fascinating lens through which to examine the interconnectedness, in evolutionary terms, of life and death. It is a truism to note that one does not exist without the other, but just how does this play out in evolutionary history? These two processes have been studied from philosophical, theoretical, experimental, and genomic angles, but no one has yet integrated the information from these various disciplines. In this work, Durand synthesizes cellular studies of life and death looking at the origin of life and the evolutionary significance of programmed cellular death. The exciting and unexpected outcome of Durand's analysis is the realization that life and death exhibit features of coevolution. The evolution of more complex cellular life depended on the coadaptation between traits that promote life and those that promote death. In an ironic twist, it becomes clear that, in many circumstances, programmed cell death is essential for sustaining life.

With the predicted increase of the human population and the subsequent need for larger food supplies, root health in crop plants could play a major role in providing sustainable highly productive crops that can cope with global climate changes. While the essentiality of roots and their relation to plant performance is broadly recognized, less is known about their role in plant growth and development. Root Genomics examines how various new genomic technologies are rapidly being applied to the study of roots, including high-throughput sequencing and genotyping, TILLING, transcription factor analysis, comparative genomics, gene discovery and transcriptional profiling, post-transcriptional events regulating microRNAs, proteome profiling and the use of molecular markers such as SSRs, DArTs, and SNPs for QTL analyses and the identification of superior genes/alleles. The book also covers topics such as the molecular breeding of crops in problematic soils and the responses of roots to a variety of stresses.

Combinatorial chemistry is used to find materials that form sensor microarrays. This book discusses the fundamentals, and then proceeds to the many applications of microarrays, from measuring gene expression (DNA microarrays) to protein-protein interactions, peptide chemistry, carbodhydrate chemistry, electrochemical detection, and microfluidics.

This interdisciplinary volume reflects on the effects of recent discoveries in genetics on a broad range of scientific fields. It shows the way in which those discoveries influence genetics itself and many other fields, and explains the impact of genetics on contemporary culture. The volume contains the most recent views of the Nobel Laureate Francois Jacob on genetics and the nature of living things."

In the dramatic and rapidly developing field of neural transplantation for CNS repair, the most powerful contributor has been the vital research focusing on stem cells. In Neural Cell Transplantation: Methods and Protocols, leading experts in the field examine tried-and-true laboratory techniques in order to supply scientists with a firm foundation upon which further advancements can be based. Written in the highly successful Methods in Molecular Biology series format, the chapters of this volume include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and Notes sections, which examine tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and easy to use, Neural Cell Transplantation: Methods and Protocols provides the most thorough and essential protocols that will allow new generations of neuroscientists to enter and contribute to this uniquely inspiring field.

This book facilitates the introduction of SAGE into the laboratory and provides a framework for interpreting and comparing data derived from SAGE experiments. SAGE studies encompass 50,000 tags and can provide detailed knowledge of the 2000 most highly expressed genes in the tissue sample. The SAGE protocols presented are detailed, fully annotated, and tested, and are all written by experienced SAGE researchers from around the world.