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 book presents a guide to building computational gene finders, and describes the state of the art in computational gene finding methods, with a focus on comparative approaches. Fully updated and expanded, this new edition examines next-generation sequencing (NGS) technology. The book also discusses conditional random fields, enhancing the broad coverage of topics spanning probability theory, statistics, information theory, optimization theory and numerical analysis. Features: introduces the fundamental terms and concepts in the field; discusses algorithms for single-species gene finding, and approaches to pairwise and multiple sequence alignments, then describes how the strengths in both areas can be combined to improve the accuracy of gene finding; explores the gene features most commonly captured by a computational gene model, and explains the basics of parameter training; illustrates how to implement a comparative gene finder; examines NGS techniques and how to build a genome annotation pipeline.

Cells in the developing embryo depend on signals from the extracellular environment to help guide their differentiation. An important mediator in this process is the extracellular matrix - secreted macromolecules that interact to form large protein networks outside the cell. During development, the extracellular matrix serves to separate adjacent cell groups, participates in establishing morphogenic gradients, and, through its ability to interact directly will cell-surface receptors, provides developmental clocks and positional information. This volume discusses how the extracellular matrix influences fundamental developmental processes and how model systems can be used to elucidate ECM function. The topics addressed range from how ECM influences early development as well as repair processes in the adult that recapitulate developmental pathways.

Transcriptome Profiling: Progress and Prospects assists readers in assessing and interpreting a large number of genes, up to and including an entire genome. It provides key insights into the latest tools and techniques used in transcriptomics and its relevant topics which can reveal a global snapshot of the complete RNA component of a cell at a given time. This snapshot, in turn, enables the distinction between different cell types, different disease states, and different time points during development. Transcriptome analysis has been a key area of biological inquiry for decades. The next-generation sequencing technologies have revolutionized transcriptomics by providing opportunities for multidimensional examinations of cellular transcriptomes in which high-throughput expression data are obtained at a single-base resolution. Transcriptome analysis has evolved from the detection of single RNA molecules to large-scale gene expression profiling and genome annotation initiatives. Written by a team of global experts, key topics in Transcriptome Profiling include transcriptome characterization, expression analysis of transcripts, transcriptome and gene regulation, transcriptome profiling and human health, medicinal plants transcriptomics, transcriptomics and genetic engineering, transcriptomics in agriculture, and phylotranscriptomics.

The discovery of stress-induced mutagenesis has changed ideas about mutation and evolution, and revealed mutagenic programs that differ from standard spontaneous mutagenesis in rapidly proliferating cells. The stress-induced mutations occur during growth-limiting stress, and can include adaptive mutations that allow growth in the otherwise growth-limiting environment. The stress responses increase mutagenesis specifically when cells are maladapted to their environments, i.e. are stressed, potentially accelerating evolution then. The mutation mechanism also includes temporary suspension of post-synthesis mismatch repair, resembling mutagenesis characteristic of some cancers. Stress-induced mutation mechanisms may provide important models for genome instability underlying some cancers and genetic diseases, resistance to chemotherapeutic and antibiotic drugs, pathogenicity of microbes, and many other important evolutionary processes. This book covers pathways of stress-induced mutagenesis in all systems. The principle focus is mammalian systems, but much of what is known of these pathways comes from non-mammalian systems.

This volume contains state-of-the-art methods tackling all aspects of small non-coding RNAs biology. Small Non-Coding RNAs: Methods and Protocols guides readers through customized dedicated protocols and technologies that will be of valuable help to all those willing to contribute deciphering the numerous functions of small non-coding RNAs. 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. Instructive and practical, Small Non-Coding RNAs: Methods and Protocols reaches out to biochemists, cellular and molecular biologists already working in the field of RNA biology and to those just starting to study small non-coding RNAs.

The work reported in this book represents an excellent example of how creative experimentation and technology development, complemented by computational data analysis, can yield important insights that further our understanding of biological entities from a systems perspective. The book describes how the study of a single RNA-binding protein and its interaction sites led to the development of the novel 'protein occupancy profiling' technology that for the first time captured the mRNA sequence space contacted by the ensemble of expressed RNA binders. Application of protein occupancy profiling to eukaryotic cells revealed that extensive sequence stretches in 3' UTRs can be contacted by RBPs and that evolutionary conservation as well as negative selection act on protein-RNA contact sites, suggesting functional importance. Comparative analysis of the RBP-bound sequence space has the potential to unravel putative cis-acting RNA elements without a priori knowledge of the bound regulators. Here, Dr. Munschauer provides a comprehensive introduction to the field of post-transcriptional gene regulation, examines state-of-the-art technologies, and combines the conclusions from several journal articles into a coherent and logical story from the frontiers of systems-biology inspired life science. This thesis, submitted to the Department of Biology, Chemistry and Pharmacy at Freie Universitat Berlin, was selected as outstanding work by the Berlin Institute for Medical Systems Biology at the Max-Delbrueck Center for Molecular Medicine, Germany.

This is a detailed history of one of the most important and dramatic episodes in modern science, recounted from the novel vantage point of the dawn of the information age and its impact on representations of nature, heredity, and society. Drawing on archives, published sources, and interviews, the author situates work on the genetic code (1953-70) within the history of life science, the rise of communication technosciences (cybernetics, information theory, and computers), the intersection of molecular biology with cryptanalysis and linguistics, and the social history of postwar Europe and the United States.
Kay draws out the historical specificity in the process by which the central biological problem of DNA-based protein synthesis came to be metaphorically represented as an information code and a writing technology--and consequently as a "book of life." This molecular writing and reading is part of the cultural production of the Nuclear Age, its power amplified by the centuries-old theistic resonance of the "book of life" metaphor. Yet, as the author points out, these are just metaphors: analogies, not ontologies. Necessary and productive as they have been, they have their epistemological limitations. Deploying analyses of language, cryptology, and information theory, the author persuasively argues that, technically speaking, the genetic code is not a code, DNA is not a language, and the genome is not an information system (objections voiced by experts as early as the 1950s).
Thus her historical reconstruction and analyses also serve as a critique of the new genomic biopower. Genomic textuality has become a fact of life, a metaphor literalized, she claims, as human genome projects promise new levels of control over life through the meta-level of information: control of the word (the DNA sequences) and its editing and rewriting. But the author shows how the humbling limits of these scriptural metaphors also pose a challenge to the textual and material mastery of the genomic "book of life."

This second edition volume discusses the revolutionary development of faster and less expensive DNA sequencing technologies from the past 10 years and focuses on general technologies that can be utilized by a wide array of plant biologists to address specific questions in their favorite model systems. This book is organized into five parts. Part I examines the tools and methods required for identifying epigenetic and conformational changes at the whole-genome level. Part II presents approaches used to determine key aspects of a gene's function, such as techniques used to identify and characterize gene regulatory networks. This is followed by a discussion of tools used to analyze the levels of mRNA, mRNA translation rates and metabolites. Part III features a compilation of forward and reverse genetic approaches that include recent implementation of high-throughput sequencing in classical methodologies such as QTL mapping. The final two parts explore strategies to facilitate and accelerate the generation and testing of functional DNA elements and basic computational tools used to facilitate the use of systems biology approached by a broad spectrum of plant researchers. 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 troubleshooting and avoiding known pitfalls. Practical and timely, Plant Functional Genomics: Methods and Protocols, Second Edition highlights the latest developments in DNA sequencing technologies that are likely to continue shaping the future of functional genomics.

This volume provides an overview on design PCR primers for successful DNA amplification. Chapters focus on primer design strategies for quantitative PCR, in silico PCR primer design, and primer design using software. 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 easily accessible, PCR Primer Design, Second Edition seeks to aid molecular biology students, researchers, professors and PCR enthusiasts.

This volume collects a series of protocols describing the kinds of infrastructures, training, and standard operating procedures currently available to actualize the potential of stem cells for regenerative therapies. Stem Cells and Good Manufacturing Practices: Methods, Protocols, and Regulations pulls together key GMP techniques from laboratories around the world. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Inclusive and authoritative, Stem Cells and Good Manufacturing Practices: Methods, Protocols, and Regulations will be an invaluable resource to both basic and clinical practitioners in stem cell biology.

This volume contains a comprehensive compilation of chromogenic and fluorescent RNA in situ hybridization (ISH) technology in many of its various shades, forms, and applications. The book is organized into a number of parts and chapters focusing on the application of ISH methodologies to different animal species as used in Evolutionary Development (EvoDevo) and Biomedical research, and covering new developments in RNA visualization by fluorescent ISH (FISH). The described (F)ISH protocols employ effective strategies for signal enhancement and target amplification allowing for high signal intensities and drastically improved signal-to-noise ratios. Chromogenic and fluorescent ISH, as specified in the various chapters, are most essential for RNA expression profiling, applied to many fields of research including cellular, developmental, and evolutionary biology, neurobiology and neuropathology. Written for the popular Neuromethods series, chapters include the kind of detail and key implementation advice that ensures successful results in the laboratory. Essential and authoritative, In Situ Hybridization Methods provides detailed protocols for newcomers to ISH, and inspires researchers familiar with the technique to seek and find up-to-date methodology for new and specialized applications.

This volume opens by covering two main types of approaches widely used to determine essential genes: single-gene knockouts and transposon mutagenesis, in both prokaryotes and Candida albicans. Given the significant advancement in the computational predictions of microbial essential genes, the second half of the book examines four main types of approaches: comparative genomics, supervised machine learning, constraint-based methods, and corrections of transposon mutagenesis data, as well as databases and servers that are often used in studying gene essentiality. Written in the highly successful Methods in Molecular Biology series format, chapters include an introduction 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, Gene Essentiality: Methods and Protocols will aid researchers who wish to further our knowledge in this vital field of study.

Over the past decade, significant efforts have been made to develop stem cell-based therapies for difficult to treat diseases. Multipotent mesenchymal stromal cells, also referred to as mesenchymal stem cells (MSCs), appear to hold great promise in regards to a regenerative cell-based therapy for the treatment of these diseases. Currently, more than 200 clinical trials are underway worldwide exploring the use of MSCs for the treatment of a wide range of disorders including bone, cartilage and tendon damage, myocardial infarction, graft-versus-host disease, Crohn's disease, diabetes, multiple sclerosis, critical limb ischemia and many others. MSCs were first identified by Friendenstein and colleagues as an adherent stromal cell population within the bone marrow with the ability to form clonogenic colonies in vitro. In regards to the basic biology associated with MSCs, there has been tremendous progress towards understanding this cell population's phenotype and function from a range of tissue sources. Despite enormous progress and an overall increased understanding of MSCs at the molecular and cellular level, several critical questions remain to be answered in regards to the use of these cells in therapeutic applications. Clinically, both autologous and allogenic approaches for the transplantation of MSCs are being explored. Several of the processing steps needed for the clinical application of MSCs, including isolation from various tissues, scalable in vitro expansion, cell banking, dose preparation, quality control parameters, delivery methods and numerous others are being extensively studied. Despite a significant number of ongoing clinical trials, none of the current therapeutic approaches have, at this point, become a standard of care treatment. Although exceptionally promising, the clinical translation of MSC-based therapies is still a work in progress. The extensive number of ongoing clinical trials is expected to provide a clearer path forward for the realization and implementation of MSCs in regenerative medicine. Towards this end, reviews of current clinical trial results and discussions of relevant topics association with the clinical application of MSCs are compiled in this book from some of the leading researchers in this exciting and rapidly advancing field. Although not absolutely all-inclusive, we hope the chapters within this book can promote and enable a better understanding of the translation of MSCs from bench-to-bedside and inspire researchers to further explore this promising and quickly evolving field.

Patient specific and disease specific stem cell lines have already introduced groundbreaking advances into the research and practice of ophthalmology. This volume provides a comprehensive and engaging overview of the latest innovations in the field. Twelve chapters discuss the fastest growing areas in ophthalmological stem cell research, from disease modelling, drug screening and gene targeting to clinical genetics and regenerative treatments. Innovative results from stem cell research of the past decade are pointing the way toward practicable treatments for retinitis pigmentosa, age related macular degeneration, and Stargardt disease. What future directions will stem cell research take? Researchers, graduate students, and fellows alike will find food for thought in this insightful guide tapping into the collective knowledge of leaders in the field. Stem Cells in Ophthalmology is part of the Stem Cells in Regenerative Medicine series dedicated to discussing current challenges and future directions in stem cell research.

GW bodies are novel cytoplasmic foci that were discovered and named by Dr. Chan's group in 2002. These bodies are now known to be active cytoplasmic foci involved with the new gene regulation process mediated by microRNA that leads to translational repression and mRNA degradation. The detailed biological functions of these cytoplasmic structures are still being uncovered and the idea for this book is to provide the history of the discovery and the major work from different laboratories that has led to the characterization and elucidation of the structure and function of these new multiple subcellular structures.

The book "STEM CELL THERAPY FOR ORGAN FAILURES" edited by Dr. S. Indumathi demonstrates the In Vitro and In vivo therapeutic strategies and applications of pre- and post-natal stem cells for treating the failures of various organ systems of our body in a wide perspective. It explores the past, present and the futuristic approach of the exciting field of stem cells and its intriguing properties involved in tissue repair and regeneration. The prime focus of this volume is to unravel the basic, advanced, therapeutic and translational approaches put-forth so far in the field of stem cells and regenerative medicine at research, pre-clinical and clinical levels. Stem cells has ushered in widespread interest and exciting possibilities for cell based therapies, albeit failures do prevail and small uncontrolled phase I/II studies are only signals generating, rather than definite proof of concept thereby limiting its applicability in curative therapeutics. Despite certain initiatives and meticulous untiring efforts, bringing this basic bench side research into advanced transitional bedside remained a challenge. Thus, this book embarked upon the expanding researches in these areas that seem decisive in improvising regenerative medical therapeutics, thereby leading to further path-breaking studies that cure all health challenges facing mankind. Overall, this book reveals the imperativeness of various stem cell sources and its utility in curative therapeutics.

This volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls. Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA.

The series Topics in Current Chemistry presents critical reviews of the present and future trends in modern chemical research. The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience. Each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field. Review articles for the individual volumes are invited by the volume editors. Readership: research chemists at universities or in industry, graduate students.

Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP) which has become a world-wide effort and the Global Ocean Sampling (GOS) surveys. The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to gather seminal contributions from the leaders in the field, and at the same time provide this information to a significant number of junior and senior scientists. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.

Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP) which has become a world-wide effort and the Global Ocean Sampling (GOS) surveys. The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to receive seminal contributions from the leaders in the field and at the same time provide this information to a significant number of junior and senior scientists, via colleges, libraries, and just through online access. This format also allows scientists in the developing world to have continued access to this growing field. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.

The ability of a single genome to give rise to hundreds of functionally distinct cell type programs is in itself remarkable. Pioneering studies over the past few decades have demonstrated that this plasticity is retained throughout development, a phenomenon of epigenetic programming and reprogramming that remains one of the most fascinating areas of modern biology, with major relevance to human health and disease. This book presents the basic biology involved, including key mechanistic insights into this rapidly growing field.

The central question of this book is whether or not particular cell entities of human origin ought to be considered human beings. The answer is crucial for making moral decisions for or against research and experimentation. Experts in the field discuss the production of embryonic-like pluripotent stem cells by altered nuclear transfer, parthenogenesis and reprogramming of adult somatic cells. They thoroughly analyse the biological and moral status of different cell entities, such as human stem cells, embryos and human-animal hybrid embryos, and make a decisive step towards establishing final criteria for what constitutes a human being. The topic is challenging in nature and of broad interest to all those concerned with current bioethical thought on embryonic human life and its implications for society.

As the largest group of extant vertebrates, fish offer an almost limitless number of striking examples of evolutionary adaptation to environmental and biotic selection pressure. The most diverse of all vertebrate groups, the higher taxa of fish traditionally have been classified by morphology and paleontology, with a much smaller input of cytogenetic information. DNA sequence data are exerting an increasingly strong influence on modern fish systematics, challenging the classification of numerous higher taxa ranging from genera to orders. The most fruitful approach, however, involves synthetic analyses of morphology, molecular phylogenetics, comparative karyology, and genome size. Karyotypes of more than 3400 species/subspecies are arranged here by fish systematics and include a list of genome size, sex chromosomes, B chromosomes, polyploidy, and locality of material fish, among others. This volume enables both beginners and advanced researchers to survey the existing literature and facilitates the implementation of an integrative approach to fish systematics. The first book on fish chromosomes in nearly 15 years, it is also the most comprehensive.

This open access book offers a comprehensive overview of the history of genomics across three different species and four decades, from the 1980s to the recent past. It takes an inclusive approach in order to capture not only the international initiatives to map and sequence the genomes of various organisms, but also the work of smaller-scale institutions engaged in the mapping and sequencing of yeast, human and pig DNA. In doing so, the authors expand the historiographical lens of genomics from a focus on large-scale projects to other forms of organisation. They show how practices such as genome mapping, sequence assembly and annotation are as essential as DNA sequencing in the history of genomics, and argue that existing depictions of genomics are too closely associated with the Human Genome Project. Exploring the use of genomic tools by biochemists, cell biologists, and medical and agriculturally-oriented geneticists, this book portrays the history of genomics as inseparably entangled with the day-to-day practices and objectives of these communities. The authors also uncover often forgotten actors such as the European Commission, a crucial funder and forger of collaborative networks undertaking genomic projects. In examining historical trajectories across species, communities and projects, the book provides new insights on genomics, its dramatic expansion during the late twentieth-century and its developments in the twenty-first century. Offering the first extensive critical examination of the nature and historicity of reference genomes, this book demonstrates how their affordances and limitations are shaped by the involvement or absence of particular communities in their production.