Featuring current resources used to discover new legume family genes and to understand genes and their interactions, Legume Genomics: Methods and Protocols provides techniques from expert researchers to study these plants that are so vitally important for food, feed, human nutrition, bioenergy, and industrial purposes. This detailed volume covers genome characterization and analysis, transcriptome analysis and miRNA identification/analysis, forward and reverse genetics, molecular markers, as well as transformation strategies used to investigate gene function and many other topics. 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 useful, Legume Genomics: Methods and Protocols aims to serve plant molecular biologists, molecular breeders, plant physiologists and biochemists, developmental biologists, and those interested in plant-microbe interactions.

Innate DNA and RNA Recognition: Method and Protocols presents validated experimental strategies to dissect nucleic acid sensing in-vitro and in-vivo sources. 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, Innate DNA and RNA Recognition: Method and Protocols provides a resource for immunologists, molecular biologists, virologists, microbiologists and researchers studying how the innate immune system handles nucleic acids from endogenous or foreign sources.

Yeast Metabolic Engineering: Methods and Protocols provides the widely established basic tools used in yeast metabolic engineering, while describing in deeper detail novel and innovative methods that have valuable potential to improve metabolic engineering strategies in industrial biotechnology applications. Beginning with an extensive section on molecular tools and technology for yeast engineering, this detailed volume is not limited to methods for Saccharomyces cerevisiae, but describes tools and protocols for engineering other yeasts of biotechnological interest, such as Pichia pastoris, Hansenula polymorpha and Zygosaccharomyces bailii. Tools and technologies for the investigation and determination of yeast metabolic features are described in detail as well as metabolic models and their application for yeast metabolic engineering, while a chapter describing patenting and regulations with a special glance at yeast biotechnology closes the volume. Written in the highly successful Methods in Molecular Biology series format, most chapters include an introduction to their respective topic, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and tips on troubleshooting and avoiding known pitfalls. Comprehensive and authoritative, Yeast Metabolic Engineering: Methods and Protocols aims to familiarize researchers with the current state of these vital and increasingly useful technologies.

Myc controls multiple cellular functions, including cell proliferation, growth, differentiation and death, both directly and indirectly, through its modulation of downstream transcriptional programs. In The Myc Gene: Methods and Protocols, experts in the field summarize the standard and novel techniques that allow the studying of Myc mechanism of action in normal and cancer cells, in vitro and in vivo, in one succinct manual. 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 key tips on troubleshooting and avoiding known pitfalls.

This book gives an overview of the current knowledge on the most common neurodegenerative diseases, including Alzheimer's disease, frontotemporal lobar degeneration, amyotrophic lateral sclerosis, and additional neurodegenerative diseases. Different aspects of each disease are reviewed, including clinical issues, treatments, basic discoveries (genetics and molecular biology), and translation of basic research into biomarkers for early diagnosis. In addition, emerging data indicate that neurodegeneration seems to also be present in classically non-degenerative disorders. Therefore, a chapter about overlapping mechanisms between dementias and psychiatric disorders is included, as well as a description of the role of neurodegeneration in multiple sclerosis. Neurodegenerative Diseases is aimed at clinicians, particularly those working in academic hospitals. This multidisciplinary book will also be of interest to basic researchers in medical fields.

This volume contains 29 engrossing chapters contributed by worldwide, leading research groups in the field of chemical biology. Topics include pre-biology; the establishment of the genetic code; isomerization of RNA; damage of nucleobases in RNA; the dynamic structure of nucleic acids and their analogs in DNA replication, extra- and intra-cellular transport; molecular crowding by the use of ionic liquids; new technologies enabling the modification of gene expression via editing of therapeutic genes; the use of riboswitches; the modification of mRNA cap regions; new approaches to detect appropriately modified RNAs with EPR spectroscopy and the use of parallel and high-throughput techniques for the analysis of the structure and new functions of nucleic acids. This volume discusses how chemistry can add new frontiers to the field of nucleic acids in molecular medicine, biotechnology and nanotechnology and is not only an invaluable source of information to chemists, biochemists and life scientists but will also stimulate future research.

In miRNomics: MicroRNA Biology and Computational Analysis, expert researchers in the field present an overview of the current state of the art and aim to put the respective areas of research into a larger perspective. These include methods and techniques ranging from miRNA biogenesis, their biological function, computational analyses to their medical implications and applications. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, miRNomics: MicroRNA Biology and Computational Analysis seeks to aid scientists in the further study into miRNA research and statistics.

In this volume expert researchers in the field detail many of the methods which are now commonly used to study RNA. These methods are presented as a guidebook to scientists who are experienced with RNA research and want to brush up on a new technique. 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 key tips on troubleshooting and avoiding known pitfalls. Thorough and intuitive, RNA-RNA Interactions: Methods and Protocols guides scientists investigating biological systems and studying RNA.

JIMD Reports publishes case and short research reports in the area of inherited metabolic disorders. Case reports highlight some unusual or previously unrecorded feature relevant to the disorder, or serve as an important reminder of clinical or biochemical features of a Mendelian disorder.

This work provides a review of biological networks as a model for analysis, presenting and discussing a number of illuminating analyses. Biological networks are an effective model for providing insights about biological mechanisms. Networks with different characteristics are employed for representing different scenarios. This powerful model allows analysts to perform many kinds of analyses which can be mined to provide interesting information about underlying biological behaviors. The text also covers techniques for discovering exceptional patterns, such as a pattern accounting for local similarities and also collaborative effects involving interactions between multiple actors (for example genes). Among these exceptional patterns, of particular interest are discriminative patterns, namely those which are able to discriminate between two input populations (for example healthy/unhealthy samples). In addition, the work includes a discussion on the most recent proposal on discovering discriminative patterns, in which there is a labeled network for each sample, resulting in a database of networks representing a sample set. This enables the analyst to achieve a much finer analysis than with traditional techniques, which are only able to consider an aggregated network of each population.

JIMD Reports publishes case and short research reports in the area of inherited metabolic disorders. Case reports highlight some unusual or previously unrecorded feature relevant to the disorder, or serve as an important reminder of clinical or biochemical features of a Mendelian disorder.

Clinical Ophthalmic Genetics and Genomics provides an accessible, clinically-focused reference for the evolving field of Genetic Ophthalmology. This well-organised, easy-to-read textbook integrates key concepts with clinical practice and is designed to enhance effective learning and retention of complex material. It includes contributions from recognised leaders in the field and provides expert guidance on the complete spectrum of genetic ophthalmic disorders.

JIMD Reports publishes case and short research reports in the area of inherited metabolic disorders. Case reports highlight some unusual or previously unrecorded feature relevant to the disorder, or serve as an important reminder of clinical or biochemical features of a Mendelian disorder.

In her study Elisabeth Salzer describes three novel monogenic diseases. For CD27 deficiency Elisabeth Salzer describes a large cohort of patients. Although all patients shared the same causative missense mutation, they displayed diverse clinical presentations. In another patient she was able to identify a mutation in PRKCD resulting in a primary immunodeficiency with severe Lupus-like autoimmunity. The patient exhibited increased mRNA levels of IL6. Therefore, treatment with Tocilizumab, a humanized anti-IL-6 receptor monoclonal antibody was suggested. In a family with a history of deaths due to inflammatory bowel disease she identified a missense mutation in IL21. She produced wild type and mutated IL-21 protein and demonstrated a loss of function phenotype. As IL-21 is in clinical trials, she proposed a potentially curative treatment option. These discoveries contributed to the understanding of the multifaceted regulatory mechanisms of the immune system and highlighted essential players in these complex signaling networks.

JIMD Reports publishes case and short research reports in the area of inherited metabolic disorders. Case reports highlight some unusual or previously unrecorded feature relevant to the disorder, or serve as an important reminder of clinical or biochemical features of a Mendelian disorder.

In Situ Hybridization Protocols, Fourth Edition contains 21 protocols that utilize the in situ hybridization technology to document or take advantage of the visualization of specific RNA molecules. 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, In Situ Hybridization Protocols, Fourth Edition seeks to aid scientists in the further discovery of new RNA species and uncovering of their cellular functions.

With the detailed genomic information that is now becoming available, we have a plethora of data that allows researchers to address questions in a variety of areas. Genome-wide association studies (GWAS) have become a vital approach to identify candidate regions associated with complex diseases in human medicine, production traits in agriculture, and variation in wild populations. Genomic prediction goes a step further, attempting to predict phenotypic variation in these traits from genomic information. Genome-Wide Association Studies and Genomic Prediction pulls together expert contributions to address this important area of study. The volume begins with a section covering the phenotypes of interest as well as design issues for GWAS, then moves on to discuss efficient computational methods to store and handle large datasets, quality control measures, phasing, haplotype inference, and imputation. Later chapters deal with statistical approaches to data analysis where the experimental objective is either to confirm the biology by identifying genomic regions associated to a trait or to use the data to make genomic predictions about a future phenotypic outcome (e.g. predict onset of disease). As part of the Methods in Molecular Biology series, chapters provide helpful, real-world implementation advice.

In the past two decades we have seen a surge forward in understanding the genetics and biochemistry underlying many pediatric orthopaedic disorders. A few projects have even progressed into the realm of clinical trials that are primarily aimed at controlling progressive disease. Meanwhile, genomic technology development has outpaced expectations and is enabling gene discovery for disorders that were previously intractable with traditional genetic methods. Included in this latter category are common disorders that display multigenic inheritance, sporadic disorders, and very rare conditions that are difficult to ascertain. Simultaneously, the study of pediatric orthopaedic disorders has been continuously refined and updated, highlighting a number of likely genetic conditions that are as yet unsolved. Molecular Genetics of Pediatric Orthopaedic Disorders updates researchers and clinicians of new developments of pediatric orthopaedic genetics. The chapters inform the audience on the revolution in new genomic methods and the impact this is having on potential study designs and the potential to discover genetic causes of many unsolved orthopaedic conditions. Recent examples have been included of pediatric orthopaedic conditions, both rare and common, that are being solved with these new methods. The book also educates pediatric orthopedic clinicians and geneticists on our understanding of the biology of "classic" genetic diseases that were derived from prior genetic studies. Chapters include biobanks and strategies for studying very rare disorders, genes and pathways causing primordial dwarfism, and notch signaling in congenital scoliosis, and more.

In Nucleic Acid Chemistry: Methods and Protocols, expert researches in the field detail techniques and approaches for the detection of DNA and RNA. These techniques include the recovery of trace amounts of DNA for amplification and analysis, new qPCR chemistries, new application of isothermal amplification techniques, assays with visual or electric signals for point-of-care diagnostics, improvement of fluorescent in situ hybridization, and new signal amplification techniques. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Nucleic Acid Chemistry: Methods and Protocols seeks to aid scientists in the further study of detection for DNA and RNA.

G protein-coupled receptors (GPCRs) are heptahelical transmembrane receptors that convert extra-cellular stimuli into intra-cellular signaling, and ultimately into biological responses. Since GPCRs are natural targets for approximately 40% of all modern medicines, it is not surprising that they have been the subject of intense research. Notwithstanding the amount of data generated over the years, discovering ligands of these receptors with optimal therapeutic properties is not straightforward and has certainly been hampered for years by the lack of high-resolution structural information about these receptors. Luckily, there has been a steady increase of high-resolution crystal structures of these receptors since 2007, and this information, integrated with dynamic inferences from computational and experimental methods, holds great potential for the discovery of new, improved drugs. This book, which provides, for the first time, state-of-the-art views on modeling and simulation of GPCRs, is divided into 4 parts. In the first part, the impact of currently available GPCR crystal structures on structural modeling is discussed extensively as are critical insights from simulations in the second part of the book. The third part reports recent progress in rational ligand discovery and mathematical modeling, whereas the fourth part provides an overview of bioinformatics tools and resources that are available for GPCRs.

This book addresses the differentiation control of skeletal muscle in different locations of the vertebrate body Particular attention is paid to novel regulatory molecules and signals as well as the heterogeneity of origin that have revealed a developmental overlap between skeletal and cardiac muscle. Different functional muscle groups are the product of the evolution of the vertebrate classes, making a phylogenetic comparison worthwhile for understanding the role of muscle stem cells and precursors in myogenesis. New insights into the hierarchy of transcription factors, particularly in the context of these different muscle groups have been gained from detailed investigations of the spatio-temporal and regulatory relationships derived from mouse and zebrafish genetics and avian microsurgery. Importantly, epigenetic mechanisms that have surfaced recently, in particular the role of MyomiRs, are also surveyed. With an eye to the human patient, encouraging results have been generated that identify parallels between embryonic myogenesis and regenerating myofibers due to common regulatory molecules. On the other hand, both processes differ considerably in quality and complexity of the processes employed. Interestingly, the heterogeneity in embryonic sources from which skeletal muscle groups in the vertebrate including the human body take origin is paralleled by differences in their susceptibility to particular muscle dystrophies as well as by the characteristics of the satellite cells involved in regeneration. The progress that has been made in the field of muscle stem cell biology, with special focus on the satellite cells, is outlined in this book by experts in the field. The authors review recent insights of the heterogeneous nature of these satellite cells regarding their gene signatures and regeneration potential. Furthermore, an improved understanding of muscle stem cells seems only possible when we study the impact of the cell environment on efficient stem cell replacement therapies for muscular dystrophies, putting embryological findings from different vertebrate classes and stem cell approaches into context.

The thymus is an evolutionarily ancient primary lymphoid organ common to all vertebrates in which T cell development takes place. Failing thymus function is associated with immunodeficiency and/or autoimmunity. In this volume, leading experts provide a comprehensive overview of recent advances in thymopoiesis research. The chapters cover the development of the thymic epithelial microenvironment, address the formation of a diverse and self-tolerant repertoire of T cell receptors as the basis for cellular immunity, discuss the mechanisms by which progenitor cells colonize the thymus and detail the molecular basis for T lineage decisions. The reviews illustrate the important role of the multifaceted process of thymopoiesis for adaptive immunity.

Regulatory Non-Coding RNAs: Methods and Protocols offers a collection of methods for those interested in the discovery, localization, and functional analysis of these non-coding transcripts that have the potential and ability to orchestrate and control gene expression. After a review of the field, this detailed volume continues with methods useful for the study of siRNAs, microRNAs and their targets, techniques concerned with long non-coding RNAs, as well as studies of the critical parameters of functional non-coding RNA protein-RNA interactions and the environment in which they act. Written for the highly successful Methods in Molecular Biology series, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and tips for troubleshooting and avoiding known pitfalls. Dependable and easy to use, Regulatory Non-Coding RNAs: Methods and Protocols provides a current, state-of-the-art collection of methods and approaches that will be of value to researchers in this expanding and fascinating field.

JIMD Reports publishes case and short research reports in the area of inherited metabolic disorders. Case reports highlight some unusual or previously unrecorded feature relevant to the disorder, or serve as an important reminder of clinical or biochemical features of a Mendelian disorder.

This is a short and self-contained introduction to the field of mathematical modeling of gene-networks in bacteria. As an entry point to the field, we focus on the analysis of simple gene-network dynamics. The notes commence with an introduction to the deterministic modeling of gene-networks, with extensive reference to applicable results coming from dynamical systems theory. The second part of the notes treats extensively several approaches to the study of gene-network dynamics in the presence of noise-either arising from low numbers of molecules involved, or due to noise external to the regulatory process. The third and final part of the notes gives a detailed treatment of three well studied and concrete examples of gene-network dynamics by considering the lactose operon, the tryptophan operon, and the lysis-lysogeny switch. The notes contain an index for easy location of particular topics as well as an extensive bibliography of the current literature. The target audience of these notes are mainly graduates students and young researchers with a solid mathematical background (calculus, ordinary differential equations, and probability theory at a minimum), as well as with basic notions of biochemistry, cell biology, and molecular biology. They are meant to serve as a readable and brief entry point into a field that is currently highly active, and will allow the reader to grasp the current state of research and so prepare them for defining and tackling new research problems.