This volume presents a valuable and readily reproducible collection of established and emerging techniques on modern genetic analyses. Chapters focus on statistical or data mining analyses, genetic architecture, the burden of multiple testing, genetic variance, measuring epistasis, multifactor dimensionality reduction, and ReliefF. 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, Epistasis: Methods and Protocols aids scientists in continuing to study elucidate epistasis in the context of modern data availability.

This unique book explores the role of retrotransposons in human health and disease. The ability of retrotransposons to affect the structure of human genes is recognized since the late 80's. However, the advances of deep-sequencing technologies have shed new light on the extent of retrotransposon-mediated genome variations. These progresses have also led to the discovery that retrotransposon activity is not restricted to the germline - resulting in inheritable genetic variations - but can also mobilize in somatic tissues, such as embryonic stem cells, neuronal progenitor cells, or in many cancers. This book covers topics related to the effects of retrotransposon insertions, and their consequences on germline and somatic genome dynamics, but also discuss the role and impact of retrotransposons sequences in a broader context, including a number of novel topics that emerged recently (long non-coding RNA, neuronal disorders, exaptation) with unexpected connections between retrotransposons, stem cell maintenance, placentation, circadian cycles or aging.

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."

This detailed volume explores the latest methods that can be used to probe mRNA decay pathways and identify mRNA-binding protein targets as well as miRNA targets. Subjects include metabolic labelling and RNAseq methods for determining RNA decay rates, approaches for discovering RNA-binding protein targets, bioinformatics, miRNA targets and novel components of the miRNA-directed decay pathway, and recently developed approaches for studying nonsense-mediated mRNA decay, among other areas. Written for the highly popular Methods in Molecular Biology series, 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, mRNA Decay: Methods and Protocols serves as an ideal guide for molecular biologists, geneticists, and developmental biologists with an interest in understanding how normal development and tissue homeostasis is regulated and how these processes are perturbed in inherited and acquired diseases.

This volume explores databases containing genome-based data and genome-wide analyses. This book covers databases from all eukaryotic taxa, except plants. The chapters describe database contents and classic use-cases, which assist in accessing eukaryotic genomic data and encouraging comparative genomic research. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Eukaryotic Genomic Databases: Methods and Protocols is a valuable resource for geneticists and molecular biologists who are interested in the latest eukaryotic genomics data. The chapters 'PomBase: The Scientific Resource for Fission Yeast' and 'The Ensembl Genome Browser: Strategies for Accessing Eukaryotic Genome Data' are available open access under a CC BY 4.0 license via link.springer.com.

Sendai virus (SeV) is not just a mouse pathogen but is evolving into a cutting-edge component of biotechnology. SeV reverse genetics originating from a pure academic need to settle long-held questions in the biology and pathogenicity of nonsegmented negative strand RNA viruses (Mononegavirales) is about to bear the impressive fruit of multipurpose cytoplasmic (non-integrating) RNA vectors. This book brings together in one source the SeV biology revealed by conventional approaches and reverse genetics, the methods to construct the first-generation SeV vector and to generate safer versions, and the applications in medical settings that have left or are about to leave the laboratory bench. The applications, which already are diverse and have high medical impact, include use as vaccine vectors against AIDS and respiratory virus infections, creation of BioKnife to resect malignant tumors, induction of "footprint (transgene) free" pluripotent stem cells, and gene therapy for peripheral arterial disease. These achievements-which are just a few of many examples-were attainable only after rigorously incorporating the rich knowledge of SeV biology that has accumulated during the several decades since the discovery of the virus. Application of SeV vector is certain to expand greatly because of its extremely high performance in transgene expression and its remarkable target cell breadth.

Human beings normally have a total of 46 chromosomes, with each chromosome present twice, apart from the X and Y chromosomes in males. Some three million people worldwide, however, have 47 chromosomes: they have a small supernumerary marker chromosome (sSMC) in addition to the 46 normal ones. This sSMC can originate from any one of the 24 human chromosomes and can have different shapes. Approximately one third of sSMC carriers show clinical symptoms, while the remaining two thirds manifest no phenotypic effects. This guide represents the first book ever published on this topic. It presents the latest research results on sSMC and current knowledge about the genotype-phenotype correlation. The focus is on genetic diagnostics as well as on prenatal and fertility-related genetic counseling. A unique feature is that research meets practice: numerous patient reports complement the clinical aspects and depict the experiences of families living with a family member with an sSMC.

This book explores Dental Stem Cell (DSC) biology, from a review of basic concepts for cell culture, to isolation, self-renewal, multipotency and differentiation, regulation by molecular medicine, and prospective research areas for regenerative medicine. The first seven chapters delve into basic DSC properties, vital signaling pathways involved in differentiation, pluripotency, iPS cell development from DSCs, and genetic engineering approaches of DSCs in accordance with the current literature. A comprehensive review of possible clinical applications and in vitro/in vivo studies follows, illustrating the future of DSC research for in the tissue engineering field. The text also discusses the political, ethical, social, and legal ramifications of the use of dental stem cells. Expertly authored and drawing from a multitude of international perspectives, Dental Stem Cells is an invaluable addition to Springer's Stem Cell Biology and Regenerative Medicine series. It is essential reading for advanced graduate students, basic researchers, and clinical investigators in the fields of stem cell therapy, biological sciences of dentistry, and regenerative medicine.

The Biogenesis of Cellular Organelles represents a comprehensive summary of recent advances in the study of the biogenesis and functional dynamics of the major organelles operating in the eukaryotic cell. This book begins by placing the study of organelle biogenesis in a historical perspective by describing past scientific strategies, theories, and findings and relating these foundations to current investigations. Reviews of protein and lipid mediators important for organelle biogenesis are then presented, and are followed by summaries focused on the endoplasmic reticulum, Golgi, lysosome, nucleus, mitochondria, and peroxisome. All chapters are written by experts in their fields and, though concentrated on particular topics, are integrated under the general themes of organelle structure, function, dynamics, and biogenesis. An understanding of these concepts is important for all researchers and students interested in general cell biology and particularly to those with interests in organelle function.

Stem Cell therapy for lysosomal diseases (LSDs) is developing rapidly. This volume discusses the history, current practice and future perspectives of stem cells in inborn errors of metabolism (IEM) and provides an international perspective on progress, limitations, and future directions (e.g. gene therapy, iPS, ES) in the field. Beginning with an overview of these diseases, the book covers the breadth of this topic from treatment options, bone marrow transplantation, and alternative treatment options, through long-term outcomes and future perspectives.

This volume focuses on cytological, biochemical, and molecular biological methods to identify and examine the function of each nuclear body, with an emphasis on the analysis of long non-coding RNAs. Chapters focus on exploring recent studies that reveal how certain long non protein-coding RNAs accumulate in specific nuclear bodies and regulate the function of the bodies by serving as architectural components or controlling the dynamics of associating protein components. 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. Authoritative and practical, Nuclear Bodies and Noncoding RNAs: Methods and Protocols serves as a guideline for further study into the sophisticated regulation of gene expression.

This detailed volume will focus on the phenomenon of RNA interference by providing comprehensive coverage of various techniques for in vivo micro/siRNA imaging including the design and synthesis of specific imaging agents and tools, the development of imaging methodologies, and their interpretation. An essential element in the development and optimization of these therapies is the ability to measure the bioavailability and functionality of the RNA/oligonucleotide molecule after administration into the body. Noninvasive imaging provides the necessary set of tools to accomplish this in authentic physiologic environments and across time. Written for the highly successful Methods in Molecular Biology series, 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, RNA Imaging: Methods and Protocols serves physicians, scientists, and graduate students who are either new to the field of RNA-based imaging and its associated therapeutic applications or who wish to be apprised of recent advances in the state of the art.

Synthetic mRNA is an attractive tool for mammalian cell reprogramming that can be used in basic research, as well as in clinical applications. Present mRNA in vitro synthesis is a rather simple procedure, which delivers a high yield of quality product. Various modifications may be introduced into the mRNA by changing the sequence of the DNA template, by modifying the reaction of transcription, or by post-transcriptional modification. mRNA, as a transfection agent, has several advantages over DNA, as mRNA expression is not dependent on nuclear entry and occurs directly in the cytosol. Synthetic Messenger RNA and Cell Metabolism Modulation: Methods and Protocols covers the typical main methods, such as mRNA synthesis, modifications, and delivery. Examples of cell reprogramming and analysis in the fields of immunotherapy and stem cell research are also 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, Synthetic Messenger RNA and Cell Metabolism Modulation: Methods and Protocols will be of interest to researchers, clinicians, and biotech companies interested in mRNA-mediated cell reprogramming.

This superbly structured text is designed for practical ease of use. Quick and easy to read, it bridges the gap between primary literature and daily practice in this specialized field. Neuro-ophthalmology encompasses lesions of both the afferent and efferent pathways, which can result from various etiologies, including tumoral, paraneoplastic, vascular, inflammatory, infectious, or hereditary just to name a few. This volume of Essentials in Ophthalmology is dedicated to the review of new developments in neuro-ophthalmology. It has been written by an array of authors with real expertise in the subject. The text includes all the latest developments, including those in diagnosis, physiology, investigations, and in therapeutic options.

Hedgehog-GLI Signaling in Human Disease represents the first compilation of up-to-date reviews by top-level scientists in this important field of research. The chapters cover a wide spectrum of related interests, from the molecular bases of morphogen function, to human genetics to cancer research. The aim of the book is to disseminate information on this exciting field, to allow students, scientists and the public in general to gain access current information from research leaders and to provide a book that encompasses different aspects of research showing the fusion of basic research in model systems and medicine. This is a timely primer on how a system of cell communication, Hedgehog-GLI signaling, plays a critical role in human disease and thus provides the background for the development of novel and rational therapies.

Recent stem cell research has revealed that miRNA and RNAi-mediated gene regulation is one of the vital determinates controlling the state of cell differentiation, with the small RNAs serving as key elements involved in regulatory network control of pluripotent cell fate determination. In RNAi and microRNA-Mediated Gene Regulation in Stem Cells: Methods, Protocols, and Applications, expert authors from laboratories across the globe contribute an accessible compendium of up-to-date, proven methods focused on the study of the titular topic. Divided into three sections, the book first gives a brief introduction to RNAi and miRNAs in stem cells, with a focus on the current status of research and future perspectives, then it continues with detailed methods and protocols for RNAi screening, transfection, and the knockdown of specific genes and pathways in several animal species, including humans and mice, concluding with a section on recently developed methods for identification of miRNAs, including a general protocol for preparation and analysis of miRNA libraries for deep sequencing, knock down of a specific gene using miRNA-based shRNA, and miRNA expression analysis using qRT-PCR. 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 highlighting tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNAi and microRNA-Mediated Gene Regulation in Stem Cells: Methods, Protocols, and Applications serves as a valuable resource for scientists and aspiring graduate students interested in the intersection of RNAi, miRNA, and stem cell molecular biology and the exciting areas of medicine, including regenerative medicine, aging, cancer, and neurological disorders, that can be advanced through this expanding area of research.

Accumulating evidence supports the role of defects in post-transcriptional gene regulation in the development of cancer. RNA and Cancer examines the recent advances in our understanding of post-transcriptional gene regulation, especially RNA processing and its role in cancer development and treatment. A particular focus is mRNA splicing, but other topics such as microRNAs, mRNA stability, the perinucleolar compartment, and oligonucleotide therapeutics are also covered in detail. All chapters have been written by internationally renowned experts. The book is intended for all with an interest in gene regulation and cancer biology, and especially for those not directly working on RNA biology, including clinicians and medical students. It is hoped that it will stimulate further innovative research collaborations between RNA biologists and cancer researchers to the benefit of patients.

* Discusses cancer cell biology in relation to Genome stability and Cell cycle regulation Unique assembly of experts in these fields who wrote a comprehensive and deep up-to-date overview Discusses models for the understanding of DNA damage-dependent signal transduction and regulation in human cells Since the establishment of the DNA structure researchers have been highly interested in the molecular basis of the inheritance of genes and of genetic disorders. Scientific investigations of the last two decades have shown that, in addition to oncogenic viruses and signalling pathways alterations, genomic instability is important in the development of cancer. This view is supported by the findings that aneuploidy, which results from chromosome instability, is one of the hallmarks of cancer cells. Chromosomal instability also underpins our fundamental principles of understanding tumourigenesis: It thought that cancer arises from the sequential acquisition of genetic alterations in specific genes. In this hypothesis, these rare genetic events represent rate-limiting bottlenecks' in the clonal evolution of a cancer, and pre-cancerous cells can evolve into neoplastic cells through the acquisition of somatic mutations. This book is written by international leading scientists in the field of genome stability. Chapters are devoted to genome stability and anti-cancer drug targets, histone modifications, chromatin factors, DNA repair, apoptosis and many other key areas of research. The chapters give insights into the newest development of the genome stability and human diseases and bring the current understanding of the mechanisms leading to chromosome instability and their potential for clinical impact to the reader.

Edward B. Lewis' science is the bridge linking experimental genetics as conducted in the first half of the 20th century, and the powerful molecular genetic approaches that revolutionized the field in its last quarter. His Nobel Prize winning studies founded the field of developmental genetics and laid the groundwork for our current understanding of the universal, evolutionarily conserved strategies controlling animal development. A lesser-known aspect of Lewis' canon is the pioneering studies he carried out on ionizing radiation and human cancer. In doing so, he was propelled into a public storm over nuclear weapons testing policy. For the first time Lewis' key publications in the fields of genetics, developmental biology, radiation and cancer are compiled within one volume. commentaries on the papers placing them in their scientific and historical context and, throughout, giving insight into Lewis' approach to science and the motivations that drove Lewis' choice of subject matter. This book will be invaluable to a wide audience of professionals in the life and biomedical sciences; including geneticists, developmental biologists, molecular biologists, radiation biologists and cancer researchers. It provides source material for advanced undergraduate and graduate level courses in genetics, developmental biology, radiation and cancer. In addition, historians of science will find it to be a valuable resource both because it contains original research publications and because of the illuminating commentary.

Ultimately, the quality of the tools available for genetic analysis and experimental disease models will be assessed on the basis of whether they provide new information that generates novel treatments for human disease. In addition, the time frame in which genetic discoveries impact clinical practice is also an important dimension of how society assesses the results of the significant public financial investment in genetic research. Because of the investment and the increased expectation that new tre- ments will be found for common diseases, allowing decades to pass before basic discoveries are made and translated into new therapies is no longer acceptable. Computational Genetics and Genomics: Tools for Understanding Disease provides an overview and assessment of currently available and developing tools for genetic analysis. It is hoped that these new tools can be used to identify the genetic basis for susceptibility to disease. Although this very broad topic is addressed in many other books and journal articles, Computational Genetics and Genomics: Tools for Understanding Disease focuses on methods used for analyzing mouse genetic models of biomedically - portant traits. This volume aims to demonstrate that commonly used inbred mouse strains can be used to model virtually all human disea- related traits. Importantly, recently developed computational tools will enable the genetic basis for differences in disease-related traits to be rapidly identified using these inbred mouse strains. On average, a decade is required to carry out the development process required to demonstrate that a new disease treatment is beneficial.

This title will focus on the study of human interphase chromosomes and its relation to health and disease. Orchestrated organization and human genome function in interphase nuclei at the chromosomal level have been repeatedly shown to play a significant role in a variety of basic biological processes involved in realization and inheritance of genetic information within and between species. Current biomedical sciences of post-genomic era refocus basic and applied studies of interphase nuclei genetics and genomics with special attention to interphase chromosome behavior in health and disease. Additionally, related processes are a target of studies elucidating the role of interphase chromosome behavior during development, chromosome/DNA replication, DNA reparation etc. Studies of interphase nuclei have an appreciable impact on different areas of biomedical sciences such as cell biology, neurobiology, cancer research, developmental biology, epigenetics, cytogenetics, and medical genetics, as a whole. Moreover, development of innovative and emergent technologies to analyze interphase nuclei are closely associated with application of these techniques in clinical, diagnostic and research practice to solve reproductive problems (including infertility and spontaneous abortions), to investigate congenital malformations (including those produced by aneuploidy and other chromosome abnormalities); genetic diseases (including cardiac, immune, neurological and psychiatric diseases), and cancer. This title will serve as a source of new valuable information and promising ideas for a wide audience of professionals in biomedicine including researchers, scientists, and healthcare professionals in human genetics, cytogenetics, and developmental biology.

This book highlights a new paradigm of translation control by regulatory nascent polypeptides, which is integrated into cellular regulatory systems. Translation lies in the hub of the central dogma of biology, in which the genetic information in the forms of 4-letter sentences is translated into 20-letter sentences: sequences of amino acids that constitute proteins, the functional molecules of life. The process involves a huge number of chemical reactions as well as physical movements of the ribosome along a messenger RNA and takes, on average, tens of seconds in prokaryotes and a few minutes in eukaryotes. Detailed knowledge about the progression of translation, called "elongation", only recently started to accumulate. Newly synthesized and growing polypeptides, called nascent polypeptides, can interact with the intra-ribosomal conduit, called the ribosomal exit tunnel, when they have some specific amino acid sequences, called "an arrest sequence". Such interaction leads to a halt in the elongation reaction. Resulting stalling of the ribosome on messenger RNA can affect the secondary structure and/or localization of the message in the cell, consequently leading to biological outputs such as elevation or reduction of a gene product. This book provides a first collection of knowledge focused on regulatory nascent polypeptides, which have been studied recently using diverse organisms including bacteria, plants, and animals. Readers will be impressed by a new paradigm showing that proteins can function even during the course of their biosynthesis and that the ribosome, the "factory" of protein production, interacts with and inspects its products to adjust the speed of completion of each product. Moreover, regulatory nascent polypeptides can sense or monitor physiological states of the cell and modulate its ability to arrest translation. Living organisms use such intricate control mechanisms of translational speed to regulate gene expression. This book will be a useful addition for established scientists while inspiring students and young scientists to gain deeper insights into the processes of expression of genetic information.

Heart disease is the leading cause of death in developed countries. Recent experimental advances featuring cellular, molecular, and genetic tools and technologies offer the potential for new therapeutic strategies directed toward remediation of inherited and acquired heart diseases. Whether these recent basic science advances will ultimately translate to clinical efficacy for patients with heart disease is unknown and is important to ascertain. Cardiac Cell and Gene Transfer: Principles, Protocols, and Applications is designed to provide the reader with up-to-date coverage of a myriad of specific methodo- gies and protocols for gene and cell transfer to the myocardium. Each chapter features a "Notes" section that provides useful "how to" problem-solving insights that are often left unstated in standard published protocols. Cardiac Cell and Gene Transfer: Principles, Protocols, and Appli- tions addresses principles and applications of cell and gene transfer to the heart, including protocols for vector production and purification. Detailed step-by-step methods and applications for first/second-generation adenoviral vectors, adeno-associated vectors, gutted adenoviral vectors, and lentiviral vectors are included. Additionally, detailed methods for cardiac cell grafting and transplantation are provided, and these chapters highlight the prospects of cell-based therapies for cardiac repair. The book also covers specific in vivo techniques for cardiac gene transfer, and specifies subsequent cellular and organ-level physiological assessment techniques and protocols. Accordingly, this book is designed for basic science and clinical researchers in the academic, pharmaceutical, and biotechnology sectors of the cardiovascular community.

This volume explores the latest developments in a novel area of molecular biology and a hot topic in the field of oncology: cancer stem cells. These chapters from expert contributing authors present concepts such as the universal stem cell, new molecular pathways, new targeted agents, the different roles that cancer stem cells seem to have according to the organ they are placed in, and the future role that targeting cancer stem cells may have in the management of patients in the clinic.

Exploring the latest research including new data from randomized trials, this book examines important proposals over the origin of cancer stem cells such as the possibility that cancer stem cells may arise from mutated stem cells or a fully differentiated cell that may undergo several mutations that drive it back to a stem-like state. The authors consider the role that stem cells seem to have in the onset, development and resistance to classical antitumoral treatments of cancer and discuss possible potential future treatment modalities for the management of advanced cancer patients.

The question, "Are stem cells involved in cancer?" may not have a simple answer, but ongoing investigations, in-depth consideration and a broad spectrum of information can be found in this book, allowing the reader to arrive at his or her own answer.

This book will appeal to researchers in the field of oncology and cancer research and biomedical scientists with an interest in stem cells.

Human beings have been using intoxicating substances for millennia. But while most people have used psychoactive substances without becoming dependent on them, a significant minority develop substance use disorders. The question remains: why does addiction occur in some and not others? The 61st installment of the Nebraska Symposium on Motivation, Genes and the Motivation to Use Substances probes the complex role of genetics in substance use and abuse across diverse methodologies, research organisms, levels of analysis and disciplines. Its combined lifespan/motivation approach to individual differences sheds necessary light on genetic vs. environmental factors in vulnerability, addiction risk, the relationship between behavioral disinhibition and substance use and the motivation to quit. While alcohol use/abuse is the focus of much of the book, its chapters provide scientific and clinical insights into substance abuse in general as well as implications for treatment. And an intriguing conclusion discusses the need to bridge the gap between genetics and neuroscience and the best scientific conditions in which this integration may thrive. Included in the coverage: * Rodent models of genetic contributions to the motivation to use alcohol. * The adolescent origins of substance abuse disorders * The developmental matrix of addictive behavior * The genetics of cannabis involvement * The DNA methylation signature of smoking * Genomics of impulsivity: integrating genetics and neuroscience. Reflecting the current state of knowledge in a field with groundbreaking potential, Genes and the Motivation to Use Substances is a fascinating resource for psychologists, psychiatrists, geneticists, neuroscientists, social workers, policymakers and researchers in addiction.