The rapid pace of microRNA (miRNA) research continues to drive the advances of techniques for miRNA expression profiling, and innovative technologies that are more sensitive, specific, quantitative, and that are compatible with a wide range of biospecimens have been developed during the past few years. In Next-Generation MicroRNA Expression Profiling Technology: Methods and Protocols, expert researchers in the field contribute detailed examinations of the most current approaches being used today. This volume includes comprehensive coverage of methodologies that have been developed for miRNA profiling, as well as next-gen sequencing technology, miRNA databases, and specialized applications, such as cancer studies and miRNA-based non-invasive biomarker development. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters feature 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 cutting-edge, Next-Generation MicroRNA Expression Profiling Technology: Methods and Protocols provides an ideal guide for novices and experts alike who are seeking to utilize these powerful technologies.

Despite a half century of structural, biophysical and biochemical investigations of ribonucleic acids, they are still mysterious. RNAs stand at fertile crossroads of disciplines, integrating concepts from genomics, proteomics, dynamics as well as biochemistry and molecular biology. From 20 years it is clear, that genetic regulation of eukaryotic organisms has been misunderstood for the last years that the expression of genetic information is effected only by proteins. Basic understanding of nucleic acids has enhanced our foundation to probe novel biological functions. This is especially evident for RNA molecules whose functionality, maturation, and regulation require formation of correct secondary structure through encoded base-pairing interactions.

After transcription in the nucleus, RNA binding proteins (RBPs) recognize cis-regulatory RNA elements within pre-mRNA sequence to form mRNA-protein (mRNP) complexes. Similarly to DNA binding proteins such as transcription factors that regulate gene expression by binding to DNA elements in the promoters of genes, RBPs regulate the fate of target RNAs by interacting with specific sequences or RNA secondary structural features within the transcribed RNA molecule. The set of functional RNA elements recognized by RBPs within target RNAs and which control the temporal, functional and spatial dynamics of the target RNA define a putative mRNP code . These cis-regulatory RNA elements can be found in the 5 and 3 untranslated regions (UTRs), introns, and exons of all protein-coding genes. RNA elements in 5 and 3 UTRs are frequently involved in targeting RNA to specific cellular compartments, affecting 3 end formation, controlling RNA stability and regulating mRNA translation. RNA elements in introns and exons are known to function as splicing enhancers or silencers during the splicing process from pre-mRNA to mature mRNA.

This book provides case studies of RNA binding proteins that regulate aspects of RNA processing that are important for fundamental understanding of diseases and development. Chapters include systems-level perspectives, mechanistic insights into RNA processing and RNA Binding proteins in genetic variation, development and disease. The content focuses on systems biology and genomics of RNA Binding proteins and their relation to human diseases."

The principle objective of this book is to help undergraduate students in the analysis of genetic problems. Many students have a great deal of difficulty doing genetic analysis, and the book will be useful regardless of which genetics text is being used. Most texts provide some kinds of problems and answers: few, if any, however, show the students how to actually solve the problem. Often the student has no idea how the answer was derived. This work emphasizes solutions, not just answers. The strategy is to provide the student with the essential steps and the reasoning involved in conducting the analysis. Throughout the book, an attempt is made to present a balanced account of genetics. Topics, therefore, center about Mendelian, cytogenetic, molecular, quantitative, and population genetics, with a few more specialized areas. Whenever possible the student is provided with the appropriate basic statistics necessary to make some the analyses. The book also builds on itself; that is, analytical methods learned in early parts of the book are subsequently revisited and used for later analyses. A deliberate attempt is made to make complex concepts simple, and sometimes to point out that apparently simple concepts are sometimes less so on further investigation. Any student taking a genetics course will find this book an invaluable aid to achieving a good understanding of genetic principles and practice.

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 volume describes a variety of protocols that will allow the readers to study different aspects of transcriptional and posttranscriptional gene expression regulation in eukaryotic cells. Chapters focus on the latest use of CRISPRi and RNAi technologies for studying various aspects of transcriptional and posttranscriptional regulation and tools to navigate protocols on key bioinformatics. 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 cutting-edge, Eukaryotic Transcription and Post-Transcription Gene Expression Regulation aims to ensure successful results in the further study of this vital field.

Basophils and mast cells are similar but unique secretory cells with a well-documented role in immediate-hypersensitivity reactions. The presence of these cells in various cell mediated hypersensitivity reactions, in tissues of multiple diseases, and as a component of the host reaction to injury and repair in numerous circumstances is well known. Release of stored and newly generated mediators of inflammation from basophils and mast cells contributes to the cascade of pathogenetic events in circumstances under which these release reactions occur. Despite insights acquired through studies of these pathologic events, the role of basophils and mast cells and their secretory products in health is not known. In this book, I review much of the structural information regarding basophils and mast cells of multiple species. Ultrastructural studies of rat mast cells historically precede and quantitatively exceed similar studies of basophils and mast cells of other species. Therefore, I first review these background studies as an entity. Then I discuss the contents of two prominent organelles-granules and lipid bodies-in basophils and mast cells of several species. The ultrastructural morphology of basophils and mast cells in three species is presented in detail to establish appropriate guidelines for their recognition and to provide general rules for analysis which are appropriate for the identification of these cells in other species as well."

This volume addresses the overlapping aspects of the fields of genomics, obesity and (non-) medical ethics. It is unique in its examination of the implications of genomics for obesity from an ethical perspective. Genomics covers the sciences and technologies involved in the pathways that DNA takes until the organism is completely built and sustained: the range of genes (DNA), transcriptor factors, enhancers, promoters, RNA (copy of DNA), proteins, metabolism of cell, cellular interactions, organisms. Genomics offers a holistic approach, which, when applied to obesity, can have surprising and disturbing implications for the existing networks tackling this phenomenon. The ethical concerns and consideration presented are inspired by the interaction between the procedural perspective emphasizing the necessity of consultative and participatory organizational relationships in the new gray zones between medicine and food, and the substantive perspective that both cherishes individual autonomy and embeds it in socio-cultural contexts.

The field of epigenetics has grown exponentially in the past decade, and a steady flow of exciting discoveries in this area has served to move it to the forefront of molecular biology. Although epigenetics may previously have been considered a peripheral science, recent advances have shown considerable progress in unraveling the many mysteries of nontraditional genetic processes. Given the fast pace of epigenetic discoveries and the groundbreaking nature of these developments, a thorough treatment of the methods in the area seems timely and appropriate and is the goal of Epigenetics Protocols. The scope of epigenetics is vast, and an exhaustive analysis of all of the techniques employed by investigators would be unrealistic. However, this (TM) volume of Methods in Molecular Biology covers three main areas that should be of greatest interest to epigenetics investigators: (1) techniques related to analysis of chromatin remodeling, such as histone acetylation and methylation; (2) methods in newly developed and especially promising areas of epigenetics such as telomere position effects, quantitative epigenetics, and ADP ribosylation; and (3) an updated analysis of techniques involving DNA methylation and its role in the modification, as well as the maintenance, of chromatin structure.

Risk, Age and Pregnancy provides an in-depth case study of the operation of a prenatal genetic screening and testing system. The methodology integrates observational, qualitative interview and survey data. The perspectives of pregnant women, hospital doctors and midwives are explored in depth, as is the communication between women and the hospital doctors who advise them. The book offers insights which are relevant to those concerned with the rapidly growing field of genetic risk management.

The term epigenetics describes regulatory and information storing mechanisms of specific genes that do not involve any change of their DNA sequence. Epigenetics is closely related to the extensively folded state, in which the genome is packaged, known as chromatin. New genomic tools nowadays allow the genome-wide assessment of, for example, chromatin states and DNA modifications, and led to the discovery of unexpected new epigenetic principles, such as epigenomic memory. This was the start of the field of epigenomics, the relation of which to human health and disease is discussed in this textbook. This book aims to summarize, in a condensed form, the role of epigenomics in defining chromatin states that are representative of active genes (euchromatin) and repressed genes (heterochromatin). Moreover, this book discusses the principles of gene regulation, chromatin stability, genomic imprinting and the reversibility of DNA methylation and histone modifications. This information should enable a better understanding of cell type identities and will provide new directions for studies of, for example, cellular reprograming, the response of chromatin to environmental signals and epigenetic therapies that can improve or restore human health. In order to facilitate the latter, we favor a high figure-to-text ratio following the rule "a picture tells more than thousand words". The content of the book is based on the lecture course "Molecular Medicine and Genetics" that is given by one of us (C. Carlberg) in different forms since 2002 at the University of Eastern Finland in Kuopio. Thematically, this book is located between our textbooks "Mechanisms of Gene Regulation" (ISBN 978-94-017-7741-4) and "Nutrigenomics" (ISBN 978-3-319-30415-1), studying of which may also be interesting to our readers. The book is sub-divided into three sections and 13 chapters. Following the Introduction (section A), section B will explain the molecular basis of epigenomics, while section C will provide examples for the impact of epigenomics in human health and disease. The lecture course is primarily designed for Master level students of biomedicine, but is also frequented by PhD students as well as by students of other bioscience disciplines. Besides its value as a textbook, Human Epigenomics will be a useful reference for individuals working in biomedicine.

Biomedical research in the first decade of the 21st century has been marked by a rapidly growing interest in epigenetics. The reasons for this are numerous, but primarily it stems from the mounting realization that research programs focused solely on DNA sequence variation, despite their breadth and depth, are unlikely to address all fundamental aspects of human biology. Some questions are evident even to non-biologists. How does a single zygote develop into a complex multicellular organism composed of dozens of different tissues and hundreds of cell types, all genetically identical but performing very different functions? Why do monozygotic twins, despite their stunning external similarities, often exhibit significant differences in personality and predisposition to disease? If environmental factors are solely the cause of such variation, why are similar differences also observed between genetically identical animals housed in a uniform environment? Over the last couple of decades, epigenetics has undergone a significant metamorphosis from an abstract developmental theory to a very dynamic and rapidly developing branch of molecular biology. This volume represents a compilation of our current understanding about the key aspects of epigenetic processes in the brain and their role in behavior. The chapters in this book bring together some of the leading researchers in the field of behavioral epigenetics. They explore many of the epigenetic processes which operate or may be operating to mediate neurobiological functions in the brain and describe how perturbations to these systems may play a key role in mediating behavior and the origin of brain diseases.

The advances in human genetics that have ocurred during the past 20 years have revolutionized our knowledge of the role played by inheritance in health and disase. It is clear that our DNA determines not only the emergence of catastrophic single-gene disorders, which affect millions of persons worldwide, but also interacts with environments to predispose individuals to cancer, allergy, hypertension, heart disease, diabetes, psychiatric disorders and even to some infectious diseases. Overall, the study of longevity and the demonstration of genes favouring a long lifespan suggest that such protective systems exist. In recent years, the study of genetic polymorphisms has made clear that some alleles have beneficial effects. These discoveries can substantially improve our understanding of the interactions between genetics and the environment, between pathogenetic mechanisms and new treatments.

This volume provides readers with a wide collection of the latest and readily reproducible technical protocols available in the field of non-viral gene delivery vectors. The chapters in this book are organized into three major parts: Part I is a section on conventional bolus gene delivery vectors that introduces typical transfection approaches relying on the addition of transfectants to the cell culture medium where the cells are grown in; Part II covers stimuli-responsive bolus transfectants and topics on gene delivery complexes made of smart polymers or stimuli-responsive polymers that change according to the environment they are in and delivered by dripping into cells; Part III discusses examples of substrate-mediated gene delivery-also termed reverse transfection-and the immobilization of a gene delivery vector onto a surface as opposed to more typical bolus delivery from the medium. 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. Cutting-edge and practical, Non-Viral Gene Delivery Vectors: Methods and Protocols is written for experimentalists, and is an essential part of many laboratory bookshelves. This book will help novice and professionals alike succeed in their research in this field.

Over the last decade Life Science has undergone an accelerated evolution, culminating in the -omics era characterized by the development of a multitude of high throughput methods that are becoming more routinely applied in biochemistry labs. In Functional Genomics: Methods and Protocols, Second Edition expert researchers in the field detail many of the methods which are now commonly used for studies in the life sciences focusing on the dynamic aspects of the transcriptome, proteome and metabolome, respectively.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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Functional Genomics: Methods and Protocols, Second Edition seeks to aid scientists in establishing or extending technologies and techniques in their laboratories.

This innovative and engaging book argues that because our genetic information is directly linked to the genetic information of others, it is impossible to assert a ‘right to privacy’ in the same way that we can in other areas of life. This position throws up questions around access to sensitive data. It suggests that we may have to abandon certain intuitions about who may access our genetic information; and it raises concerns about discrimination against people with certain genetic characteristics. But the author asserts that regulating access to genetic information requires a more nuanced perspective that does not rely on the familiar language of rights. The book proposes new ways in which we may think about who has access to what genetic information, and on what basis they do so. Conceptually challenging, the book will prove engaging reading for scholars and students interested in the area of bioethics and medical law, as well as policy makers working with these pressing issues.

In 2009 the University Medicine Greifswald launched the "Greifswald Approach to Individualized Medicine" (GANI_MED) to implement biomarker-based individualized diagnostic and therapeutic strategies in clinical settings. Individualized Medicine (IM) has led not only to controversies about its potentials, but also about its societal, ethical and health economic implications. This anthology focusses on these areas and includes - next to clinical examples illustrating how the integrated analysis of biomarkers leads to significant improvement of therapeutic outcomes for a subgroup of patients - chapters about the definition, history and epistemology of IM. Additionally there is a focus on conceptual philosophical questions as well as challenges for applied research ethics (informed consent process, the IT-based consent management and the handling of incidental findings). Finally it pays attention to health economic aspects. The possibilities of IM to initiate a paradigm shift in the German health care provision are investigated. Furthermore, it is asked whether the G-DRG system is ready for the implementation of such approaches into clinical routine.

This volume covers a wide range of various fields of research, with the common thread being Next Generation Sequencing (NGS) related methods and applications, as well as analysis and interpretation of the data obtained. Chapters guide readers through the highly dynamic processes of translational and transcriptional profiling of a cell, method to detect copy number alterations (CNAs), targeted sequencing applications, method called "Hi-Plex" to characterize known polymorphic loci, single-cell of DNA or RNA, identify and characterize rare circulating CD4 T cells, and computational pipeline for RNAseq analysis. 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, Next Generation Sequencing: Methods and Protocols aims to be useful and informative for further study into this vital field.

Induced pluripotent stem cells in cardiovascular research.- TRPs in the brain.-The channel physiology of the skin."

Anyone interested in comparative biology or the history of science will find this myth-busting work genuinely fascinating. It draws attention to the seminal studies and important advances that have shaped systematic and biogeographic thinking. It traces concepts in homology and classification from the 19th century to the present through the provision of a unique anthology of scientific writings from Goethe, Agassiz, Owen, Naef, Zangerl and Nelson, among others.

The three-dimensional organization of the DNA inside the eukaryotic cell nucleus has emerged a critical regulator of genome integrity and function. Increasing evidence indicates that nuclear pore complexes (NPCs), the large protein channels that connect the nucleus to the cytoplasm, play a critical role in the establishment and maintenance of chromatin organization and in the regulation of gene activity. These findings, which oppose the traditional view of NPCs as channels with only one: the facilitation of nucleocytoplasmic molecule exchange, have completely transformed our understanding of these structures. This book describes our current knowledge of the role of NPCs in genome organization and gene expression regulation. It starts by providing an overview of the different compartments and structures of the nucleus and how they contribute to organizing the genome, then moves to examine the direct roles of NPCs and their components in gene expression regulation in different organisms, and ends by describing the function of nuclear pores in the infection and genome integration of HIV, in DNA repair and telomere maintenance, and in the regulation of chromosome segregation and mitosis. This book provides an intellectual backdrop for anyone interested in understanding how the gatekeepers of the nucleus contribute to safeguarding the integrity and function of the eukaryotic genome.

Mitochondrial cytopathies are mutations in the inherited maternal mitochondrial genome, or the nuclear DNA-mutation. Mitochondrial respiratory chain disorders (RCD) are a group of genetically and clinically heterogeneous diseases, due to the fact that protein components of the respiratory chain are encoded by both mitochondrial and nuclear genomes and are essential in all cells. In addition, the biogenesis, structure and function of mitochondria, including DNA replication, transcription, and translation, all require nuclear encoded genes. Since mitochondria are present in every cell, every tissue, mitochondrial disorder usually affects multiple organs.

This book presents pioneering findings on the characterization of cellular regulation and function for three recently identified protein posttranslational modifications (PTMs): lysine malonylation (Kmal), glutarylation (Kglu) and crotonylation (Kcr). It addresses three main topics: (i) Detecting Kmal substrates using a chemical reporter, which provides important information regarding the complex cellular networks modulated by Kmal; (ii) Identifying Kglu as a new histone PTM and assessing the direct impact of histone Kglu on chromatin structure and dynamics; and (iii) Revealing Sirt3's value as a regulating enzyme for histone Kcr dynamics and gene transcription, which opens new avenues for examining the physiological significance of histone Kcr. Taken together, these studies provide information critical to understanding how these protein PTMs are associated with various human diseases, and to identifying therapeutic targets for the dysregulation of these novel protein markers in various human diseases.

This book highlights key technologies and identifies areas for further development in proteogenomics. The utility and usefulness of very large Omics data sets (Next Gen Sequencing of DNA, RNA-seq, ribosome profiling, mass spectrometry- and antibody-based proteomics) is discussed and opportunities and challenges of related bioinformatics applications are outlined. The reader will be able to appreciate the interdisciplinary nature of the continuously evolving area of proteogenomics, which has already grown beyond its original concept of verifying gene annotations by proteomics. The chapters presented in this book are arranged to offer a general overview, rather than to provide detailed descriptions of technologies. The selected applications will provide useful insight into the level of detail that can be obtained in relation to certain diseases areas, including cancer biology and personalized medicine. The readers will find that each chapter delivers a comprehensive approach to proteogenomics, each from the point of view of a specific application. Research scientists interested in innovative processes that can offer a unique and at the same time a more complete access to technological developments and concepts that in turn can contribute to a better understand biological functions should read this book.