Together with early theoretical work in population genetics, the debate on sources of genetic makeup initiated by proponents of the neutral theory made a solid contribution to the spectacular growth in statistical methodologies for molecular evolution. Evolutionary Genomics: Statistical and Computational Methods is intended to bring together the more recent developments in the statistical methodology and the challenges that followed as a result of rapidly improving sequencing technologies. Presented by top scientists from a variety of disciplines, the collection includes a wide spectrum of articles encompassing theoretical works and hands-on tutorials, as well as many reviews with key biological insight. Volume 2 begins with phylogenomics and continues with in-depth coverage of natural selection, recombination, and genomic innovation. The remaining chapters treat topics of more recent interest, including population genomics, -omics studies, and computational issues related to the handling of large-scale genomic data. Written in the highly successful Methods in Molecular Biology (TM) series format, this work provides the kind of advice on methodology and implementation that is crucial for getting ahead in genomic data analyses. Comprehensive and cutting-edge, Evolutionary Genomics: Statistical and Computational Methods is a treasure chest of state-of the-art methods to study genomic and omics data, certain to inspire both young and experienced readers to join the interdisciplinary field of evolutionary genomics.

According to the National Institute of Health, a genome-wide association study is defined as any study of genetic variation across the entire human genome that is designed to identify genetic associations with observable traits (such as blood pressure or weight), or the presence or absence of a disease or condition. Whole genome information, when combined with clinical and other phenotype data, offers the potential for increased understanding of basic biological processes affecting human health, improvement in the prediction of disease and patient care, and ultimately the realization of the promise of personalized medicine. In addition, rapid advances in understanding the patterns of human genetic variation and maturing high-throughput, cost-effective methods for genotyping are providing powerful research tools for identifying genetic variants that contribute to health and disease. (good paragraph)
This burgeoning science merges the principles of statistics and genetics studies to make sense of the vast amounts of information available with the mapping of genomes. In order to make the most of the information available, statistical tools must be tailored and translated for the analytical issues which are original to large-scale association studies. This book will provide researchers with advanced biological knowledge who are entering the field of genome-wide association studies with the groundwork to apply statistical analysis tools appropriately and effectively. With the use of consistent examples throughout the work, chapters will provide readers with best practice for getting started (design), analyzing, and interpreting data according to their research interests. Frequently used tests will be highlighted and a critical analysis of the advantages and disadvantage complimented by case studies for each will provide readers with the information they need to make the right choice for their research. Additional tools including links to analysis tools, tutorials, and references will be available electronically to ensure the latest information is available.
* Easy access to key information including advantages and disadvantage of tests for particular applications, identification of databases, languages and their capabilities, data management risks, frequently used tests
* Extensive list of references including links to tutorial websites
* Case studies and Tips and Tricks

Due to their novel concepts and extraordinary high-throughput sequencing capacity, the "next generation sequencing" methods allow scientists to grasp system-wide landscapes of the complex molecular events taking place in various biological systems, including microorganisms and microbial communities. These methods are now being recognized as essential tools for a more comprehensive and deeper understanding of the mechanisms underlying many biological processes. In High-Throughput Next Generation Sequencing: Methods and Applications, experts in the field explore the most recent advances in the applications of next generation sequencing technologies with an emphasis on microorganisms and their communities; however, the methods described in this book will also offer general applications relevant to the study of any living organisms. 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. Comprehensive and cutting-edge, High-Throughput Next Generation Sequencing: Methods and Applications is an excellent collection of chapters to aid all scientists who wish to apply these innovative research tools to enhance their own pursuits in microbiology and also biology in general.

Recent developments in stem cell biology have opened new directions in cell therapy. This book provides the state-of-the-art developments in using biomaterials as artificial niches for engineering stem cells, both for the purpose of better understanding their biology under 3D biomimetic conditions as well as for developing new strategies for efficient long term maintenance and directed differentiation of stem cells into various therapeutic lineages. Animal and human stem cells of both embryonic and adult origin are discussed with applications ranging from nerve regeneration, orthopedics, cardiovascular therapy, blood cell generation and cancer therapy. Both synthetic and natural biomaterials are reviewed with emphasis on how material-stem cell interactions direct specific signaling pathways and ultimately modulate the cell fate. This book is valuable for biomaterial scientists, tissue engineers, clinicians as well as stem cell biologists involved in basic research and applications of adult and embryonic stem cells.

Two sigma receptor subtypes have been proposed, sigma1 and 2. Much of our understanding of this system is based on biochemical and pharmacological characterization of the cloned sigma1 receptor subtype (Sigma1). It has become clear that sigma receptors are not canonical receptors. Sigma1 is highly conserved among mammalian species, however, it does not share significant homology with any other mammalian protein. Although a range of structurally diverse small molecules bind Sigma1 with high affinity, and it has been associated with a broad range of signaling systems, Sigma1 itself has no known signaling or enzymatic activity. The evolution of this field over nearly four decades has more recently led to a fundamental shift in the concept of "sigma receptors" to what may more accurately and generally be called sigma proteins. Largely based on traditional pharmacologic approaches, the Sigma1 protein has been associated with a broad range of signaling systems, including G-protein coupled receptors, NMDA receptors, and ion channels. Sigma proteins have been linked to a range of physiological processes, including intracellular calcium signaling, neuroprotection, learning, memory, and cognition. Emerging genetic, clinical, and mechanism focused molecular pharmacology data demonstrate the involvement of proteins in a range of pathophysiologies and disorders including neurodegenerative disease, pain, addiction, psychomotor stimulant abuse, and cancer. However, an understanding of the physiological role of sigma proteins has remained elusive. Emerging data associate Sigma1 with chaperone-like activities or molecular scaffold functions. This book aims to provide an updated perspective on this rapidly evolving field undergoing changes in fundamental concepts of key importance to the discipline of pharmacology. It focusses on the reported roles of sigma proteins in pathophysiology and on emergent therapeutic initiatives.

Neuropsychiatric disorders such as schizophrenia, mood disorders, Alzheimer s disease, epilepsy, alcoholism, substance abuse and others are one of the most debilitating illnesses worldwide characterizing by the complexity of the causes, and lacking the laboratory tests that may promote diagnostic and prognostic procedures. Recent advances in neuroscience, genomic, genetic, proteomic and metabolomic knowledge and technologies have opened the way to searching biomarkers and endophenotypes, which may offer powerful and exciting opportunity to understand the etiology and the underlying pathophysiological mechanisms of neuropsychiatric disorders. The challenge now is to translate these advances into meaningful diagnostic and therapeutic advances. This book offers a broad synthesis of the current knowledge about diverse topics of the biomarker and endophenotype strategies in neuropsychiatry.

The book is organized into four interconnected volumes: Neuropsychological Endophenotypes and Biomarkers (with overview of methodological issues of the biomarker and endophenotype approaches in neuropsychiatry and some technological advances), Neuroanatomical and Neuroimaging Endophenotypes and Biomarkers, Metabolic and Peripheral Biomarkers and Molecular Genetic and Genomic Markers . The contributors are internationally and nationally recognized researchers and experts from 16 countries. This four-volume handbook is intended for a broad spectrum of readers including neuroscientists, psychiatrists, neurologists, endocrinologists, pharmacologists, clinical psychologists, general practitioners, geriatricians, health care providers in the field of neurology and mental health interested in trends that have crystallized in the last decade, and trends that can be expected to further evolve in the coming years. It is hoped that this book will also be a useful resource for the teaching of psychiatry, neurology, psychology and mental health. "

"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.

Progress in functional proteomics has been limited for a long time, partially caused by limitations in assay sensitivity and sample capacity; however, protein microarrays have the ability to overcome these limitations so that a highly parallel analysis of hundreds of proteins in thousands of samples is attainable. In Protein Microarrays: Methods and Protocols, expert researchers in the field present an up-to-date collection of robust strategies in the field of protein microarrays and summarize recent advantages in the field of printing technologies, the development of suitable surface materials, as well as detection and quantification technologies. 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 notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Protein Microarrays: Methods and Protocols aims to stimulate the application and further advancement of this powerful technology in labs worldwide.

Circadian rhythms are such an innate part of our lives that we rarely pause to speculate why they even exist. Some studies have suggested that the disruption of the circadian system may be causal for obesity and manifestations of Metabolic Syndrome (MetS). Shift-work, sleep-deprivation and bright-light-exposure at night are related to increased adiposity (obesity) and prevalence of MetS. It has been provided evidence of clock genes expression in human adipose tissue and demonstrated its association with different components of the MetS. Moreover, current studies are illustrating the particular role of different clock genes variants and their predicted haplotypes in MetS.

The purpose of Chronobiology and Obesity is to describe the mechanisms implicated in the interaction between chonodisruption and metabolic-related illnesses, such as obesity and MetS, with different approaches."

This volume provides a collection of methods and protocols detailing extracellular RNA and hopes to be a useful resource for those interested in this exciting and emerging field. Chapters are divided into four sections covering an overview of the field, approaches for the isolation of exRNA, protocols for detection and quantitation of exRNA, and approaches that can be useful for studies to evaluate potential therapeutic 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Extracellular RNA: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Many fundamental discoveries concerning epigenetics and the elucidation of mechanisms of epigenetic regulation have developed from studies performed in plants. In Plant Epigenetics and Epigenomics: Methods and Protocols, leading scientists in the epigenetics field describe comprehensive techniques that have been developed to understand the plant epigenetic landscape. These include recently developed methods and techniques for analysis of epigenetically regulated traits, such as flowering time, transposon activation, genomic imprinting and genome dosage effects. 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 avoidance of known pitfalls. Authoritative and practical, Plant Epigenetics and Epigenomics: Methods and Protocols seek to aid scientists in the further study of plant epigenetic phenomena using advanced contemporary methods.

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 Gene Regulatory Sequences and Human Disease, the Editor will introduce the different technological advances that led to this breakthrough. In addition, several examples will be provided of nucleotide variants in noncoding sequences that have been shown to be associated with various human diseases.

Fluorescence in situ Hybridization (FISH) belongs to that special category of well-established molecular biology techniques that, since their inception a few decades ago, have succeeded in keeping a prominent position within the constantly expanding list of laboratory pro- dures for biomedical research and clinical diagnostics. The design simplicity and cost-effectiveness of the early FISH protocols, combined with the signifcant acceleration of discoveries in related technical areas such as fuor- cence microscopy, digital imaging, and nucleic acid technology have prompted the div- sifcation of the original technique into an outstanding number of imaginative and useful applications, and thus have not only held back its outmoding but have also promoted its expansion into different areas of basic and applied research in the post-genomic era. The 34 chapters included in this book aim at portraying the vibrant complexity and diversity of the current FISH protocol landscape, providing cutting-edge examples of va- ous applications for genetic and developmental research, cancer research, reproductive medicine, diagnostic and prognostic purposes, microbial ecology, and evolutionary st- ies. The book is divided in four parts: (I) Core Techniques, (II) Technical Advancements and Novel Adaptations, (III) Translational FISH: Applications for Human Genetics and Medicine, and (IV) Protocols for Model Organisms.

The field of genetics is rapidly evolving, and new medical breakthroughs are occurring as a result of advances in our knowledge of genetics. This series continually publishes important reviews of the broadest interest to geneticists and their colleagues in affiliated disciplines. This thematicvolume reviews the latest research findings in the area of vascular proteomics related to the receptors of the vascular endothelium, and expands insights into diseases that exhibit distinct vascular characteristics, including cancer, obesity, andinflammation.

* Provides contrasting roles of VEGF, givingresearchers a better understanding of the underlying mechanisms of VEGF *Includeschapters that review research employing a variety of organisms, allowing researchers to compare and contrast *Focuses onmaterial that translates basic research to real-life treatment applications, showing primary researchers how the basic science is being used in the clinical setting"

In Polyadenylation: Methods and Protocols, expert researchers in the field detail many of the protocols which are now commonly used to study polyadenylation. Focusing on recent advances in the fast-moving polyadenylation filed, that has recently been recognized as a key contributor to the complexity of mammalian gene expression. 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 evolved from the editors strong belief that the information and new developments that were evolving from the rapidly growing field of genomics and that are happening primarily in the developed world have not happened at a parallel rate in the developing world. One would have hoped that by now the technologies and approaches would have been adapted on a far greater scale. In addition to this, the associated information is not always easily accessible, and is not disseminated in a format that can become a useful reference for scientists, students and others who reside in developing countries.

This manual offers detailed protocols for fluorescence in situ hybridization (FISH) and comparative genomic hybridization approaches, which have been successfully used to study various aspects of genomic behavior and alterations. Methods using different probe and cell types, tissues and organisms, such as mammalians, fish, amphibians (including lampbrush-chromosomes), insects, plants and microorganisms are described in 57 chapters. In addition to multicolor FISH procedures and special applications such as the characterization of marker chromosomes, breakpoints, cryptic aberrations, nuclear architectures and epigenetic changes, as well as comparative genomic hybridization studies, this 2nd edition describes how FISH can be combined with other techniques. The latter include immunostaining, electron microscopy, single cell electrophoresis and microdissection. This well-received application guide provides essential protocols for beginning FISHers and FISH experts alike working in the fields of human genetics, microbiology, animal and plant sciences.

This volume provides the reader with a pathophysiological perspective on the role of CNS in puberty and adolescence, starting from genetic/molecular aspects, going through structural/imaging changes and leading to physical/behavioral characteristics. Therefore, renowned investigators involved in both animal and human research shared recent data as well as overall appraisal of relevant questions around CNS control of puberty and adolescence. No doubt that this volume will inspire those involved in either scientific research or clinical practice or both in the fascinating field of puberty and adolescence.

Epigenetics has emerged recently as an important area of molecular biological studies. Epigenetic modifications lead to potentially heritable but reversible alterations in the expression of genes that determine cell fate. Epigenetic misregulation is thus often linked to degenerative diseases, cancer and neuronal disorders. Recent biomedical interest in this regulatory system stems from the fact that epigenetic, in contrast to genetic, alterations are in principle amenable to pharmacological intervention. A few epigenetically active drugs, for example histone deacetylase inhibitors (HDACi) and DNA methyltransferase (DNMT) inhibitors, have been approved by FDA for treatment of cancers such as CTCL, MDS, and AML. This volume explores the scientific background for clinical applications of epigenetically active drugs. Included are descriptions of epigenetic controls over gene expression, the post-transcriptional silencing of genes by RNA interference (RNAi) and microRNAs, as well as new findings from stem cell research which are relevant to pharmacological applications. Content Level Research

Together with early theoretical work in population genetics, the debate on sources of genetic makeup initiated by proponents of the neutral theory made a solid contribution to the spectacular growth in statistical methodologies for molecular evolution. Evolutionary Genomics: Statistical and Computational Methods is intended to bring together the more recent developments in the statistical methodology and the challenges that followed as a result of rapidly improving sequencing technologies. Presented by top scientists from a variety of disciplines, the collection includes a wide spectrum of articles encompassing theoretical works and hands-on tutorials, as well as many reviews with key biological insight. Volume 1 includes a helpful introductory section of bioinformatician primers followed by detailed chapters detailing genomic data assembly, alignment, and homology inference as well as insights into genome evolution from statistical analyses. Written in the highly successful Methods in Molecular Biology (TM) series format, this work provides the kind of advice on methodology and implementation that is crucial for getting ahead in genomic data analyses. Comprehensive and cutting-edge, Evolutionary Genomics: Statistical and Computational Methods is a treasure chest of state-of the-art methods to study genomic and omics data, certain to inspire both young and experienced readers to join the interdisciplinary field of evolutionary genomics.

Ataxia-telangiectasia (A-T) is a rare and severe genetic disorder affecting children. A-T is a multisystem disease characterized by progressive neurodegeneration, immunodeficiency and cancer predisposition. This detailed volume explores the ever expanding field of research into the ATM (ataxia-telangiectasia, mutated) gene and the role played by ATM kinase in DNA damage signaling and diverse cellular processes. What follows is a handy desktop reference for both seasoned A-T researchers and postgraduate students, as it demonstrates the breadth of recent developments in A-T studies. 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. Both classic and cutting-edge techniques are described, including ATM gene mutation detection, assays for radiosensitivity and radioresistant DNA synthesis, new methods to measure ATM kinase activity by imaging microscopy and high content screening as well as proteomics, phosphoproteomics and bioinformatics approaches to decipher ATM-dependent signalling pathways. Additional methods include generation of patient-specific stem cells and approaches to study ATM functions in the nervous system. Comprehensive and practical, ATM Kinase: Methods and Protocols aims to ignite and attract the interest of colleagues from diverse fields to A-T research in an effort to bring their expertise and fresh ideas to resolve many A-T puzzles still waiting to be pieced together and to alleviate the suffering of A-T children and their families.

Since the discovery of microRNAs, developmental biologists have striven to understand the role of miRNAs in development and disease. MicroRNAs in Development: Methods and Protocols collects contributions from expert researchers in order to provide practical guidelines to this complex study. Divided into three convenient sections, this detailed volume covers various techniques to detect and profile miRNA expression, followed by protocols to manipulate the activity of miRNAs in various organisms, and it concludes with a section that outlines different methods to identify and validate miRNA targets in animals and plants. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, MicroRNAs in Development: Methods and Protocols serves as a practical guide for scientists of all backgrounds and conveys the appropriate sense of fascination associated with this vital field of research.

Genetic Diseases of the Kidney identifies and analyzes genetic abnormalities causing renal diseases in human subjects. Although in a sense the genome contains all the instructions required for the formation of a phenotype, the information is encoded in an extremely complicated fashion. In primary genetic diseases, the genetic instruction specifies a phenotype clearly linked with a discreet lesion confined to the kidney. However, the genetic disturbance may be imbedded in a complicated physiologic ensemble, so that the nexus between the genetic disturbance and the phenotype may be obscured; in consequence, the causal sequence is extremely difficult to unravel. In many instances the renal disease is one component of a complicated systemic hereditary disease, either monogenic or polygenic. Indeed, renal disease may arise as the sum of minor inputs from many different, seemingly unrelated genes, so that the genetic contributions may be difficult to identify. Confounding the problem further are environmental influences, originating either in the chromosomal environment from modifier genes, or in the extra-chromosomal environmental from intrauterine or postnatal influences. These considerations have determined both the organization of the text as well as the detailed description of the genetic disorders and the physiologic derangements that emerge.
* Lays the essential foundation of mammalian genetics principles for medical professionals with little to no background in genetics
* Analyzes specific renal diseases - both monogenic disorders confined to the kidney as well as systemic diseases with renal involvement - and explains their genetic causes.
*World-renowned editors andauthors offer expert frameworks for understanding the links between genes and complex clinical disorders (i.e., lupus, diabetes, HIV, and hypertension)

DNA Tumor Viruses will focus on the DNA viruses in the human population that are associated with cancers. It will cover most of the viruses that are thought to contribute to human malignancy.

This book will represent a comprehensive review of the field of DNA tumor virology. Right now, while there are books out there that cover individual viruses that will be also covered in this book, there is no single book that covers this topic comprehensively.

The main textbook in this market, Fields, which is referred to by both reviewers, covers some of these topics but on a lower level. The only two books that are nearly as comprehensive as this one are Human Tumor Viruses, which was published by the American Society for Microbiology in 1998 and is quite outdated, and Viruses, Cell Transformation, and Cancer, which was published by Elsevier in 2001. Our book will be the only current, comprehensive review of its kind in the market.