This detailed volume provides comprehensive practical guidance on transcriptome data analysis for a variety of scientific purposes. Beginning with general protocols, the collection moves on to explore protocols for gene characterization analysis with RNA-seq data as well as protocols on several new applications of transcriptome 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. Authoritative and useful, Transcriptome Data Analysis: Methods and Protocols serves as an ideal guide to the expanding purposes of this field of study.

This book helps transform the awareness of the anticipatory perspective into actionable methods for practitioners of medicine. It provides guidance for those who design new means and methods inspired by epigenetics, in particular to those who advance sustainable alternatives.

This detailed book presents a comprehensive collection of state-of-the-art protocols on muscular dystrophy therapeutics, covering therapeutics using antisense oligonucleotides, gene replacement, genome editing, small molecules, stem cells, and antibodies. Written by leaders in the field, the volume explores techniques that are currently in use and are starting an exciting therapeutic revolution in muscular dystrophy. As a part of 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 and readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Muscular Dystrophy Therapeutics: Methods and Protocols serves as an ideal resource to inspire readers and provide tips, strategies, and advice to develop new therapeutic technologies for this group of diseases.

After volume 33, this book series was replaced by the journal "Evolutionary Biology." Please visit www.springer.com/11692 for further information.

The nature of science is to work on the boundaries between the known and the unknown. These boundaries shift as new methods are developed and as new concepts are elaborated (e.g., the theory of the gene, or more recently, the coalescence framework in population genetics). These tools allow us to address questions that were previously outside the realm of science, and, as a consequence, the boundary between the knowable and unknowable has shifted. A study of limits should reveal and clarify the boundaries and make sharper the set of questions. This book examines and analyzes these new limits as they are applied to evolutionary biology and population genetics. It does this by framing the analysis within four major classes of problems - establishing the fact of evolution; understanding the evolutionary pathways that led to today's biological world; mechanisms of evolutionary change (e.g., models of social behavior, sexual selection, macro evolution); and, finally, prediction.

Recent progress in high-throughput technologies and genome wide transcriptome studies have lead to a significant scientific milestone of discovering non-coding RNAs (ncRNAs) which spans through a major portion of the genome. These RNAs most often act as riboregulators, and actively participate in the regulation of important cellular functions at the transcriptional and/or post-transcriptional levels rather than simply being an intermediated messenger between DNA and proteins. As the appreciation for the importance of ncRNAs continues to emerge, it is also increasingly clear that these play critical roles in gene regulatory processes during development and differentiation. Further, regulatory RNAs are useful biomarkers for diagnosis of diseases. Hence these RNA regulators are essential to the development of therapeutics. This book on "Regulatory RNAs" offers a comprehensive view on our current understanding of these regulatory RNAs viz. siRNA, miRNA, piRNA, snoRNA, long non-coding RNA, small RNA etc. It addresses both the biogenesis and mechanism of action of regulatory RNAs with a primary focus on their annotation, experimental methodologies (microarray, next-gen sequencing etc.) for their discovery, computational tools for their prediction, and above all, applications of these revolutionary regulatory molecules in understanding biological systems and diseases, including therapeutics. This comprehensive volume is intended for readers with research or teaching interests in ncRNA biology and will provide a major information resource on current research in the fast-moving fields of RNA and gene expression regulation. Cutting-edge and concise, "Regulatory RNAs: Basics, Methods and Applications" promises to support vital research in the field of regulatory RNAs, ever-continuing to grow rapidly and gain increasing importance in basic and translational biology.

This book explores mental disorders from a uniquely evolutionary perspective. Although there have been many attempts to mathematically model neural processes and, to some extent, their dysfunction, there is very little literature that models mental function within a sociocultural, socioeconomic, and environmental context. Addressing this gap in the extant literature, this book explores essential aspects of mental disorders, recognizing the ubiquitous role played by the exaptation of crosstalk between cognitive modules at many different scales and levels of organization, the missing heritability of complex diseases, and cultural epigenetics. Further, it introduces readers to valuable control theory tools that permit the exploration of the environmental induction of neurodevelopmental disorders, as well as the study of the synergism between culture, psychopathology and sleep disorders, offering a distinctively unique resource.

Despite the many milestones in cystic fibrosis (CF) research, progress towards curing the disease has been slow, and it is increasingly difficult to grasp and use the already wide and still growing range of diverse methods currently employed to study CF so as to understand it in its multidisciplinary nature. Cystic Fibrosis: Diagnosis and Protocols aims to provide the CF research community and related researchers with a very wide range of high-quality experimental tools, as an easy way to grasp and use classical and novel methods applied to cystic fibrosis. Volume I: Approaches to Study and Correct CFTR Defects focuses on the cystic fibrosis transmembrane conductance regulator (CFTR) and its expression, biogenesis, structure, and function in terms of the defects causing CF. 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 tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, Cystic Fibrosis: Diagnosis and Protocols will provide readers with optimal working tools to address pressing questions in the best technical way, while helping all of us, as a research and clinical community, to move faster hand-in-hand toward unravelling the secrets of this challenging disorder and cure it.

The field of epigenetics has played a major role at the forefront not only of molecular biology, but also of medical genetics and clinical medicine. Few disciplines have experienced growth comparable to that which we have witnessed for epigenetics in the past decade. The goal of "Epigenetics Protocols, Second Edition "is to highlight select techniques that have been mainstays in the field as well as to cover methods that are especially relevant to extant discoveries in epigenetics. This volume focuses on the two broad areas of epigenetics: DNA methylation and chromatin modifications, and also covers the complex topic of computational methods for epigenetic analyses which is essential to a complete understanding of the vast body of information that is being derived with the use of these newly-developed tools. Written in the highly successful "Methods in Molecular Biology " 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, "Epigenetics Protocols, Second Edition" serves as an ideal guide to advanced students, basic scientists and clinical researchers as well as clinicians and biotechnology investigators who wish to continue exploring this exciting and progressive research field."

Germ cells in sexually reproducing metazoa, through the germline lineage, are the route by which genetic material and cytoplasmic constituents are passed from one generation to the next in the continuum of life. Chapters in this book review germ cell development in the model organism Caenorhabditis elegans, discussing the biology, the genetics and the molecular mechanisms for various processes, as well as drawing comparisons with other organisms. Processes discussed include specification of germ cell fate, meiosis, gametogenesis, environmental/ physiological controls, epigenetics and translational control, fertilization and the oocyte-to-embryo transition. This book thus provides a comprehensive picture of the germline lineage and the continuum of life for the worm.

Chemotherapy has made a dramatic difference to improved survival in patients with cancer. However, not all patients respond and some experience serious side effects.

"Pharmacogenetics: Making cancer treatment safer and more effective" is an up to date summary of the exciting new field of how genetic testing can tailor more effective prescription in oncology.

It is targeted at oncologists and professionals involved in the treatment of patients with cancer. It provides a core background in genetics and pharmacological principles before providing chapters from acknowledged experts in the field on genetic tests in specific cancer types, including breast, bowel and lung cancer. Clinical cases are used to illustrate the practical application of this knowledge.

Chapters on ethics, health economics and the industry aspects of pharmacogenetics set out the challenges and opportunities afforded by this new science.

This third edition provides new and updated chapters on design PCR primers for successful DNA amplification. Chapters are divided into seven parts, including primer design strategies for quantitative PCR, genotyping, multiplex PCR, in silico PCR primer design, and primer design to identify plant and animal viruses. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, PCR Primer Design, Third Edition aims to be useful for various fields of molecular biology, including biotechnology, molecular genetics, and recombinant DNA technology.

Research into ancient DNA began more than 25 years ago with the publication of short mitochondrial DNA sequence fragments from the quagga, an extinct relative of the zebra. Ancient DNA research really gained momentum following the invention of PCR, which allowed millions of copies to be made of the few remaining DNA molecules preserved in fossils and museum specimens. In Ancient DNA: Methods and Protocols expert researchers in the field describe many of the protocols that are now commonly used to study ancient DNA. These include instructions for setting up an ancient DNA laboratory, extraction protocols for a wide range of different substrates, details of laboratory techniques including PCR and NGS library preparation, and suggestions for appropriate analytical approaches to make sense of the sequences obtained. 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, Ancient DNA: Methods and Protocols seeks to aid scientists in the further study of ancient DNA and the methodological approaches in ancient research.

This book illustrates the role of randomness and noise in living organisms. Traditionally, the randomness and noise have been used in understanding signal processing in communications. This book is divided into two sections, the first of which introduces readers to the various types and sources of noise and the constructive role of noise in non-linear dynamics. It also analyses the importance of randomness and noise in a variety of science and engineering applications. In turn, the second section discusses in detail the functional role of noise in biological processes for example, in case of brain function at the level of ion channel, synaptic level and even at cognitive level. These are described in various chapters. One of the challenging issue finding the neuronal correlates of various meditative states is to understand how brain controls various types of noise so as to reach a state of synchronized oscillatory state of the brain corresponding to the state of Samadhi. This is described in details in one chapter called Noise, Coherence and meditation. The concept of noise and the role of randomness in living organism raise lot of controversy for last few decades. This is discussed in a separate chapter. Finally, the epistemic and ontic nature of randomness as discussed in physical science are investigated in the context of living organism.

Genetic counselors translate the findings of scientific investigation into meaningful accounts that enable individuals and families to make decisions about their lives. This collection of original papers explores the history, values, and norms of that process, with some focus on the value of nondirectiveness in counseling practice. The contributors; examination of genetic counseling issues serves as a foundation from which to address other ethical, legal, and policy considerations in the expanding universe of clinical genetics.

This volume provides researchers with up-to-date protocols and takes a close look at current research and promising applications. Optogenetics: Methods and Protocols contains a collection of recently developed technical protocols on optogenetic applications in neuroscience, brain mapping, treatment of neurological disorders, and restoration of visual function. Several introductory and discussion chapters offer a wide overview about sources and diversity of optogenetic tools, design strategies, and potential applications in other fields like plant research. 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 thorough, Optogenetic: Methods and Protocols, delivers an interdisciplinary view of optogenetic applications and its potential to develop as a valuable tool for basic research, as well as biomedical and biotechnological applications.

This book focuses on histone mutations, especially those mutations closely related to cancer. Genetic mutations and epigenetic alterations contribute to the development of a variety of cancers: recent genetic studies have identified e.g. H3K27M and H3G34R/V mutation in over 75% of DIPG cases, H3.3K36M mutation in more than 90% of chondroblastoma cases, and H3G34W/L mutation in over 90% of giant cell tumors of bone. Given the high incidence and tumorigenesis effects of histone H3 mutations, they are also referred to as oncohistones. This book highlights the advances made in the area over the past 10 years, and offers a state-of-the-art summary of epigenetic alternation, gene expression, protein structure, drug discovery, immunotherapy, and mouse modeling of histone H3 mutations in various tumors. Chiefly intended to provide researchers and graduate students with an overall picture of these mutations, it will also be of interest to researchers in basic oncology, clinical oncology, and epigenetics, as well as academics and clinical oncology practitioners.

This fourth, updated edition contains the latest developments in preanalytical knowledge. An international team of authors summarizes the information on biological influences, analytical interferences and on the variables affecting the collection, transport and storage, as well as preparation of samples. In so doing, they cover age, gender, race, pregnancy, diet, exercise and altitude, plus the effects of stimulants and drugs. National and international standards are described for sampling procedures, transport, sample identification and all safety aspects, while quality assurance procedures are shown for total laboratory management.

In addition, this practical book is rounded off by a glossary explaining all terms being used.

This book is a must-have for everyone involved in patient care and using or performing laboratory tests.

Arising from firm foundations laid by mathematical population genetics, clinical genetics, and statistical epidemiology, genetic epidemiology attempts to identify the many components of risk

attributable to genes, environments, and interactions, and the course of its research can follow many diverse paths. In "Genetic Epidemiology," the success of genome-wide association studies in their identification of hundreds of disease susceptibility loci has inspired renowned experts to contribute thorough methodologies, which aim to bring together bioinformaticians, geneticists, clinicians, statisticians, and epidemiologists in the study of this vital field. The volume opens with chapters covering the basics; however, it quickly moves on to coverage of more specialist topics such as twin studies, Mendelian randomization, genetic association studies, more advanced areas, as well as case studies. As a part of the highly successful "Methods in Molecular Biology " series, this work provides the detailed description of the application and analysis of the most commonly employed methods that are necessary for a firm grounding in the field.

Authoritative and cutting-edge, "Genetic Epidemiology" aims to provide a basic framework for crucial interdisciplinary communication and understanding suited to newcomers to the field as well as experienced researchers and graduate level students."

Pocket Guide to Gene Level Diagnostics in Clinical Practice is an abbreviated, pocket-size, quick-reference guide that provides a point-by-point synopsis of the vast wealth of information contained in CRC Handbook of Gene Level Diagnostics in Clinical Practice. All sections and subsections in the Pocket Guide are cross-referenced to corresponding pages in the Handbook. The book works well on its own as a quick reference, but also can be used in conjunction with the larger Handbook for detailed coverage and references to specific information. Pocket Guide to Gene Level Diagnostics in Clinical Practice also includes extensive supplements featuring material not included in the Handbook. These are intended to provide an up-dated, practical source of information useful to anyone involved in molecular diagnostic research and/or service. Supplements are cross-referenced to the main text of the Pocket Guide, that complement and enhance the material covered. Pocket Guide to Gene Level Diagnostics in Clinical Practice will be a handy reference for professionals and students in pathology, biotechnology, biology, and medicine.

This book presents the latest knowledge and the most recent research results on glycobiology of innate immunology. Innate immunity is the crucial part of the immunological defense system that exerts their distinct functions through binding to certain functional glycoproteins. They play a role in various human diseases and also function against microbial invaders and self-associated molecular patterns. Co-regulated expression of glycan-binding is associated with many biological components such as cellular oncotransformation, phenotype change, neuronal or embryonic development, regulation of cell division, cell-cell interaction, cell attachment, adhesion, and motility, and intracellular signaling via protein-carbohydrate or carbohydrate-carbohydrate interactions. This book opens by providing the key background on glycans in innate immunity and its mechanisms behind the Dendritic cell interactions during infection and inflammation are examined in depth, and the concluding chapter is devoted to signaling tumor immunotherapy. Up-to-date information is then presented on all aspects of glycan structure-recognizing signaling. The book should assist in the further development of new strategies against emerging infectious agents and intractable diseases.

With very few exceptions, eukaryotic cells possess two interdependent genomes, chromosomal and extra-chromosomal. Over the past several decades, cancer - search has focused primarily on deciphering the intricate alterations in the chro- somal genome, with until recently, very little attention to its cytoplasmic counterpart. In spite of the enormous complexity of the nuclear genome, which we now fully appreciate after completion of the human genome project, the efforts of cancer researchers are commendable in terms of the tremendous gains made in unraveling the numerous genetic changes in cancer. These changes include d- coveries of tumor suppressor genes, oncogenes, and caretaker genes that are often mutated in cancer. Recent studies of genomic pro?les are uncovering even more altered and mutated genes in cancer. Besides these ?ndings, several therapeutic targets for chemotherapy are currently made from studies of altered nuclear genetic pathways. Inspite of all these positive efforts, the war on cancer, declared in 1971 by Richard Nixon, is far from being worn. Indeed, the failure of chemotherapy is obvious to clinicians, oncologists, and their patients alike. Moreover, the global incidence and prevalence of cancer continue to rise. What are we missing? Which direction should we be taking? Of course, modern integrated nuclear genomics, proteomics, and metabolomics should provide important clues to carcinogenesis, but the contribution of cytoplasmic genetic alterations to carcinogenesis cannot be neglected.

This second edition provides a broad spectrum of methods used in long non-coding RNAs (lncRNA) research, ranging from computational annotation of lncRNA genes to molecular and cellular analyses of the function of individual lncRNA. Chapters guide readers through studies used to circular RNAs, RNA splicing, and findings on lncRNA in human diseases. 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, Long Non-Coding RNAs: Methods and Protocols,Second Edition aims to ensure successful results in the further study of this vital field.

This volume contains cutting-edge techniques to study the function of enhancers and promoters in depth. Chapters are divided into six sections and describe enhancer-promoter transcripts, nucleosome occupancy, DNA accessibility, chromatin interactions, protein-DNA interactions, functional analyses, and DNA methylation assays. Written in the Methods in Molecular Biology series format, chapters include comprehensive introductions, lists of the necessary materials and reagents, step-by-step laboratory protocols, and useful suggestions for troubleshooting. Authoritative and cutting-edge, Enhancers and Promoters: Methods and Protocols is a useful guide for future experiments. Chapters 4 and 11 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com

Next Generation Sequencing (NGS) is the latest high throughput technology to revolutionize genomic research. NGS generates massive genomic datasets that play a key role in the big data phenomenon that surrounds us today. To extract signals from high-dimensional NGS data and make valid statistical inferences and predictions, novel data analytic and statistical techniques are needed. This book contains 20 chapters written by prominent statisticians working with NGS data. The topics range from basic preprocessing and analysis with NGS data to more complex genomic applications such as copy number variation and isoform expression detection. Research statisticians who want to learn about this growing and exciting area will find this book useful. In addition, many chapters from this book could be included in graduate-level classes in statistical bioinformatics for training future biostatisticians who will be expected to deal with genomic data in basic biomedical research, genomic clinical trials and personalized medicine.

About the editors:

Somnath Datta is Professor and Vice Chair of Bioinformatics and Biostatistics at the University of Louisville. He is Fellow of the American Statistical Association, Fellow of the Institute of Mathematical Statistics and Elected Member of the International Statistical Institute. He has contributed to numerous research areas in Statistics, Biostatistics and Bioinformatics.

Dan Nettleton is Professor and Laurence H. Baker Endowed Chair of Biological Statistics in the Department of Statistics at Iowa State University. He is Fellow of the American Statistical Association and has published research on a variety of topics in statistics, biology and bioinformatics."

The Mutator Transposable Element Family of Maize.- Protein Phosphorylation and the Regulation of Cellular Processes by the Homologous Two-Component Systems of Bacteria.- The Peculiar Nature of Codon Usage in Primates.- The Role of Nodulation Genes in Bacterium-Plant Communication.- Regulation of Gene Expression by Epidermal Growth Factor.- Machinery for Protein Import into Chloroplasts and Mitochondria.- High-Level Expression of Foreign Genes in Mammalian Cells.- Aromatic Hydrocarbon Degradation: A Molecular Approach.- Employment of Fibroblasts for Gene Transfer Applications for Grafting into the Central Nervous System.- The Molecular Biology of Amino Acid Biosynthesis in Plants.- Genetic Manipulation of Bacillus Thuringiensis Insectidal Crystal Protein Genes in Bacteria.- Progress Towards Gene Targeting in Plants.- Molecular Biology of Mating-Type Determination in Schizophyllum Commune.- Functions of Intracellular Protein Degradation in Yeast.- Transgenic Fish for Aquaculture.