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Naturally occurring RNA always contains numerous biochemically altered nucleotides. They are formed by enzymatic modification of the primary transcripts during the complex RNA maturation process designated RNA modification. A large number of enzymes catalyzing the formation of these modified nucleosides or converting one canonical base into another at the posttranscriptional level have been studied for many years, but only recently have systematic and comparative studies begun. The functions of individual enzymes and/or the modified/edited nucleosides in RNA, however, have remained largely ignored. This book provides advance information on RNA modification, including the associated editing machinery, while offering the reader some perspective on the significance of such modifications in fine-tuning the structure and functions of mature RNA molecules and hence the ability to influence the efficiency and accuracy of genetic expression. Outstanding scientists who are actively working on RNA modification/editing processes have provided up-to-date information on these intriguing cellular processes that have been generated over the course of millions of years in all living organisms. Each review has been written and illustrated for a large audience of readers, not only specialists in the field, but also for advanced students or researchers who want to learn more about recent progress in RNA modification and editing.
This volume is a timely and comprehensive description of the many facets of DNA and RNA modification-editing processes and to some extent repair mechanisms. Each chapter offers fundamental principles as well as up to date information on recent advances in the field (up to end 2008). They ended by a shortconclusion and future prospect' section and
This volume provides a comprehensive collection of current methods and protocols to study posttranscriptional base modifications in RNA with special focus on methylation. The protocols in this book discuss state-of-the-art methods for investigating aspects of RNA methylation on different types of RNA. The protocols cover topics such as wet-lab techniques for the detection of methylation, instructions for bioinformatics analyses of transcriptome-scale data, and protocols for the functional examination of RNA modifications and enzymes. 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, RNA Methylation: Methods and Protocols is a valuable resource for biochemists and molecular biologists, from various fields, who wish to investigate different types of RNA methylations.
This book reviews a novel and exciting field of cellular and molecular biology called epitranscriptomics, which focuses on changes in an organism’s cells resulting from the posttranscriptional modification of cellular RNA. RNA-binding proteins (RBPs) play a crucial role in these posttranscriptional modifications and also support several cellular processes necessary for maintaining RNA homeostasis. Exploring the mechanisms underlying RNA modifications and RBP function is an emerging area of biomedical research, taking the study of gene regulation a step beyond epigenetics. This book reveals that the RNA molecule is not just an information-carrying molecule with some secondary structures. Accordingly, how RNA is modified, regulated, packaged, and controlled is an important aspect. Leading experts address questions such as where the over 170 distinct posttranscriptional RNA modifications are located on the genome, what percentage of mRNAs and noncoding RNAs these modifications include, and how an RNA modification impacts a person’s biology. In closing, the book reviews the role of RNA modifications and RBPs in a variety of diseases and their pathogenesis. Addressing some of the most exciting challenges in epitranscriptomics, this book provides a valuable and engaging resource for researchers in academia and industry studying the phenomena of RNA modification.
This volume is comprised of 18 chapters, covering various aspects of DNA modification and RNA modified bases. It also discusses in detail circular RNA, therapeutic oligonucleotides and their different properties. The chemical nature of DNA, RNA, protein and lipids makes these macromolecules easily modifiable, but they are also susceptible to damage from both endogenous and exogenous agents. Alkylation and oxidation show a potential to disrupt the cellular redox equilibrium and cause cellular damage leading to inflammation and even chronic disease. Furthermore, DNA damage can drive mutagenesis and the resulting DNA sequence changes can induce carcinogenesis and cancer progression. Modified nucleosides can occur as a result of oxidative DNA damage and RNA turnover, and are used as markers for various diseases. To function properly some RNA needs to be chemically modified post-transcriptionally. Dysregulation of the RNA-modification pattern or of the levels of the enzymes that catalyze these modifications alters RNA functionality and can result in complex phenotypes, likely due to defects in protein translation. While modifications are best characterized in noncoding ribonucleic acids like tRNA and rRNA, coding mRNAs have also been found to contain modified nucleosides. This book is a valuable resource, not only for graduate students but also researchers in the fields of molecular medicine and molecular biology.
Learn, understand, and implement deep neural networks in a math- and programming-friendly approach using Keras and Python. The book focuses on an end-to-end approach to developing supervised learning algorithms in regression and classification with practical business-centric use-cases implemented in Keras. The overall book comprises three sections with two chapters in each section. The first section prepares you with all the necessary basics to get started in deep learning. Chapter 1 introduces you to the world of deep learning and its difference from machine learning, the choices of frameworks for deep learning, and the Keras ecosystem. You will cover a real-life business problem that can be solved by supervised learning algorithms with deep neural networks. You’ll tackle one use case for regression and another for classification leveraging popular Kaggle datasets. Later, you will see an interesting and challenging part of deep learning: hyperparameter tuning; helping you further improve your models when building robust deep learning applications. Finally, you’ll further hone your skills in deep learning and cover areas of active development and research in deep learning. At the end of Learn Keras for Deep Neural Networks, you will have a thorough understanding of deep learning principles and have practical hands-on experience in developing enterprise-grade deep learning solutions in Keras. What You’ll Learn Master fast-paced practical deep learning concepts with math- and programming-friendly abstractions. Design, develop, train, validate, and deploy deep neural networks using the Keras framework Use best practices for debugging and validating deep learning models Deploy and integrate deep learning as a service into a larger software service or product Extend deep learning principles into other popular frameworks Who This Book Is For Software engineers and data engineers with basic programming skills in any language and who are keen on exploring deep learning for a career move or an enterprise project.
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The second edition of a highly acclaimed handbook and ready reference. Unmatched in its breadth and quality, around 100 specialists from all over the world share their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints. They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins. Throughout, they bear the practising bench scientist in mind, providing quick and reliable access to a plethora of solutions for practical questions of RNA research, ranging from simple to highly complex. This broad scope allows the treatment of specialized methods side by side with basic biochemical techniques, making the book a real treasure trove for every researcher experimenting with RNA.
This Comprehensive, current text explores the manifold ways in which living cells respond to genomic injury and alterations, including both spontaneous and environmentally induced DNA damage. With more than 4,000 complete references to primary research literature and over 380 color figures throughout, this book is an important text for all courses in DNA repair and mutagenesis. It will also serve as a major reference for all molecular biologists working in cancer biology, recombination, transcription and gene regulation, DNA replication, environmental studies, and biological evolution.