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RISINGTIDEFALLINGSTAR: In Search of the Soul of the Sea
by Philip Hoare“Every day is an anxiety in my ways of getting to the water. . . . I’ve become so attuned to it, so scared of it, so in love with it that sometimes I can only think by the sea. It is the only place I feel at home.” Many of us visit the sea. Admire it. Even profess to love it. But very few of us live it. Philip Hoare does. He swims in the sea every day, either off the coast of his native Southampton or his adopted Cape Cod. He watches its daily and seasonal changes. He collects and communes with the wrack—both dead and never living—that it throws up on the shingle. He thinks with, at, through the sea. All of which should prepare readers: RISINGTIDEFALLINGSTAR is no ordinary book. It mounts no straight-ahead argument. It hews to no single genre. Instead, like the sea itself, it moves, flows, absorbs, transforms. In its pages we find passages of beautiful nature and travel writing, lyrical memoir, seams of American and English history and much more. We find Thoreau and Melville, Bowie and Byron, John Waters and Virginia Woolf, all linked through a certain refusal to be contained, to be strictly defined—an openness to discovery and change. Running throughout is an air of elegy, a reminder that the sea is an ending, a repository of lost ships, lost people, lost ways of being. It is where we came from; for Hoare, it is where he is going. “Every swim is a little death,” Hoare writes, “but it is also a reminder that you are alive.” Few books have ever made that knife’s edge so palpable. Read RISINGTIDEFALLINGSTAR. Let it settle into the seabed of your soul. You’ll never forget it.
RNA 3D Structure Analysis and Prediction
by Eric Westhof Neocles LeontisWith the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.
RNA Abundance Analysis: Methods and Protocols (Methods in Molecular Biology #2170)
by Hailing Jin Isgouhi KaloshianThis updated book covers a wide range of techniques on RNA extraction, detection, quantification, visualization, and genome-wide profiling, from conventional methods to state-of-the-art high throughput approaches. It includes detailed techniques to examine mRNAs, small non-coding RNAs, protein-associated small RNAs, organelle RNAs, endosymbiont RNAs, and alternatively spliced RNA variants from various organisms. RNA editing and the computational data processing for genome-wide datasets is also discussed. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Abundance Analysis: Methods and Protocols, Second Edition provides a comprehensive set of techniques and methods on isolating and analyzing mRNAs, small RNAs, and other RNA variants, in order to assist researchers in their gene expression studies.
RNA Activation
by Long-Cheng LiThis book offers an essential guide to RNA activation (RNAa), an emerging and fascinating new field. RNAa is a small RNA-guided and Argonaute-dependent gene regulation phenomenon in which promoter-targeted short double-stranded RNAs (dsRNAs) induce target gene expression at the transcriptional level. It occurs primarily in the nucleus and can be mediated by artificially designed short duplex RNAs that target regulatory sequences (e.g., promoters, genes’ 3’ termini and enhancers) and naturally occurring small RNAs (e.g., miRNAs and C. elegans 22G-RNAs). With contributions from internationally respected RNA experts, this book provides comprehensive coverage of different RNAa mechanisms and a timely update on recent advances in RNAa research, with a focus on developing RNAa-based therapeutics. Special chapters are also devoted to the topics of gene activation induced by antisense oligonucleotides and the CRISPR system. As the first book to cover RNAa, it will be of interest to a wide audience, from scientists in academia and the pharmaceutical industry to clinicians who wish to further explore the biology of RNAa and related phenomena, so as to harness their full potential for use in biotechnology and drug development.
RNA Amplification and Analysis: Methods and Protocols (Methods in Molecular Biology #2822)
by Mekbib AstatkeThis volume provides methods to analyze RNA and gain insight to a number of critical cellular functions. Chapters detail RNA isolation and enrichment, RNA amplification and detection, RNA sequencing, analysis of RNA modification, RNA delivery approaches, and analysis of RNA binding and catalytic activity. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA Amplifications and Analysis: Methods and Protocols aims to present researchers with cutting-edge technologies with detailed explanations of critical steps, while providing a clear understanding of the overall protocol.
RNA Binding Proteins
by Zdravko LorkovicGene expression in eukaryotes is regulated at different levels, which need to be coordinated to implement the information in the genome. Now it is clear that post-transcriptional regulation of gene expression such as pre-mRNA splicing, mRNA transport, editing, turnover and translation are as important as the control of transcription. In all aspects
RNA Bioinformatics
by Ernesto PicardiThis volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls. Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA.
RNA Bioinformatics (Methods in Molecular Biology #2284)
by Ernesto PicardiThis detailed book aims to provide an overview of novel bioinformatics resources for exploring diverse aspects of RNA biology. This edition focuses on methods dealing with non-coding RNA (miRNAs, circRNAs or lncRNAs), RNA modifications (m6A or RNA editing), single cell RNA-seq and statistical models to handle count data from RNA-seq experiments. The book also includes chapters based on the classical RNA bioinformatics methods, such as those for deciphering secondary and tertiary RNA structures; however, they are revised to take into account deep sequencing data. Finally, chapters describing methods to analyze RNA sequencing data from emerging third generation sequencing technologies that could provide interesting insights into the transcriptional process and its regulation are also included. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of expert implementation advice that encourages quality results. Comprehensive and up-to-date, RNA Bioinformatics, Second Edition serves as an ideal guide for researchers digging ever-deeper into the depths of the study of RNAs.The chapter 'RNA-Seq Data Analysis in Galaxy' is open access under a CC BY 4.0 license.
RNA Chaperones: Methods and Protocols (Methods in Molecular Biology #2106)
by Tilman HeiseThis book provides a wide spectrum of methods to study RNA chaperones in vitro, at the single molecule level, and protocols useful for cell-based assays. Beginning with a section on a number of bacterial proteins for study, the volume also explores proteins from eukaryotic cells and how to delve into the complex interactions between RNA chaperones and the folding and unfolding of proteins. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Chaperones: Methods and Protocols serves as an ideal guide for scientists and students interested in RNA biology and RNA chaperones.Chapter 3 is available Open Access under a Creative Commons Attribution 4.0 International License via link.springer.com.
RNA Damage and Repair
by Ioly Kotta-LoizouRibonucleic acid (RNA) is a macromolecule that plays a central role in cell physiology: RNA molecules act as intermediates between the deoxyribonucleic acid (DNA), where genetic information is stored, and proteins, which perform the necessary functions within the cell. Traditionally, the structural and functional properties of RNA are closely linked to gene expression. However, RNA-based enzymes, called ribozymes, are also involved in catalysis and small RNAs regulate key cellular processes, such as cell growth, division, differentiation, aging and death. RNA is a sensitive macromolecule that can be easily damaged by environmental conditions (ultraviolet radiation, oxidative stress) and biological factors (ribonucleases, ribotoxins, CRISPR-Cas systems). Therefore, cells have developed mechanisms to protect and/or repair RNA molecules. This book presents an overview of the biology of RNA damage, protection and repair in prokaryotes and eukaryotes. Individual chapters cover the expression regulation, enzymology and physiological role of such systems, and link them to important human diseases such as cancer and degenerative diseases.
RNA Delivery Function for Anticancer Therapeutics (Nanotechnology for Drugs, Vaccines and Smart Delivery Systems)
by Loutfy H. MadkourThis book presents an overview of the current status of translating the RNAi cancer therapeutics in the clinic, a brief description of the biological barriers in drug delivery, and the roles of imaging in aspects of administration route, systemic circulation, and cellular barriers for the clinical translation of RNAi cancer therapeutics, and with partial content for discussing the safety concerns. It then focuses on imaging-guided delivery of RNAi therapeutics in preclinical development, including the basic principles of different imaging modalities, and their advantages and limitations for biological imaging. With growing number of RNAi therapeutics entering the clinic, various imaging methods will play an important role in facilitating the translation of RNAi cancer therapeutics from bench to bedside. RNAi technique has become a powerful tool for basic research to selectively knock down gene expression in vitro and in vivo. Our scientific and industrial communities have started to develop RNAi therapeutics as the next class of drugs for treating a variety of genetic disorders, such as cancer and other diseases that are particularly hard to address with current treatment strategies. Key Features Provides insight into the current advances and hurdles of RNAi therapeutics. Accelerates RNAi, miRNAs, and siRNA drug development for cancer therapy from bench to bedside. Addresses various modifications and novel delivery strategies for miRNAs, piRNAs and siRNA delivery in anticancer therapeutics. Explores the need for the interaction of hematologists,cell biologists, immunologists, and material scientists in the development of novel cancer therapies. Describes the current status of clinical trials related to miRNA and siRNA-based cancer therapy Presents remaining issues that need to be overcome to establish successful therapies.
RNA Design: Methods and Protocols (Methods in Molecular Biology #2847)
by Alexander Churkin Danny BarashThis volume provides comprehensive methods on RNA design. Chapters details traditional RNA design in secondary structure, RNA design in tertiary structure, and RNA design applications and assessments. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA Design: Methods and Protocols aims to ensure successful results in the further study of this vital field.
RNA Detection and Visualization
by Jeffrey E. GerstWith its complex and extensively regulated metabolism, the study of the RNA lifecycle demands tools that allow for the localization of RNAs to be observed either in an in situ setting or, preferably, under in vivo conditions. In RNA Detection and Visualization: Methods and Protocols, the best and brightest investigators provide an up-to-date and in-depth description of basic methods and protocols used for detecting and visualizing mRNAs in both fixed and live cells, from bacteria to mammals. For novices and experts alike, this mix of classic in situ hybridization and advanced live imaging techniques, cell fractionation and affinity purification procedures, and bioinformatics tools gives researchers the most complete and extensive array of research aids possible. As a volume written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and expert tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA Detection and Visualization: Methods and Protocols offers well-honed techniques in order to inspire researchers around the world to further our knowledge of the vital biological significance of RNA.
RNA Detection: Methods And Protocols (Methods In Molecular Biology #1649)
by Imre GasparThis volume introduces different concepts and methods of detecting RNA in biological material in a variety of model systems. The chapters in this book discuss methods that will answer numerous biological questions that arise in the study of RNAs. Some of the topics covered in this book are single mRNA molecule detection in embryos and neurons; detection of mRNA and associated molecules by ISH-IEM on frozen sections; optimizing molecular beacons for intracellular analysis of RNA; imaging translation dynamics of single mRNA molecules in live cells; preparation of high-throughput sequencing libraries; and capturing RNA binding proteins in embryos and in cell-culture. 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 comprehensive, RNA Detection: Methods and Protocols is a valuable resource for novel and experiences scientist in the expanding field of RNAs.
RNA Folding
by Christina WaldsichFocusing on in vitro and intracellular RNA structure formation, RNA Folding: Methods and Protocols provides a comprehensive collection of experimental protocols which are suitable to dissect RNA folding pathways and to characterize the structure of RNA folding intermediates at nucleotide or even atomic resolution. The presented techniques include powerful tools with a long tradition in RNA research as well as more advanced, novel methods, thus the methods span multiple disciplines, including molecular biology, biochemistry, biophysics, and computational biology. 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. Practical and authoritative, RNA Folding: Methods and Protocols serves as a vital reference for researchers attempting to gain insights into the secrets of this astounding macromolecule.
RNA Folding: Methods and Protocols (Methods in Molecular Biology #2726)
by Ronny LorenzTo understand and predict the behavior and function of RNAs, sophisticated tools are required to simulate and analyze their potential for forming structures. This volume discusses the various levels of prediction and algorithmic approaches to RNA folding. The chapters in this book cover topics such as energy parameters of the nearest-neighbor (NN) energy model; classified dynamic programming to address exponential growth of candidate structures that an RNA molecule may fold into; sequence evolution and conserved structures among multiple RNA sequences; the latest framework capable of handling both positive and negative RNA sequence design objectives; and kinetic folding approaches that look at the dynamic nature of RNA folding. 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 comprehensive, RNA Folding: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this important and developing field.
RNA Genetics: Volume I: RNA-Directed Virus Replication
by Esteban DomingoFirst Published in 2018. Routledge is an imprint of Taylor & Francis, an Informa company.
RNA Genetics: Volume II: Retroviruses, Viroids, and RNA Recombination
by Esteban DomingoThis book describes the basic features of virus replication, and points out how these features lead into the diverse biologies and genetics of the various viruses.
RNA Genetics: Volume III: Variability of RNA Genomes
by Esteban DomingoThis book reviews the early evidence of genetic variability of rhabdoviruses. It describes data on the variability in the genomes of closely related virus strains and the variability that can be observed within a given virus strain.
RNA Imaging
by Zdravka MedarovaThis detailed volume will focus on the phenomenon of RNA interference by providing comprehensive coverage of various techniques for in vivo micro/siRNA imaging including the design and synthesis of specific imaging agents and tools, the development of imaging methodologies, and their interpretation. An essential element in the development and optimization of these therapies is the ability to measure the bioavailability and functionality of the RNA/oligonucleotide molecule after administration into the body. Noninvasive imaging provides the necessary set of tools to accomplish this in authentic physiologic environments and across time. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Imaging: Methods and Protocols serves physicians, scientists, and graduate students who are either new to the field of RNA-based imaging and its associated therapeutic applications or who wish to be apprised of recent advances in the state of the art.
RNA Interference
by Mouldy SioudRNA Interference: Challenges and Therapeutic Opportunities provides readers with recent advances in siRNA design, delivery, targeting and methods to minimize siRNA's unwanted effects. Preclinical and clinical use of synthetic siRNAs, the roles of miRNAs in cancer and the promise of extracellular miRNAs for diagnosis are also covered in this meticulous collection, along with novel methods for identifying endogenous siRNAs and the annotation of small RNA transcriptomes. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and key implementation advice that ensures successful results in the laboratory. Comprehensive and cutting-edge, RNA Interference: Challenges and Therapeutic Opportunities will aid researchers, clinicians, teachers and biotechnologists interested in the power of RNA-based therapies.
RNA Interference (Life Science Research Fundamentals)
by WileyThe 2006 Nobel Prize in Physiology or Medicine was awarded to Andrew Z. Fire and Craig C. Mello for their discovery of RNA interference (RNAi). RNAi is a biological process in which RNA molecules can silence (inhibit) or up- or down-regulate gene expression, typically by causing the destruction of specific messenger RNA (mRNA) molecules. This collection of articles begins with an introduction to RNAi, and proceeds to describe uses of this technology in various approaches to disease treatment, including gene therapy. Several laboratory protocols for silencing genes via RNAi are also provided, as are protocols for down-regulating and then rescuing those down-regulated genes, which demonstrates specificity of the approach. This e-book — a curated collection from eLS, WIREs, and Current Protocols — offers a fantastic introduction to the field of RNA interference for students or interdisciplinary collaborators.
RNA Interference and CRISPR Technologies: Technical Advances and New Therapeutic Opportunities (Methods in Molecular Biology #2115)
by Mouldy SioudThis volume explores the uses of RNAi and CRISPR interferences as a general method for inhibiting gene expression, with focus on their biological functions, design, chemical modifications, delivery, and preclinical/clinical applications. In addition to relevant backgrounds, the chapters in this book discuss simple and accurate protocols dealing with the latest advances in RNAi and CRISPR applications and look at how these methods differ from one another. 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.Comprehensive and cutting-edge, RNA Interference and CRISPR Technologies: Technical Advances and New Therapeutic Opportunities is a valuable resource for any scientist, teachers, graduate student, postdoc, and clinician interested in this field. This book also benefits anyone in research and development in biotech and pharmaceutical companies who want to understand more about these technologies, and their applications in biology and medicine.
RNA Interference, Editing, and Modification
by Jonatha M. GottA comprehensive collection of cutting-edge methods for elucidating the function of new genes and altering gene expression. These readily reproducible techniques can be used either in transient and stable gene splicing applied to worms, flies, trypanosomes, mammals, and plants, or in studying RNA editing mechanisms in a wide range of organisms, including systems that involve the conversion of one base to another and insertion/deletion editing. Topics of interest include stable and transient RNA interference, gene silencing, RNA editing, bioinformatics, small noncoding RNAs, and RNomics. Special attention is given to methods for the identification and characterization of small RNAs involved in RNA interference or modification.
RNA Isolation and Characterization Protocols
by Ralph Rapley David L. ManningInnovative biological investigators offer a powerful and highly useful collection of up-to-date methods for the isolation of RNA from a variety of sources, including bacterial, plant, and mammalian cells. These fine-tuned protocols take both the experienced and inexperienced investigator through the nuances of RNA manipulation, from extraction to in vitro translation. The book also includes protocols for the analysis and characterization of isolated RNA species and extensive troubleshooting hints and tips to ensure easy reproducibility. RNA Isolation and Characterization Protocols is the single best collection of easily reproducible, step-by-step RNA techniques now available for today's bench scientists.