Download or read book RNA Detection and Visualization written by Jeffrey E. Gerst and published by Humana Press. This book was released on 2011-04-06 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: With 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.
Download or read book Visualizing RNA Dynamics in the Cell written by and published by Academic Press. This book was released on 2016-05-27 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: Methods in Enzymology: Visualizing RNA Dynamics in the Cell continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods visualizing RNA dynamics in the cell, and includes sections on such topics as identification of RNA cis-regulatory sequences, IRAS, IMAGEtags, MERFISH, plant RNA labeling using MS2, and visualization of 5S dynamics in live cells using photostable corn probe. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods in visualizing RNA dynamics in the cell Contains sections on such topics as identification of RNA cis-regulatory sequences, IRAS, IMAGEtags, MERFISH, plant RNA labeling using MS2 and visualization of 5S dynamics in live cells using photostable corn probe
Download or read book RNA Detection written by Imre Gaspar and published by Humana Press. This book was released on 2017-11-15 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: This 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.
Download or read book RNA Probing Methods written by and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, RNA’s structure and function has been increasingly analyzed through the utilization of experimental methods, such as RNA in situ hybridization (ISH) and electrophoretic mobility shift assays. Oligonucleotide probes are used for the detection and visualization of target RNAs for obtaining greater insight into the mechanism of gene expression and RNA function. RNA Fluorescence In-Situ Hybridization (FISH) and molecular beacons are popular tools used to detect and track endogenous RNAs. An additional tool utilized to study RNA function is the triplex forming oligonucleotide (TFO), which is a short probe that can bind to a purine-rich double stranded region within a target RNA to form a triple helix. In our study, a new probe was designed and evaluated for its efficiency in detecting a model RNA using peptide nucleic acid (PNA) TFOs. The PNA TFO probe was tested to determine the extent to which it formed a triple helix with a model RNA hairpin using two methods: 1) spectrofluorometer assays and 2) gel electrophoresis. Triplex formation was confirmed using the gel electrophoresis assay. Moreover, new theoretical probes were designed using the PinMol and TFOFinder software. Moving forward, these probes will be further tested using the experimental methodologies described in this study to evaluate their efficiency in detecting and visualizing endogenous RNA in live and fixed tissue.
Download or read book Fluorescence based Methods for Visualization of RNA in Living Cells written by Eman Ahmad Ageely and published by . This book was released on 2016 with total page 162 pages. Available in PDF, EPUB and Kindle. Book excerpt: Knowledge about ribonucleic acids (RNAs) and their roles has recently been expanded by extensive studies seeking to uncover novel RNAs using biochemical techniques. These techniques visualize specific RNA in situ to understanding the regulatory mechanisms of gene expression. Lately, a variety of photo labeling techniques has been developed for imaging RNA in vivo to locate and track it with high accuracy. This study focuses on fluorescence-based methods of in vivo RNA visualization. Using fluorescent light has transformed the study of micro-molecular components due to its many advantages. Molecular beacons targeting repeat expansion of RNA can differentiate between normal repeat sizes and repeat expansions in the pathogenic range. With modification and testing, molecular beacons have the potential to serve as probes for sensing repeat structure accessibility and for use in diagnostics assays. Broccoli GFP-mimic RNAs have different instability and metal ion preferences than Baby Spinach, a truncated version of the Spinach aptamer, that are primarily associated with the sequence and structure of predicted quadruplex-flanking stem structures. Unique duplex-to-quadruplex transitions in GFP-mimic RNAs, which likely explains their sensitivity to magnesium due to its stability and fluorescence. RNA Mango is an RNA aptamer that binds thiazole Orange (TO1) dye and its derivative with nanomolar binding affinity, unlike MS2 and Spinach systems. Mango is superior in its detection of bacterial fluorescence compared with Spinach, which requires 200uM of the fluorophore. Inserting a Mango aptamer with TO1-Biotin, a derivative of TO1, genetically into the cell can be used to monitor the expression of RNA in real time by measuring the fluorescence signal that comes from the TO1-Biotin.
Download or read book RNA Detection written by Imre Gaspar and published by Humana Press. This book was released on 2018-08-30 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: This 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.
Download or read book RNA Abundance Analysis written by Hailing Jin and published by Humana Press. This book was released on 2016-05-01 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book examines 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.
Download or read book RNA protein Interactions written by Kiyoshi Nagai and published by Oxford University Press, USA. This book was released on 1994 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
Download or read book Visualization and Analysis of RNA Processing written by Sabine Paula Snaar and published by . This book was released on 2003 with total page 160 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Understanding Diverse RNA Function Using Quantum Dot Based Fluorescence in Situ Hybridization written by Norman Huang and published by . This book was released on 2020 with total page 125 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ribonucleic acids (RNAs) serve as one of the main building blocks of organic life and with the advent of new understanding beyond an intermediary for protein coding, understanding its function becomes imperative. Previous tools study RNA expression from cell populations such as tissue or cell lines, however, an expansive area of research has developed for the individual cells. The recognition of cell heterogeneity in normal and diseased tissues further highlighted the importance of accurate RNA detection in single cells. Single molecule RNA fluorescence in situ hybridization (smRNA-FISH) has revolutionized RNA detection and quantification by visualizing single RNA transcripts. The work in this dissertation improves upon smRNA-FISH by developing quantum dot based fluorescent in situ technologies that uses hybridization of quantum dot-labeled single stranded DNA oligonucleotides to the RNA targets for visualization and quantification. In chapter 2, we demonstrate our proof-of-concept quantum dot single molecule RNA-FISH (qdot-smRNA-FISH) by comparing the sensitivity and specificity of qdot-smRNA-FISH against commercialized smRNA-FISH. In chapter 3, we describe qdot-smRNA-FISH for detection of isoforms (isoFISH), where different from smFISH that requires dozens of hybridization probes per gene, isoFISH requires only two hybridization probes per splicing variant. In chapter 4, we used the co-localization of multi-color quantum dot FISH (CoQ-FISH) to observe for the first time a fusion transcript formation of Eml4-Alk in non-small cell lung cancer biopsy samples from trans-splicing and not chromosomal rearrangement. In chapter 5, we develop cell surface qDot RNA-FISH (Surface-FISH), a method for visualization of RNAs on the cell surface. We identified RNA targets using RNA-seq on membrane coated nanoparticles from EL4 and applied Surface-FISH to observe regions of Malat1 and Neat1. In chapter 6, we developed Surface-PromFISH that uses randomized antisense probes to promiscuously label as many csRNAs as possible and made it compatible with co-staining of cell membrane proteins. We subjected the hybridization targets to RNA sequencing (Surface-FISHseq), which led to 51 putative PBMC csRNAs and we identified a potential function where antisense blocking of FNDC3B and CTSS lowers monocyte attachment.
Download or read book Visualization of Nucleic Acids written by Gerard Morel and published by CRC Press. This book was released on 1995-03-30 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a review of the principle approaches for visualizing DNA and RNA. Using scanning tunneling and atomic force microscopes, the three-dimensional image of the surface of nucleic acids can be seen at atomic-scale resolutions. Spreading methods provide useful details on structural features of isolated molecules, but the major constituent of living matter is water, and the cryomicroscope makes it possible to look at DNA in its aqueous environment. Genes can be detected simultaneously in situ in chromosomes using fluorescent probes, and also at the electron microscopic level. In cells, nucleic acids are localized and quantified by dyes; electron microscopy is used with cytochemical, immunocytological, nuclease, and in situ hybridization methods. The main potential applications for pathological studies are shown with particular aspects such as viral nucleic acids and in situ PCR.
Download or read book RNA Trafficking and Nuclear Structure Dynamics written by Philippe Jeanteur and published by Springer. This book was released on 2007-11-03 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores nuclear structure and trafficking involving or relevant to RNA and RNPs. Topics include advances and current problems in the structural organization of different subnuclear compartments, Cajal bodies and gems, speckles containing splicing factors, and PML bodies characteristic of ProMyelocytic leukemia. The book also describes the dynamic aspects of RNA trafficking and the latest technologies for live cell imaging of mRNA.
Download or read book Visualization of Single RNA Transcripts in Situ written by Andrea M. Femino and published by . This book was released on 2001 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book A Strategy to Label RNA for Visualization written by Chinmoyee Karmakar and published by . This book was released on 2014 with total page 110 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Histochemical and Cytochemical Methods of Visualization written by Jean-Marie Exbrayat and published by CRC Press. This book was released on 2013-06-05 with total page 355 pages. Available in PDF, EPUB and Kindle. Book excerpt: Histochemistry and cytochemistry are important fields for studying the inner workings of cells and tissues of the body. While visualization techniques have been in use for many years, new methods of detection developed recently help researchers and practitioners better understand cell activity. Histochemical and Cytochemical Methods of Visualization describes the essential techniques that can be used for histochemical investigations in both light and transmission electron microscopy. The book begins by discussing techniques in light microscopy. It reviews classical methods of visualization, histochemical and histoenzymatic methods, and methods used to visualize cell proliferation and apoptosis. Next, the book examines the cytochemical methods used in electron microscopy with traditional techniques, as well as more specialized methods. The final section provides an overview of image analysis and describes how image processing methods can be used to extract vital information. A 16-page insert supplies color illustrations to enhance the text. Techniques will continue to adapt to the latest technological innovations, allowing more and more precise quantification of images. These developments are essential to the biological as well as the medical sciences. This manual is a critical resource for novice and experienced researchers, technicians, and students who need to visualize what happens in the cell, the molecules expressed, the main enzymatic activities, and the repercussions of the molecular activities upon the structure of the cells in the body.
Download or read book In Situ Hybridization Methods written by Giselbert Hauptmann and published by Humana. This book was released on 2016-10-05 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains a comprehensive compilation of chromogenic and fluorescent RNA in situ hybridization (ISH) technology in many of its various shades, forms, and applications. The book is organized into a number of parts and chapters focusing on the application of ISH methodologies to different animal species as used in Evolutionary Development (EvoDevo) and Biomedical research, and covering new developments in RNA visualization by fluorescent ISH (FISH). The described (F)ISH protocols employ effective strategies for signal enhancement and target amplification allowing for high signal intensities and drastically improved signal-to-noise ratios. Chromogenic and fluorescent ISH, as specified in the various chapters, are most essential for RNA expression profiling, applied to many fields of research including cellular, developmental, and evolutionary biology, neurobiology and neuropathology. Written for the popular Neuromethods series, chapters include the kind of detail and key implementation advice that ensures successful results in the laboratory. Essential and authoritative, In Situ Hybridization Methods provides detailed protocols for newcomers to ISH, and inspires researchers familiar with the technique to seek and find up-to-date methodology for new and specialized applications.
Download or read book RNA Amplification and Analysis written by Mekbib Astatke and published by Springer Nature. This book was released on with total page 469 pages. Available in PDF, EPUB and Kindle. Book excerpt:
