Download or read book siRNA and miRNA Gene Silencing written by Mouldy Sioud and published by Humana Press. This book was released on 2008-11-26 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA interference has become a key method in the suppression of gene expression and the development of therapeutic agents, yet there is still the problem of delivery, stability, and the danger of off-target effects such as the silencing of unwanted genes and activation of innate immunity. In siRNA and miRNA Gene Silencing: From Bench to Bedside, expert researchers explore the most recent advances in siRNA design, expression, delivery, in vivo imaging, and methods to minimize siRNA’s unwanted effects and promote successful use in patients. As part of the highly successful Methods in Molecular BiologyTM series, the chapters focus on their respective subjects with easy-to-use, up-to-date information, including several step-by-step laboratory protocols on topics such as new delivery formulations and strategies with promising applications in vitro and in vivo, validated therapeutic target genes, and components of miRNA function, biogenesis, and interference with virus infection. Comprehensive and cutting-edge, siRNA and miRNA Gene Silencing: From Bench to Bedside offers an excellent collection of chapters to aid all those with an interest in RNAi, gene regulation, and new therapies.
Download or read book RNAi Technology written by R. K. Gaur and published by CRC Press. This book was released on 2016-04-19 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNAi technology is used for large-scale screens that systematically shut down each gene in the cell, which can help identify the components necessary for a particular cellular process or an event such as cell division. Exploitation of the pathway is also a promising tool in biotechnology and medicine. Introducing new technology in the study of RNA
Download or read book Introduction to Epigenetics written by Renato Paro and published by Springer Nature. This book was released on 2021-03-23 with total page 215 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access textbook leads the reader from basic concepts of chromatin structure and function and RNA mechanisms to the understanding of epigenetics, imprinting, regeneration and reprogramming. The textbook treats epigenetic phenomena in animals, as well as plants. Written by four internationally known experts and senior lecturers in this field, it provides a valuable tool for Master- and PhD- students who need to comprehend the principles of epigenetics, or wish to gain a deeper knowledge in this field. After reading this book, the student will: Have an understanding of the basic toolbox of epigenetic regulation Know how genetic and epigenetic information layers are interconnected Be able to explain complex epigenetic phenomena by understanding the structures and principles of the underlying molecular mechanisms Understand how misregulated epigenetic mechanisms can lead to disease
Download or read book Plant MicroRNAs written by Stefan de Folter and published by Humana Press. This book was released on 2019-01-31 with total page 363 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed volume provides a collection of protocols for the study of miRNA functions in plants. Beginning with coverage of miRNA function, biogenesis, activity, and evolution in plants, the book continues by guiding readers through methods on the identification and detection of plant miRNAs, bioinformatic analyses, and strategies for functional analyses of miRNAs. 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, Plant MicroRNAs: Method and Protocols aims to ensure successful results in the further study of this vital area of plant science.
Download or read book RNA Silencing written by Gordon Carmichael and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 343 pages. Available in PDF, EPUB and Kindle. Book excerpt: A collection of readily reproducible methods for the design, preparation, and use of RNAs for silencing gene expression in cells and organisms. The techniques range widely and include methods addressing the biochemical aspects of the silencing machinery, RNA silencing in non-mammalian organisms, and the in vivo delivery of siRNAs and silencing vectors. There are also techniques for designing, preparing, and using RNAs to silence gene expression, for fine-tuning regulation by targeting specific isoforms of a given gene, and for the study and use of microRNAs. The protocols follow the successful Methods in Molecular BiologyTM series format, each offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.
Download or read book Plant Small RNA written by Praveen Guleria and published by Academic Press. This book was released on 2020-02-19 with total page 638 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant Small RNA: Biogenesis, Regulation and Application describes the biosynthesis of small RNA in plant systems. With an emphasis on the various molecular mechanisms affected by small RNA and their applications in supporting plant growth and survival, this books presents the basics and most recent advancements in small RNA mediated plant genomics, metabolomics, proteomics and physiology. In addition, it emphasizes the various molecular mechanisms affected by small RNA and their applications in supporting plant growth and survival. Final sections cover the most recent advancements in small RNA mediated plant genomics, metabolomics, proteomics and physiology. - Presents foundational information about small RNA biology and regulation in plants - Includes small RNA pathway advances - Describes the application and scope of small RNA technology for agricultural stability
Download or read book MicroRNA Interference Technologies written by Zhiguo Wang and published by Springer Science & Business Media. This book was released on 2009-06-11 with total page 198 pages. Available in PDF, EPUB and Kindle. Book excerpt: MicroRNAs (miRNAs), endogenous noncoding regulatory mRNAs of around 22-nucleotides long, have rapidly emerged as one of the key governors of the gene expression regulatory program in cells of varying species, with ever-increasing implications in the control of the fundamental biological processes and in the pathogenesis of adult humans. The exciting findings in this field have inspired us with a premise and a promise that miRNAs will ultimately be taken to the heart for therapy of human disease. While miRNAs have been considered potential therapeutic targets for disease treatment, it remains obscured what strategies we can use to achieve the goal. In the past years, we have witnessed a rapid evolving of many creative, innovative, inventive strategies and methodologies pertinent to miRNA research and applications. These technologies have convincingly demonstrated their efficacy and reliability in producing gain-of-function or loss-of-function of miRNAs through targeting miRNA expression/biogenesis/function, providing new tools for elucidating miRNA functions and opening up a new avenue for the development of new agents targeting miRNAs for therapeutic aims. The present book provides comprehensive descriptions of these technologies and their applications to miRNA research and to new drug design for miRNA-related diseases. It starts with an overview of up-to-date knowledge of miRNA biology and the potential of miRNAs as therapeutic targets for human disease, followed by an introduction of the new concept of miRNA interference (miRNAi) and the perspectives of miRNAi technologies in general terms. In the following, each chapter introduces one of the miRNAi technologies with detailed descriptions of state-of-the-art design, procedures, principles and applications to basic research, R and D and clinical therapy.
Download or read book Current Perspectives in microRNAs miRNA written by Shao-Yao Ying and published by Springer Science & Business Media. This book was released on 2008-09-12 with total page 461 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nearly 97% of the human genome is the non-coding DNA, which varies from one species to another, and changes in these sequences are frequently noticed to manifest clinical and circumstantial malfunction. Numerous non-protein-coding genes are recently found to encode microRNAs, which are responsible for RNA-mediated gene silencing through RNA interference (RNAi)-like pathways. MicroRNAs (miRNAs), small single-stranded 17–25 nucleotide RNAs capable of interfering with intracellular messenger RNAs (mRNAs) that contain either complete or partial complementarity, are useful for the design of new therapies against cancer polymorphism and viral mutation. Currently over 1000 native miRNA species found in vertebrates and many more new miRNA homologs continue to be identified; however, most of their functions remain to be determined. In this book, many new perspectives of the miRNA research are reviewed and discussed, including their roles in stem cell maintenance, embryonic development, tissue differentiation, adult physiology, disease pathology, cancer research, viral infection, genetic engineering in plants, and utility in cosmetic applications. These new findings may not only provide significant insight into the various mechanisms of miRNAs but also offer a great opportunity in developing new therapeutic interventions.
Download or read book Arabidopsis written by Detlef Weigel and published by CSHL Press. This book was released on 2002 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: The thale cress Arabidopsis thaliana is increasingly popular among plant scientists: it is small, easy to grow, and makes flowers, and the sequence of its small and simple genome was recently completed. This is the most complete and authoritative laboratory manual to be published on this model organism and the first to deal with genomic and proteomic approaches to its biology.
Download or read book Nanoparticle mediated SiRNA miRNA Delivery to Mesenchymal Stem Cells written by Dominic W.. Malcolm and published by . This book was released on 2017 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Small interfering RNA (siRNA) and microRNA (miRNA) are short double stranded RNA molecules that mediate posttranscriptional gene silencing via RNA interference by binding to or degrading complimentary target mRNA in the cytosol to inhibit translation. Though > 30 siRNA and miRNA candidates are in clinical trials for a variety of indications, none have yet to receive FDA-approval. Successful delivery is the critical barrier to therapeutic translation, and necessitates the need for multifunctional drug delivery systems (DDS). Barriers to delivery include nuclease-mediated degradation and phospholipid membrane impermeability. Furthermore, any DDS used must be cytocompatible and avoid off-target effects. The study herein provides a comprehensive characterization of a pH-responsive diblock copolymer nanoparticle (NP) siRNA DDS and its effects on mesenchymal stem cells (MSCs) for applications in regenerative medicine. Reversible addition-fragmentation chain transfer (RAFT) polymerization was used to synthesize a library of diblock copolymers to determine how polymer properties affect siRNA delivery. Results show this NP-siRNA delivery is effective in multiple therapeutic cell types in vitro, and that increasing NP core hydrophobicity provides greater cytocompatibility and gene silencing. This is achieved by increased pHresponsive membrane lytic activity allowing for better endosomal escape. Additionally, in vitro treatment conditions were identified that resulted in potent gene silencing with no acute cytotoxicity. However, NP-siRNA treatment resulted in a sustained reduction in hMSC metabolic activity, and RNAseq with enrichment analysis shows upregulation of anti-apoptotic gene expression and immune signaling pathways associated with siRNA immune stimulation. Colloidal stability is critical for effective NP DDS, and can be significantly altered in the presence of biological proteins. Therefore, an extensive characterization of this NP-siRNA DDS in the presence of serum reveals NP-siRNA aggregation, which significantly diminishes siRNA delivery in vitro. When delivered locally in vivo, cells take up NP-siRNA complexes in a non-aggregated state, emphasizing the importance of local delivery. Taken together this in-depth characterization of NP-mediated siRNA delivery establishes a solid foundation for the design of next generation NP-siRNA DDS for the delivery of siRNA/miRNA to MSCs."--Pages xiv-xv.
Download or read book RNA Interference written by Dr. Tim Doran and published by CABI. This book was released on 2009 with total page 269 pages. Available in PDF, EPUB and Kindle. Book excerpt: This methods manual provides an introduction to RNA interference, the theory behind its many applications, and specific protocols for RNAi, in organisms from plants and C.elegans to Drosophila and mammals. There are also chapters covering small hairpin RNAs and viral-induced gene silencing.
Download or read book Rna Silencing written by Esra Galun and published by World Scientific Publishing Company. This book was released on 2005-04-22 with total page 469 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on an emerging, central issue in molecular genetics and the development of eukaryotes: the control of gene expression by small species of RNA. As an exciting new field of endeavor, it is the first book by a single author to deal comprehensively with RNA silencing.The book provides the historical background of the field preceding the seminal work by Fire and associates in 1998 on the impact of small double-stranded RNA on the expression of nematode genes, which is considered the beginning of RNA silencing research. RNA silencing is described in a wide range of plants and animals including protozoa, simple metazoa, insects, non-mammalian vertebrates, and mammals. In each case the experimental results are provided with the accompanying background and with illustrations. There is also an appendix on the prospective use of RNA silencing in gene therapy, which is intended as a guide for investigators wishing to explore this possibility.
Download or read book Sirna Design written by Debra J. Taxman and published by Humana Press. This book was released on 2016-05-01 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: A fresh addition to Springer s successful series Methods in Molecular Biology, this publication updates researchers and technicians with the latest protocols in RNA interference, the gene silencing methodology that is revolutionizing biological research."
Download or read book Plant Gene Silencing written by M.A. Matzke and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is an up-to-date and comprehensive collection of reviews on various aspects of epigenetic gene silencing in plants. Research on this topic has undergone explosive growth during the past decade and has revealed novel features of gene regulation and plant defense responses that also apply to animals and fungi. Gene silencing is relevant for agricultural biotechnology because stable expression of transgenes is required for the successful commercialization of genetically engineered crops. The reviews have been written by distinguished authors who have made significant contributions to plant gene silencing research. This volume supersedes other books on gene silencing by focussing on plant systems, where many pioneering experiments have been performed, and by including the latest developments from top laboratories. The book is geared toward advanced students of genetics and plant sciences as well as applied and basic research scientists who work with transgenic organisms and epigenetic regulation of gene expression.
Download or read book Modulating Short Interfering RNA Off target Effects Through Nucleobase Modifications written by Rachel Anne P. Valenzuela and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Small noncoding RNAs, called short interfering RNA (siRNA) and microRNA (miRNA), regulate messenger RNA (mRNA) transcripts through Watson-Crick base complementarity in a process called RNA interference (RNAi). Both siRNA and miRNA-mediated gene silencing occur by binding to Argonaute (Ago), an integral protein in the RNA-induced silencing complex (RISC) where the antisense or “guide” strand is preferentially loaded, targeting an mRNA through sequence complementarity. RNAi has caught the attention of the pharmaceutical industry because of its therapeutic promise, and a substantial amount of research has focused on developing siRNA as a potential therapeutic. However, significant hurdles such as off-target effects, serum stability, and delivery, have slowed down the development of RNAi-based drugs. The focus of my dissertation research is using nucleobase modification as a tool to improve siRNA performance, mainly to reduce immune stimulation, improve target specificity, and improve human Argonaute 2 (hAgo2) binding. Immune stimulation triggered by siRNAs is one of the major challenges in the development of safe RNAi-based therapeutics. Within an immunostimulatory siRNA sequence, this hurdle is commonly addressed by using ribose modifications (e.g. 2’-OMe or 2’-F), which results in decreased cytokine production. However, since immune stimulation by siRNAs is a sequence-dependent phenomenon, recognition of the nucleobases by the trigger receptor(s) is also likely. Our 2014 report in Chembiochem details the use of the recently published crystal structures of Toll-like receptor 8 (TLR8) bound to small molecule agonists to generate computational models for ribonucleotide binding by this immune receptor. Our modeling suggested that modification of either the Watson-Crick or Hoogsteen face of adenosine would disrupt nucleotide/TLR8 interactions. We employed chemical synthesis to alter either the Watson-Crick or Hoogsteen face of adenosine and evaluated the effect of these modifications in an siRNA guide strand by measuring the immunostimulatory and RNA interference properties. For the siRNA guide strand tested, we found that modifying the Watson-Crick face is generally more effective at blocking TNF[alpha] production in human peripheral blood mononuclear cells (PBMCs) than modification at the Hoogsteen edge. We also observed that modifications near the 5' end were more effective at blocking cytokine production than those placed at the 3' end. This work advances our understanding of how chemical modifications can be used to mitigate siRNA immune stimulation. We studied the effect of 7-substituted-8-aza-7-deazaadenosine nucleobase analogs in enhancing target specificity of siRNA. We evaluated the IC50s of the unmodified and modified guide strands, and tested the knockdown of on- and off-targets (PIK3CB, FADD, and YY1) using a dual luciferase assay. We also assessed the knockdown of an endogenous off-target protein (YY1), using western blot. We found that modifying adenosines within the siRNA guide strand could decrease miRNA-like off-targeting in a position-dependent manner. We discovered that incorporating this modification at position 6 completely abrogrates binding to two off-target mRNA transcripts, called FADD and YY1. Furthermore, we studied the effects of incorporating 1-ethynyl ribose (1-ER) modifications at the 5’ and 3’ ends of an siRNA guide strand on hAgo2 binding and target specificity. We found that a 1-ER phenyl imidazole triazole modification in the 5’-end of a siRNA guide strand enhances on-target knockdown activity and preserves hAgo2 MID domain binding. MacRae and coworkers, our collaborators from The Scripps Research Institute, were able to co-crystallize hAgo2 bound to a siRNA modified with our 1-ER triazole analog. This crystal structure is integral in understanding the importance of the phenyl ring in the enhancement of the knockdown activity and improvement in the target specificity of the siRNA. We also tested a methyl imidazole triazole analog and to investigate the effect of a smaller alkyl substituent on MID domain binding, off-targeting, and RNAi activity.Lastly, we investigated the effects of 1-ER modifications on target specificity and PAZ domain binding. The PAZ domain of hAgo2 binds the 3’ end of a siRNA guide strand upon loading to the RISC. We incorporated 1-ER and its corresponding triazoles on the 3’ end of the guide strand, both on the terminal and penultimate positions. We evaluated the effect of these base replacements on on- and off-target knockdown as well as on endogenous off-target protein expression. We found that the 1-ER is the most effective way to reduce miRNA-like off-targeting without compromising on-target potency. We also purified the PAZ domain in order to study the relationship of the PAZ domain binding affinity to target specificity.
Download or read book RNA Nanotechnology written by Bin Wang and published by CRC Press. This book was released on 2014-04-02 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the past few decades there has been incredible growth in "bionano"-related research, which has been accompanied by numerous publications in this field. Although various compilations address topics related to deoxyribonucleic acid (DNA) and protein, there are few books that focus on determining the structure of ribonucleic acid (RNA) and using RNA as building blocks to construct nanoarchitectures for biomedical and healthcare applications. RNA Nanotechnology is a comprehensive volume that details both the traditional approaches and the latest developments in the field of RNA-related technology. This book targets a wide audience: a broad introduction provides a solid academic background for students, researchers, and scientists who are unfamiliar with the subject, while the in-depth descriptions and discussions are useful for advanced professionals. The book opens with reviews on the basic aspects of RNA biology, computational approaches for predicting RNA structures, and traditional and emerging experimental approaches for probing RNA structures. This section is followed by explorations of the latest research and discoveries in RNA nanotechnology, including the design and construction of RNA-based nanostructures. The final segment of the book includes descriptions and discussions of the potential biological and therapeutic applications of small RNA molecules, such as small/short interfering RNAs (siRNAs), microRNAs (miRNAs), RNA aptamers, and ribozymes.
Download or read book MicroRNA Protocols written by Shao-Yao Ying and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 365 pages. Available in PDF, EPUB and Kindle. Book excerpt: MicroRNA Protocols provides diverse, novel, and useful descriptions of miRNAs in several species, including plants, worms, flies, fish, chicks, mice, and humans. These include some useful adaptations and applications that could be relevant to the wider research community who are already familiar with the identification of miRNAs. This volume will stimulate the reader to explore diverse ways to understanding the mechanism in which miRNAs facilitate the molecular aspects of the biomedical research.
