Download or read book Insights Into the Functions of RNA Post transcriptional Modifications Gained Through Studies in Cellular Stress written by Kevin Charles Baldridge and published by . This book was released on 2017 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, the explosion of knowledge regarding functional roles for RNA in biology have uncovered the need for detailed molecular understanding of the relationship between the chemistry of RNA and its function. Post-transcriptional modifications in RNA are changes to the chemistry of the four basic RNA nucleotides, which can be thought of as expansions to the genetic alphabet of RNA. By subtly changing the chemistry of the standard RNA nucleotides, post-transcriptional modifications (PTMs) can act to modulate RNA function through a variety of mechanisms ranging from altering the basic physicochemical properties of an RNA molecule to fine-tuning complex regulation processes in higher organisms such as humans. While a number of functions have been ascribed to RNA post-transcriptional modifications, we still lack a comprehensive picture of how subtle changes in RNA chemistry can alter cellular function. Therefore, my dissertation focuses on applying cellular stress models as a way to interrogate how RNA post-transcriptional modifications can modulate RNA function. First, I provide a thorough discussion of how ribosomal RNA methylations help Escherichia coli adapt to stressful environmental conditions by protecting the vital protein translation process. Furthermore, by performing a targeted meta-analysis of publicly available stress-induced gene expression data, I identify specific ribosomal RNA methylations which may be important for E. coli adaptation to particular stresses including oxidative, heat, and cold stresses. Next, I examined the question of how RNA chemistry is affected directly by an external stress using a model system for simulated air pollution exposure with human lung cell cultures to demonstrate that cellular RNA oxidation is a reliable consistent indicator of oxidative stress from air pollution exposure. Building upon this air pollution exposure model system, I further explored how chemical oxidation of RNAs can be specifically enriched in certain RNA transcripts under oxidative stress induced by air pollution exposure. This work highlights specific oxidation of mRNAs involved in regulatory pathways as a possible mechanism for air-pollution related disease, suggesting that accumulation of oxidized mRNAs might interfere with processing or gene regulation. Additionally, examination of specific RNA oxidation associated with pre- and post-stress differential gene expression after exposure to air pollution highlights the potential that the oxidized RNA base 8-oxoguanosine might function as an epitranscriptomic mark affecting transcription. Lastly, I characterized how RNA modification machinery can contribute to cellular stress associated with expression of engineered transfer RNAs for applications in expanding the genetic code in E. coli. Using a suite of suppressor tRNAs designed by directed evolution, I demonstrated that the evolved lower expression level minimizes the impact of stress caused by interactions with E. coli post-transcriptional modification machinery, resulting in high performing tRNAs that remain functional regardless of their interactions with host PTM machinery. Collectively, the studies described in this dissertation demonstrate the power of employing cellular stress models to interrogate functional roles of RNA post-transcriptional modifications and highlight the myriad roles that PTMs can play in responding to and contributing to cellular stress
Download or read book Endoplasmic Reticulum Stress in Health and Disease written by Patrizia Agostinis and published by Springer Science & Business Media. This book was released on 2012-08-13 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Endoplasmic Reticulum (ER) is an organelle with extraordinary signaling and homeostatic functions. It is the organelle responsible for protein folding, maturation, quality control and trafficking of proteins destined for the plasma membrane or for secretion into the extracellular environment. Failure, overloading or malfunctioning of any of the signaling or quality control mechanisms occurring in the ER may provoke a stress condition known as ‘ER stress’. Accumulating evidence indicates that ER stress may dramatically perturb interactions between the cell and its environment, and contribute to the development of human diseases, ranging from metabolic diseases and cancer to neurodegenerative diseases, or impact therapeutic outcome. This book primarily focuses on the pathophysiology of ER stress. It introduces the molecular bases of ER stress, the emerging relevance of the ER-mitochondria cross-talk, the signaling pathways engaged and cellular responses to ER stress, including the adaptive Unfolded Protein Response (UPR), autophagy as well as cell death. Next the book addresses the role of ER stress in physiology and in the etiology of relevant pathological conditions, like carcinogenesis and inflammation, neurodegeneration and metabolic disease. The last chapter describes how ER stress pathways can be targeted for therapeutic benefit. Altogether, this book will provide the reader with an exhaustive view of ER stress biology and the latest insights in the role of ER stress in relevant human diseases.
Download or read book Alternative Splicing Regulation in Plants written by Ezequiel Petrillo and published by Frontiers Media SA. This book was released on 2020-09-02 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Download or read book DNA and RNA Modification Enzymes written by Henri Grosjean and published by CRC Press. This book was released on 2009-06-11 with total page 682 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Synthetic mRNA written by Robert E. Rhoads and published by Humana. This book was released on 2016-05-29 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents detailed laboratory protocols for in vitro synthesis of mRNA with favorable properties, its introduction into cells by a variety of techniques, and the measurement of physiological and clinical consequences such as protein replacement and cancer immunotherapy. Synthetic techniques are described for structural features in mRNA that provide investigational tools such as fluorescence emission, click chemistry, photo-chemical crosslinking, and that produce mRNA with increased stability in the cell, increased translational efficiency, and reduced activation of the innate immune response. Protocols are described for clinical applications such as large-scale transfection of dendritic cells, production of GMP-grade mRNA, redirecting T cell specificity, and use of molecular adjuvants for RNA vaccines. 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Synthetic mRNA: Production, Introduction into Cells, and Physiological Consequences is a valuable and cutting-edge resource for both laboratory investigators and clinicians interested in this powerful and rapidly evolving technology.
Download or read book mRNA Processing and Metabolism written by Daniel R. Schoenberg and published by Humana. This book was released on 2004-02-05 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cells possess a wealth of posttranscriptional control mechanisms that impact on every conceivable aspect of the life of an mRNA. These processes are intimately intertwined in an almost baroque manner, where promoter context influences the recruitment of splicing factors, where the majority of pre-mRNAs undergo alternative splicing, and where proteins deposited during nuclear processing impact distal cytoplasmic processing, translation, and decay. If there is a unifying theme to mRNA Processing and Metabolism: Methods and Protocols, it is that mRNA processing and metabolism are integrated processes. Many of the techniques used to study mRNA have been described in a previous volume of this series (RNA–Protein Interaction Protocols, Susan Haynes, ed.) and specialized methods journals. In selecting topics for mRNA Processing and Metabolism: Methods and Protocols, I sought input on new and novel techniques and approaches that build on this foundation using technological advances in microscopy, whole genome sequencing, microarrays, mass spectrometry, fluorescent detection methodologies, and RNA interference. I have tried not to bias this book toward any single model organism, and approaches described in the various chapters use yeast, Drosophila, Xenopus, mice, plants, and cultured mammalian cells.
Download or read book The Nucleolus written by Mark O. J. Olson and published by Springer Science & Business Media. This book was released on 2011-09-15 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: Within the past two decades, extraordinary new functions for the nucleolus have begun to appear, giving the field a new vitality and generating renewed excitement and interest. These new discoveries include both newly-discovered functions and aspects of its conventional role. The Nucleolus is divided into three parts: nucleolar structure and organization, the role of the nucleolus in ribosome biogenesis, and novel functions of the nucleolus.
Download or read book Poly ADP Ribosyl ation written by Alexander Bürkle and published by Springer Science & Business Media. This book was released on 2008-01-11 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the most comprehensive, up-to-date reference on this post-translational modification of proteins, which is intimately linked with DNA repair, maintenance of genomic stability, transcriptional regulation, cell death and a variety of other cellular phenomena as well as with a variety of pathophysiological conditions, including ischemia-reperfusion damage, Parkinson’s disease, Type I diabetes mellitus, hemorrhagic and septic shock and other inflammatory conditions. Richly illustrated, it offers 19 chapters written by international experts.
Download or read book Recoding Expansion of Decoding Rules Enriches Gene Expression written by John F. Atkins and published by Springer Science & Business Media. This book was released on 2010-03-10 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: The literature on recoding is scattered, so this superb book ?lls a need by prov- ing up-to-date, comprehensive, authoritative reviews of the many kinds of recoding phenomena. Between 1961 and 1966 my colleagues and I deciphered the genetic code in Escherichia coli and showed that the genetic code is the same in E. coli, Xenopus laevis, and guinea pig tissues. These results showed that the code has been c- served during evolution and strongly suggested that the code appeared very early during biological evolution, that all forms of life on earth descended from a c- mon ancestor, and thus that all forms of life on this planet are related to one another. The problem of biological time was solved by encoding information in DNA and retrieving the information for each new generation, for it is easier to make a new organism than it is to repair an aging, malfunctioning one. Subsequently, small modi?cations of the standard genetic code were found in certain organisms and in mitochondria. Mitochondrial DNA only encodes about 10–13 proteins, so some modi?cations of the genetic code are tolerated that pr- ably would be lethal if applied to the thousands of kinds of proteins encoded by genomic DNA.
Download or read book Ribosomes Structure Function and Dynamics written by Marina V. Rodnina and published by Springer Science & Business Media. This book was released on 2011-12-10 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ribosome is a macromolecular machine that synthesizes proteins with a high degree of speed and accuracy. Our present understanding of its structure, function and dynamics is the result of six decades of research. This book collects over 40 articles based on the talks presented at the 2010 Ribosome Meeting, held in Orvieto, Italy, covering all facets of the structure and function of the ribosome. New high-resolution crystal structures of functional ribosome complexes and cryo-EM structures of translating ribosomes are presented, while partial reactions of translation are examined in structural and mechanistic detail, featuring translocation as a most dynamic process. Mechanisms of initiation, both in bacterial and eukaryotic systems, translation termination, and novel details of the functions of the respective factors are described. Structure and interactions of the nascent peptide within, and emerging from, the ribosomal peptide exit tunnel are addressed in several articles. Structural and single-molecule studies reveal a picture of the ribosome exhibiting the energy landscape of a processive Brownian machine. The collection provides up-to-date reviews which will serve as a source of essential information for years to come.
Download or read book RNA Modification written by and published by Academic Press. This book was released on 2015-08-03 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA Modification provides a useful examination of the science and its role in biological regulation, the current frontier of life science research, and includes various RNA modications and their role in gene expression. It represents the most up-to-date knowledge and protocols available today.
Download or read book Applications of RNA Seq and Omics Strategies written by Fabio Marchi and published by BoD – Books on Demand. This book was released on 2017-09-13 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: The large potential of RNA sequencing and other "omics" techniques has contributed to the production of a huge amount of data pursuing to answer many different questions that surround the science's great unknowns. This book presents an overview about powerful and cost-efficient methods for a comprehensive analysis of RNA-Seq data, introducing and revising advanced concepts in data analysis using the most current algorithms. A holistic view about the entire context where transcriptome is inserted is also discussed here encompassing biological areas with remarkable technological advances in the study of systems biology, from microorganisms to precision medicine.
Download or read book RNA Infrastructure and Networks written by Lesley J. Collins and published by Springer Science & Business Media. This book was released on 2011-09-15 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNAs form complexes with proteins and other RNAs. The RNA‐infrastructure represents the spatiotemporal interaction of these proteins and RNAs in a cell‐wide network. RNA Infrastructure and Networks brings together these ideas to illustrate the scope of RNA‐based biology, and how connecting RNA mechanisms is a powerful tool to investigate regulatory pathways. This book is but a taste of the wide range of RNA‐based mechanisms that connect in the RNA infrastructure.
Download or read book Modified Nucleic Acids in Biology and Medicine written by Stefan Jurga and published by Springer. This book was released on 2016-07-29 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Plant Long Non Coding RNAs written by Julia A. Chekanova and published by Humana Press. This book was released on 2019-04-20 with total page 480 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on various approaches to studying long non-coding RNAs (lncRNAs), including techniques for finding lncRNAs, localization, and observing their functions. The chapters in this book cover how to catalog lncRNAs in various plant species; determining subcellular localization; protein interactions; structures; and RNA modifications. 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 innovative, Plant Long Non-Coding RNAs: Methods and Protocols is a valuable resource that aids researchers in understanding the functions of lncRNAs in different plant species, and helps them explore currently uncharted facets of plant biology.
Download or read book Insights into Human Neurodegeneration Lessons Learnt from Drosophila written by Mousumi Mutsuddi and published by Springer Nature. This book was released on 2019-12-05 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is aimed at generating an updated reservoir of scientific endeavors undertaken to unravel the complicated yet intriguing topic of neurodegeneration. Scientists from Europe, USA and India who are experts in the field of neurodegenerative diseases have contributed to this book. This book will help readers gain insight into the recent knowledge obtained from Drosophila model, in understanding the molecular mechanisms underlying neurodegenerative disorders and also unravel novel scopes for therapeutic interventions. Different methodologies available to create humanized fly models that faithfully reflects the pathogenicities associated with particular disorders have been described here. It also includes information on the exciting area of neural stem cells. A brief discussion on neurofibrillary tangles, precedes the elaborate description of lessons learnt from Drosophila about Alzheimer's, Parkinson’s, Spinomuscular Atrophy, Huntington’s diseases, RNA expansion disorders and Hereditary Spastic Paraplegia. We have concluded the book with the use of Drosophila for identifying pharmacological therapies for neurodegenerative disorders. The wide range of topics covered here will not only be relevant for beginners who are new to the concept of the extensive utility of Drosophila as a model to study human disorders; but will also be an important contribution to the scientific community, with an insight into the paradigm shift in our understanding of neurodegenerative disorders. Completed with informative tables and communicative illustrations this book will keep the readers glued and intrigued. We have comprehensively anthologized the lessons learnt on neurodegeneration from Drosophila and have thus provided an insight into the multidimensional aspects of pathogenicities of majority of the neurodegenerative disorders.
Download or read book Fine Tuning of RNA Functions by Modification and Editing written by Henri Grosjean and published by Springer. This book was released on 2005-05-11 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
