RNA Technologies – serie

Many breakthroughs in experimental devices, advanced software, as well as analytical methods for systems biology development have helped shape the way we study DNA, RNA and proteins, on the genomic, transcriptional, translational and posttranslational level. This book highlights the comprehensive topics that encompass systems biology with enormous progress in the development of genome sequencing, proteomic and metabolomic methods in designing and understanding biological systems.Topics covered in this book include fundamentals of modelling networks, circuits and pathways, spatial and multi cellular systems, image-driven systems biology, evolution, noise and decision-making in single cells, systems biology of disease and immunology, and personalized medicine. Special attention is paid to epigenomics, in particular environmental conditions that impact genetic background. The breadth of exciting new data towards discovering fundamental principles and direct applicationof epigenetics in agriculture is also described.The chapter “Deciphering the Universe of RNA Structures and Trans RNA-RNA Interactions of Transcriptomes in vivo - from Experimental Protocols to Computational Analyses” is available open access under a CC BY 4.0 license via link.springer.com.

This book reviews the chemical, regulatory, and physiological mechanisms of protein arginine and lysine methyltransferases, as well as nucleic acid methylations and methylating enzymes.

This book reviews the chemical, regulatory, and physiological mechanisms of protein arginine and lysine methyltransferases, as well as nucleic acid methylations and methylating enzymes.

Transcriptomic studies have demonstrated that the majority of genomes found in complex organisms are expressed in highly dynamic and cell-specific patterns, producing huge numbers of intergenic, antisense and intronic long non-protein-coding RNAs (lncRNAs).

Transcriptomic studies have demonstrated that the majority of genomes found in complex organisms are expressed in highly dynamic and cell-specific patterns, producing huge numbers of intergenic, antisense and intronic long non-protein-coding RNAs (lncRNAs).

This book reviews a novel and exciting ?eld of cellular and molecular biology called epitranscriptomics, which focuses on changes in an organism’s cells resulting from the posttranscriptional modification of cellular RNA.

This book reviews a novel and exciting ?eld of cellular and molecular biology called epitranscriptomics, which focuses on changes in an organism’s cells resulting from the posttranscriptional modification of cellular RNA.

Formulations that protect the mRNA from nucleases and accelerate its cellular uptake, combined with improvements to the mRNA molecules themselves, have been critical advancements for mRNAs to become viable therapeutics.

Formulations that protect the mRNA from nucleases and accelerate its cellular uptake, combined with improvements to the mRNA molecules themselves, have been critical advancements for mRNAs to become viable therapeutics.

This book focuses on the current status of our understanding of RNA, a key biological molecule. The various RNAs covered are messenger RNA, ribosomal RNA, transfer RNA, noncoding RNAs, modified nucleosides, and RNA enzymes. The different chapters detail methods to investigate RNA structure and function, the chemistry of modified RNAs, and the latest advances in our understanding of the vast array of biological processes in which RNA is involved.RNA, in one form or another, touches almost everything in a cell. RNA has both structural and catalytic properties. RNA fulfills a broad range of functions. These molecules are no longer seen as passive elements transferring the genetic information from DNA into proteins but regulate the activity of genes during development, cellular differentiation, and changing environments. RNAs are involved in various aspects of cell physiology and disease development. Discoveries of RNA with unexpected diverse functions in healthy and diseased cells,such as the role of RNA as both the source and countermeasure to cancer or severe viral infection, stimulate new trends, passion, and solutions for molecular medicine.In this book, fundamental questions about the biochemical and genetic importance of RNA, how mRNAs are generated and used to produce proteins, how noncoding and catalytic RNAs mediate key cellular processes, how to determine RNA structure and how to apply RNA in treatment of diseases.This book is an essential resource for researches in academia and industry contributing to the development of new RNA therapeutics. The book is geared toward scientists from the graduate level on up and particularly appeals to active investigators in RNA biology, molecular biology, and biochemistry.

This book focuses on the current status of our understanding of RNA, a key biological molecule. The various RNAs covered are messenger RNA, ribosomal RNA, transfer RNA, noncoding RNAs, modified nucleosides, and RNA enzymes. The different chapters detail methods to investigate RNA structure and function, the chemistry of modified RNAs, and the latest advances in our understanding of the vast array of biological processes in which RNA is involved.RNA, in one form or another, touches almost everything in a cell. RNA has both structural and catalytic properties. RNA fulfills a broad range of functions. These molecules are no longer seen as passive elements transferring the genetic information from DNA into proteins but regulate the activity of genes during development, cellular differentiation, and changing environments. RNAs are involved in various aspects of cell physiology and disease development. Discoveries of RNA with unexpected diverse functions in healthy and diseased cells,such as the role of RNA as both the source and countermeasure to cancer or severe viral infection, stimulate new trends, passion, and solutions for molecular medicine.In this book, fundamental questions about the biochemical and genetic importance of RNA, how mRNAs are generated and used to produce proteins, how noncoding and catalytic RNAs mediate key cellular processes, how to determine RNA structure and how to apply RNA in treatment of diseases.This book is an essential resource for researches in academia and industry contributing to the development of new RNA therapeutics. The book is geared toward scientists from the graduate level on up and particularly appeals to active investigators in RNA biology, molecular biology, and biochemistry.

Modern biology is moving away from reductionist approaches towards holistic studies that encompass whole genomes, transcriptomes, proteomes, and metabolomes. Systems biology is an approach to studying complex biological systems by looking at many biomolecules in a comprehensive way. The aim is to gain a thorough understanding of the biological functions of different classes of molecules and their interactions.Systems Biology II is an up-to-date and comprehensive guide to the latest developments in systems biology, with a particular focus on RNA-based technologies. This book is the second volume in the RNA Technologies series dedicated to this topic. It presents cutting-edge approaches and tools for modelling and analyzing complex biological systems at different levels, from molecular interactions to cellular networks and beyond.With contributions from leading experts in the field, the book covers a wide range of topics, including gene regulatory networks, epigenetics, synthetic biology, omics data analysis, network inference, and more. It explores applications in various areas of the life sciences and biomedicine, such as vaccine development, cancer research, transplantation research and pathogenic processes.This volume is an essential resource for scientists and students working in systems biology, bioinformatics, synthetic biology, and related fields, as well as anyone interested in the latest advances in RNA technologies and their applications in biology and medicine.

This book focuses on the close relationship between aging and neurodegeneration. By highlighting the reversible nature of epigenetic changes, it provides a comprehensive overview of how these modifications can regulate gene expression without altering the DNA sequence, offering promising solutions for clinical intervention.Aging induces a gradual decline in cerebral function, leading to cognitive impairment, memory loss, motor dysfunction, and eventually functional decline and death. It is accompanied by the decline of organismal functions induced by whole genome alterations leading to neurodegeneration. Epigenetic modifications, including chromatin modifications, DNA methylation, and changes in regulatory RNAs, have a major impact on neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Huntington's disease.The chapters in this book address critical issues such as the contribution of epigenetic mechanisms to aging, the interaction between genetic and environmental factors in neurodegeneration, and the potential for epigenetic therapies to delay aging and mitigate disease progression.This volume, part of the RNA Technologies book series, is an invaluable resource for researchers and advanced students in genetics and neuroscience. It provides a deep understanding of the molecular basis of neurodegenerative diseases and offers innovative strategies to address the challenges of aging and neurodegeneration.

The aim of molecular diagnostics is preferentially to detect a developing disease before any symptoms appear. There has been a significant increase, fueled by technologies from the human genome project, in the availability of nucleic acid sequence information for all living organisms including bacteria and viruses. When combined with a different type of instrumentation applied, the resulting diagnostics is specific and sensitive. Nucleic acid-based medical diagnosis detects specific DNAs or RNAs from the infecting organism or virus and a specific gene or the expression of a gene associated with a disease. Nucleic acid approaches also stimulate a basic science by opening lines of inquiry that will lead to greater understanding of the molecules at the center of life. One can follow Richard Feynman’s famous statement “What I cannot create, I do not understand.”

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 levelsof 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.

The aim of molecular diagnostics is preferentially to detect a developing disease before any symptoms appear. There has been a significant increase, fueled by technologies from the human genome project, in the availability of nucleic acid sequence information for all living organisms including bacteria and viruses. When combined with a different type of instrumentation applied, the resulting diagnostics is specific and sensitive. Nucleic acid-based medical diagnosis detects specific DNAs or RNAs from the infecting organism or virus and a specific gene or the expression of a gene associated with a disease. Nucleic acid approaches also stimulate a basic science by opening lines of inquiry that will lead to greater understanding of the molecules at the center of life. One can follow Richard Feynman’s famous statement “What I cannot create, I do not understand.”

This book presents, in 26 chapters, the status quo in epigenomic profiling. It discusses how functional information can be indirectly inferred and describes the new approaches that promise functional answers, collectively referred to as epigenome editing. It highlights the latest important advances in our understanding of the functions of plant epigenomics and new technologies for the study of epigenomic marks and mechanisms in plants. Topics include the deposition or removal of chromatin modifications and histone variants, the role of epigenetics in development and response to environmental signals, natural variation and ecology, as well as applications for epigenetics in crop improvement. Discussing areas ranging from the complex regulation of stress and heterosis to the precise mechanisms of DNA and histone modifications, it presents breakthroughs in our understanding of complex phenotypic phenomena.

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.

Discussing areas ranging from the complex regulation of stress and heterosis to the precise mechanisms of DNA and histone modifications, it presents breakthroughs in our understanding of complex phenotypic phenomena.

Many breakthroughs in experimental devices, advanced software, as well as analytical methods for systems biology development have helped shape the way we study DNA, RNA and proteins, on the genomic, transcriptional, translational and posttranslational level. This book highlights the comprehensive topics that encompass systems biology with enormous progress in the development of genome sequencing, proteomic and metabolomic methods in designing and understanding biological systems.Topics covered in this book include fundamentals of modelling networks, circuits and pathways, spatial and multi cellular systems, image-driven systems biology, evolution, noise and decision-making in single cells, systems biology of disease and immunology, and personalized medicine. Special attention is paid to epigenomics, in particular environmental conditions that impact genetic background. The breadth of exciting new data towards discovering fundamental principles and direct applicationof epigenetics in agriculture is also described.The chapter “Deciphering the Universe of RNA Structures and Trans RNA-RNA Interactions of Transcriptomes in vivo - from Experimental Protocols to Computational Analyses” is available open access under a CC BY 4.0 license via link.springer.com.

RNA technologies are the driving forces of modern medicine and biotechnology. They combine the fields of biochemistry, chemistry, molecular biology, cell biology, physics, nanotechnology and bioinformatics. The combination of these topics is set to revolutionize the medicine of tomorrow. After more than 15 years of extensive research in the field of RNA technologies, the first therapeutics are ready to reach the first patients. Thus we are witnessing the birth of a very exciting time in the development of molecular medicine, which will be based on the methods of RNA technologies. This volume is the first of a series. It covers various aspects of RNA interference and microRNAs, although antisense RNA applications, hammerhead ribozyme structure and function as well as non-coding RNAs are also discussed. The authors are internationally highly respected experts in the field of RNA technologies.

In the most recent years, each of the RNA silencing pathways of plants have appeared to generate ncRNAs with dedicated functions, specialized biological activities and specific functional scopes.RNA silencing plays a crucial role in coordinating the expression, stability, protection and inheritance of eukaryotic genomes. It compromises several mechanisms, that invariably depend on core small non coding RNAs and that achieve dedicated sequence-specific functions. RNA silencing has been recognized to carry critical developmental, stress-response and bodyguard functions be coordinating the expression, protection, stability and inheritance of virtually all eukaryotic genomes. Thus, the ncRNAs encompass a wide set of mechanisms that achieve specialized functions.

RNA technologies are the driving forces of modern medicine and biotechnology. They combine the fields of biochemistry, chemistry, molecular biology, cell biology, physics, nanotechnology and bioinformatics. The combination of these topics is set to revolutionize the medicine of tomorrow. After more than 15 years of extensive research in the field of RNA technologies, the first therapeutics are ready to reach the first patients. Thus we are witnessing the birth of a very exciting time in the development of molecular medicine, which will be based on the methods of RNA technologies. This volume is the first of a series. It covers various aspects of RNA interference and microRNAs, although antisense RNA applications, hammerhead ribozyme structure and function as well as non-coding RNAs are also discussed. The authors are internationally highly respected experts in the field of RNA technologies.

In the most recent years, each of the RNA silencing pathways of plants have appeared to generate ncRNAs with dedicated functions, specialized biological activities and specific functional scopes.RNA silencing plays a crucial role in coordinating the expression, stability, protection and inheritance of eukaryotic genomes. It compromises several mechanisms, that invariably depend on core small non coding RNAs and that achieve dedicated sequence-specific functions. RNA silencing has been recognized to carry critical developmental, stress-response and bodyguard functions be coordinating the expression, protection, stability and inheritance of virtually all eukaryotic genomes. Thus, the ncRNAs encompass a wide set of mechanisms that achieve specialized functions.

Despite a half century of structural, biophysical and biochemical investigations of ribonucleic acids, they are still mysterious. RNAs stand at fertile crossroads of disciplines, integrating concepts from genomics, proteomics, dynamics as well as biochemistry and molecular biology. From 20 years it is clear, that genetic regulation of eukaryotic organisms has been misunderstood for the last years that the expression of genetic information is effected only by proteins. Basic understanding of nucleic acids has enhanced our foundation to probe novel biological functions. This is especially evident for RNA molecules whose functionality, maturation, and regulation require formation of correct secondary structure through encoded base-pairing interactions.

This book will provide latest insights in the functional potentials of ribonucleic acids in medine and the use of Spiegelmer and Spiegelzyme systems. It will also deal with a new type of delivery systems for cellular targeting.

Despite a half century of structural, biophysical and biochemical investigations of ribonucleic acids, they are still mysterious. RNAs stand at fertile crossroads of disciplines, integrating concepts from genomics, proteomics, dynamics as well as biochemistry and molecular biology. From 20 years it is clear, that genetic regulation of eukaryotic organisms has been misunderstood for the last years that the expression of genetic information is effected only by proteins. Basic understanding of nucleic acids has enhanced our foundation to probe novel biological functions. This is especially evident for RNA molecules whose functionality, maturation, and regulation require formation of correct secondary structure through encoded base-pairing interactions.

This book will provide latest insights in the functional potentials of ribonucleic acids in medine and the use of Spiegelmer and Spiegelzyme systems. It will also deal with a new type of delivery systems for cellular targeting.

This volume contains 29 engrossing chapters contributed by worldwide, leading research groups in the field of chemical biology. Topics include pre-biology; the establishment of the genetic code; isomerization of RNA; damage of nucleobases in RNA; the dynamic structure of nucleic acids and their analogs in DNA replication, extra- and intra-cellular transport; molecular crowding by the use of ionic liquids; new technologies enabling the modification of gene expression via editing of therapeutic genes; the use of riboswitches; the modification of mRNA cap regions; new approaches to detect appropriately modified RNAs with EPR spectroscopy and the use of parallel and high-throughput techniques for the analysis of the structure and new functions of nucleic acids. This volume discusses how chemistry can add new frontiers to the field of nucleic acids in molecular medicine, biotechnology and nanotechnology and is not only an invaluable source of information to chemists, biochemists and life scientists but will also stimulate future research.