Jan Barciszewski - Böcker

General inspection of a role performed in the cell by RNAs allows us to distinguish three major groups of transcripts: i.) protein-coding mRNAs and ii.) non-coding housekeeping and iii.) regulatory RNAs. The housekeeping RNAs include RNA classes that are generally, constitutively expressed and whose presence is required for normal function and viability of the cells. On the other hand, a group of regulatory RNAs includes RNA species that are expressed at certain stages of organism development or cell differentiation or as a response to external stimuli and can affect expression of other genes on the levels of transcription or translation. Non-coding RNA transcripts form a heterogeneous class of RNAs that can not be characterized by a single specific function. Initially, the term non-coding RNA (ncRNA) was used primarily to describe polyadenylated and a capped eukaryotic RNAs transcribed by RNA polymerase II, but lacking long open reading frames. Now, this definition can be extended to cover all RNA transcripts that do not show protein-coding capacity and is sometimes used to describe any RNA that does not encode protein, including introns.This book is an in-depth look at the function of Non-Coding RNAs and their relationship to Molecular Biology and Molecular Biology.

This text describes various aspects of nucleic acid and protein structure, mainly RNA structure and proteins, interacting with specific RNA species. Papers deal with DNA protein interactions, telomerase, aminoacyl-tRNA synthetases, elongation factor Tu, DNA repair, RNA structure, NMR technology, RNA aptamer interaction of biological macromolecules with metal ions. Two papers deal with theoretical aspects of RNA structure production and computer modelling. Many papers describe the possibility of commercial application of RNA biotechnology. One article discusses the impact of direct democracy on basic science supporting biotechnology.

This text describes various aspects of nucleic acid and protein structure, mainly RNA structure and proteins, interacting with specific RNA species. Papers deal with DNA protein interactions, telomerase, aminoacyl-tRNA synthetases, elongation factor Tu, DNA repair, RNA structure, NMR technology, RNA aptamer interaction of biological macromolecules with metal ions. Two papers deal with theoretical aspects of RNA structure production and computer modelling. Many papers describe the possibility of commercial application of RNA biotechnology. One article discusses the impact of direct democracy on basic science supporting biotechnology.

General inspection of a role performed in the cell by RNAs allows us to distinguish three major groups of transcripts: I. protein-coding mRNAs, II. non-coding housekeeping and III. regulatory RNAs. The housekeeping RNAs include RNA classes that are generally, constitutively expressed and whose presence is required for normal function and viability of the cells. On the other hand, a group of regulatory RNAs includes RNA species that are expressed at certain stages of organism development or cell differentiation or as a response to external stimuli and can affect expression of other genes on the levels of transcription or translation. Non-coding RNA transcripts form a heterogeneous class of RNAs that can not be characterized by a single specific function. Initially, the term non-coding RNA (ncRNA) was used primarily to describe polyadenylated and a capped eukaryotic RNAs transcribed by RNA polymerase II, but lacking long open reading frames. Now, this definition can be extended to cover all RNA transcripts that do not show protein-coding capacity and is sometimes used to describe any RNA that does not encode protein, including introns. This book is an in-depth look at the function of Non-Coding RNAs and their relationship to Molecular Biology and Molecular Biology.

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.

Developments over the past few years have revealed the remarkable versatility of RNA in any compartment of the cell, tasks that had been thought to be exclusively in the realm of proteins and even beyond. The chapters in this book written by leading investigators in the field provide insight into various promising avenues where RNA and nucleic acid derivatives including antisense RNAs, such as siRNA, miRNAs, amplification/selection (SELEX) generated aptamers as well as ribozymes are at the threshold of impacting medicine.

In this book the authors review the field and explore the potential role of RNAi and other RNA technologies in cardiovascular medicine and research. They highlight the impressive recent progress but also the hurdles that still must be overcome before this promising technology is finally ready for translation and clinical use.

In the past few years nucleic acids technologies have grown into a powerful analytical and also increasingly therapeutic tool. It has been applied not only to the uncovering of gene functions in many organisms, but also to pathogenetic analysis and recently also for the treatment of human diseases. The book discusses in depth the potential of these innovative methods in the broad field of central nervous system and brain tumours particularly. Whereas there is currently no comprehensive overview on potential and challenges of nucleic acids technologies for basic brain tumours and for the clinical management of patients with brain tumours, this book does explicitly cover the many other aspects of the "RNA World" (pathogenic and therapeutic potential of microRNAs, aptamer technology, etc.), too. With this significantly broadened scope as compared to currently existing books it appears to be an urgently needed new publication.

Developments over the past few years have revealed the remarkable versatility of RNA in any compartment of the cell, tasks that had been thought to be exclusively in the realm of proteins and even beyond. The chapters in this book written by leading investigators in the field provide insight into various promising avenues where RNA and nucleic acid derivatives including antisense RNAs, such as siRNA, miRNAs, amplification/selection (SELEX) generated aptamers as well as ribozymes are at the threshold of impacting medicine.

In this book the authors review the field and explore the potential role of RNAi and other RNA technologies in cardiovascular medicine and research. They highlight the impressive recent progress but also the hurdles that still must be overcome before this promising technology is finally ready for translation and clinical use.