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Dissecting Regulatory Interactions of RNA and Protein
The work described in this book is an excellent example of interdisciplinary research in systems biology. It shows how concepts and approaches from the field of physics can be efficiently used to answer biological questions and reports on a novel methodology involving creative computer-based analyses of high-throughput biological data. Many of the findings described in the book, which are the result of collaborations between the author (a theoretical scientist) and experimental biologists and between different laboratories, have been published in high-quality peer-reviewed journals such as Molecular Cell and Nature. However, while those publications address different aspects of post-transcriptional gene regulation, this book provides readers with a complete, coherent and logical view of the research project as a whole. The introduction presents post-transcriptional gene regulation from a distinct angle, highlighting aspects of information theory and evolution and laying the groundwork for the questions addressed in the subsequent chapters, which concern the regulation of the transcriptome as the primary functional carrier of active genetic information.
RNA Structure and Function
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 f...
Modelling and implementation of a microscopic traffic simulation system
This thesis presents the foundations, the initial state, and the progress made in modelling and implementing a real-world and real-time online microscopic traffic simulation system for highway traffic. To successfully model and implement such a simulation system, this thesis recommends the use of a number of formal methods applied at the right places. As part of the recommendation, this thesis proposes a microscopic traffic simulation system. To explore the feasibility and the potential of the recommended methods, it observes and examines the proposed system from multiple views and under various different aspects. As part of the examination, this thesis provides a (semi-)formal specification...
Introducing Epigenetics
Epigenetics is the most exciting field in biology today, developing our understanding of how and why we inherit certain traits, develop diseases and age, and evolve as a species. This non-fiction comic book introduces us to genetics, cell biology and the fascinating science of epigenetics, which is rapidly filling in the gaps in our knowledge, allowing us to make huge advances in medicine. We'll look at what identical twins can teach us about the epigenetic effects of our environment and experiences, why certain genes are 'switched on' or off at various stages of embryonic development, and how scientists have reversed the specialization of cells to clone frogs from a single gut cell. In Introducing Epigenetics, Cath Ennis and Oliver Pugh pull apart the double helix, examining how the epigenetic building blocks and messengers that interpret and edit our genes help to make us, well, us.
The DNA, RNA, and Histone Methylomes
This book reviews the chemical, regulatory, and physiological mechanisms of protein arginine and lysine methyltransferases, as well as nucleic acid methylations and methylating enzymes. Protein and nucleic acid methylation play key and diverse roles in cellular signalling and regulating macromolecular cell functions. Protein arginine and lysine methyltransferases are the predominant enzymes that catalyse S-adenosylmethionine (SAM)-dependent methylation of protein substrates. These enzymes catalyse a nucleophilic substitution of a methyl group to an arginine or lysine side chain nitrogen (N) atom. Cells also have additional protein methyltransferases, which target other amino acids in peptidy...
Stochastic Transport in Complex Systems
The first part of the book provides a pedagogical introduction to the physics of complex systems driven far from equilibrium. In this part we discuss the basic concepts and theoretical techniques which are commonly used to study classical stochastic transport in systems of interacting driven particles. The analytical techniques include mean-field theories, matrix product ansatz, renormalization group, etc. and the numerical methods are mostly based on computer simulations. In the second part of the book these concepts and techniques are applied not only to vehicular traffic but also to transport and traffic-like phenomena in living systems ranging from collective movements of social insects ...
Essentials of Noncoding RNA in Neuroscience
Essentials of Noncoding RNA in Neuroscience: Ontogenetics, Plasticity of the Vertebrate Brain focuses on the role of miRNAs in neurogenesis, gliogenesis, neuronal network formation, and the cell biology of forebrain development. The important role miRNAs play in neuronal maturation, neocortex function, and in some neurodevelopmental disorders is discussed, as are the computational challenges and methods used in the identification of miRNA targets. This book is a valuable reference for neuroscientists who wish to better understand the role of miRNAs in complex processes. It is of strong interest to those working to develop enabling technologies to detect and monitor miRNA expression and funct...
Pacific Symposium on Biocomputing 2008
The Pacific Symposium on Biocomputing (PSB) 2008 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2008 will be held on January 4?8, 2008 at the Fairmont Orchid, Big Island of Hawaii. Tutorials will be offered prior to the start of the conference.PSB 2008 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It...
