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The work reported in this book represents an excellent example of how creative experimentation and technology development, complemented by computational data analysis, can yield important insights that further our understanding of biological entities from a systems perspective. The book describes how the study of a single RNA-binding protein and its interaction sites led to the development of the novel ‘protein occupancy profiling’ technology that for the first time captured the mRNA sequence space contacted by the ensemble of expressed RNA binders. Application of protein occupancy profiling to eukaryotic cells revealed that extensive sequence stretches in 3’ UTRs can be contacted by RBPs and that evolutionary conservation as well as negative selection act on protein-RNA contact sites, suggesting functional importance. Comparative analysis of the RBP-bound sequence space has the potential to unravel putative cis-acting RNA elements without a priori knowledge of the bound regulators. Here, Dr. Munschauer provides a comprehensive introduction to the field of post-transcriptional gene regulation, examines state-of-the-art technologies, and combines the conclusions from several journal articles into a coherent and logical story from the frontiers of systems-biology inspired life science. This thesis, submitted to the Department of Biology, Chemistry and Pharmacy at Freie Universität Berlin, was selected as outstanding work by the Berlin Institute for Medical Systems Biology at the Max-Delbrueck Center for Molecular Medicine, Germany. .
Engineering. --- Biomedical Engineering. --- Systems Biology. --- Computational Biology/Bioinformatics. --- Bioinformatics. --- Biological models. --- Biomedical engineering. --- Ingénierie --- Bio-informatique --- Modèles biologiques --- Génie biomédical --- Health & Biological Sciences --- Biomedical Engineering --- RNA-protein interactions. --- RNA polymerases. --- DNA-dependent RNA polymerases --- DNA-directed RNA polymerases --- Polymerases, RNA --- Ribonucleate nucleotidyltransferases --- RNA nucleotidyltransferases --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Systems biology. --- Protein binding --- Transferases --- Biomedical Engineering and Bioengineering. --- Bio-informatics --- Biological informatics --- Biology --- Information science --- Computational biology --- Systems biology --- Models, Biological --- Clinical engineering --- Medical engineering --- Bioengineering --- Biophysics --- Engineering --- Medicine --- Data processing --- Bioinformatics --- Biological systems --- Molecular biology
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Now in two-colour throughout, the fourth edition of Eukaryotic Transcription Factors has been completely rewritten and restructured to take into account the tremendous advances in our understanding of transcription factors and the mechanisms by which they act. Considerable emphasis has been given to the interaction between transcription factors and chromatin structure. Also included is an entirely new section on the mediator complex and expansion of the space devoted to co-activators and co-repressors.This book is essential reading for all those who wish to understand the impac
Eukaryotic Cells. --- Gene Expression Regulation. --- Transcription Factors. --- Transcription, Genetic. --- Transcription factors. --- Genetic transcription --- Eukaryotic cells. --- Facteurs de transcription --- Transcription génétique --- Cellules eucaryotes --- Regulation. --- Régulation --- Genetic transcription. --- Genetic regulation --- Genetic transcription factors --- Proteins --- Transcription factors --- Eukaryotic cells --- MOLECULAR STRUCTURE --- BASE SEQUENCE --- DNA-BINDING PROTEINS --- GENETIC PREDISPOSITION TO DISEASE --- TRANSCRIPTION, GENETIC --- DNA-DIRECTED RNA POLYMERASES --- CHROMATIN --- TRANSCRIPTION FACTORS --- ULTRASTRUCTURE
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This thesis describes research into the mode of function, inhibition, and evolution of the ribosomal catalytic center, the Peptidyl Transferase Center (PTC)--research that has already led to attempts at improving PTC antibiotics. The PhD candidate carried out two parallel studies. One using a combination of X-ray crystallography, biochemistry, molecular biology, and theoretical studies to obtain crystal structures of ribosomal particles with antibiotics that target the PTC, revealing the modes of action, resistance, cross-resistance and discrimination between ribosomes of eubacterial pathogens and eukaryotic hosts. In the second parallel study, the candidate synthesized a ribosomal substructure--one that may represent the minimal entity capable of catalyzing peptide bond formation--shedding light on the origin of the ribosome itself.
Antibiotics -- Biotechnology. --- Ribosomes. --- RNA polymerases. --- Chemistry --- Physical Sciences & Mathematics --- Biochemistry --- Enzymes. --- Biocatalysts --- Ferments --- Soluble ferments --- Ribonucleoprotein particles --- Life sciences. --- Organic chemistry. --- Nucleic acids. --- Proteins. --- Life Sciences. --- Nucleic Acid Chemistry. --- Protein Science. --- Organic Chemistry. --- Catalysts --- Proteins --- Enzymology --- Cell organelles --- Microsomes --- Nucleoproteins --- Protoplasm --- Biochemistry. --- Chemistry, Organic. --- Organic chemistry --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Biology --- Medical sciences --- Polynucleotides --- Biomolecules --- Composition --- Proteins . --- Proteids --- Polypeptides --- Proteomics
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Our common knowledge on oxidative stress has evolved substantially over the years and has been mostly focused on the fundamental chemical reactions and the most relevant chemical species involved in the human pathophysiology of oxidative stress-associated diseases. Thus, reactive oxygen species and reactive nitrogen species (ROS and RNS) were identified as the key players initiating, mediating, and regulating the cellular and biochemical complexity of oxidative stress either as physiological (acting pro-hormetic) or as pathogenic (causing destructive vicious circle) process. The papers published in this particular Special Issue of the Cells demonstrate the impressive pathophysiological relevance of ROS and RNS in a range of contexts, including the relevance of second messengers of free radicals like 4-hydroxynonenal, allowing us to assume that even more detailed mechanisms of their positive and negative effects lie in wait, and should assist in better monitoring of the major modern diseases and the development of advanced integrative biomedicine treatments.
toxicity --- toll-like receptors --- acrolein --- hydroxyapatite-based biomaterials --- LC-MS/MS --- blood–brain barrier --- NADPH-oxidase --- human neuroblastoma SH-SY5Y cells --- NRF2-NQO1 axis --- granulocytes --- free radicals --- antioxidant --- plaque vulnerability --- bEnd.3 --- relaxation --- Ca2+ --- keratinocytes --- oxidative metabolism of the cells --- lipid peroxidation --- intermittent hypoxia --- osteoblast growth --- UV radiation --- ROS --- bEnd5 --- cyclopurines --- NF?B --- glucose deprivation --- antimicrobial --- endothelial cells --- 4-hydroxynonenal (4-HNE) --- histamine --- glutamine deprivation --- optical coherence tomography --- antioxidants --- DNA damage --- glutathione --- NQO1 transcript variants --- xeroderma pigmentosum --- cancer cells --- VAS2870 --- reactive oxygen species (ROS) --- TP53 mutation --- DNA and RNA polymerases --- viability --- oxidative burst --- macrophages --- inflammation --- Nrf2 --- von Willebrand factor --- reactive oxygen species --- growth control --- intracellular signaling --- MFN2 --- nuclear factor erythroid 2–related factor 2 --- fusion/fission --- IMR-90 --- calcium --- proliferation --- mitochondria --- pathophysiology of oxidative stress --- redox balance --- 4-hydroxynonenal --- cannabidiol --- oxidative homeostasis --- rs1800566 --- neuronal cell death --- heme-oxygenase-1 --- vitamins --- cell signaling --- TRPM2 channel --- aorta --- cancer --- growth --- cancer regression --- oxidative stress --- nucleotide excision repair
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