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The means by which proteins and RNAs are exchanged between cytoplasm and nucleus have interested cell biologists for many years, and the field has seen a number of exciting recent advances. Much has been learned about the intricate architecture of the nuclear pore-complex, the mechanisms by which transport substrates are sorted, and the supply of energy for exchange processes. This book attempts a general review of the growing body of knowledge. However, the authors challenge the presumptions implicit in some interpretations of the evidence, re-examining the concept of "transport" within cells, and suggesting that lessons learned from nucleocytoplasmic transport studies can elucidate wider aspects of cell biology.
Dysfunction of nuclear-cytoplasmic transport systems has been associated with many human diseases. Thus, understanding of how functional this transport system maintains, or through dysfunction fails to maintain remains the core question in cell biology. In eukaryotic cells, the nuclear envelope (NE) separates the genetic transcription in the nucleus from the translational machinery in the cytoplasm. Thousands of nuclear pore complexes (NPCs) embedded on the NE selectively mediate the bidirectional trafficking of macromolecules such as RNAs and proteins between these two cellular compartments. In this book, the authors integrate recent progress on the structure of NPC and the mechanism of nuclear-cytoplasmic transport system in vitro and in vivo.
Selective yet efficient transport between the cell nucleus and cytoplasm is critical to cellular function as the nuclear pore complex is a major point of regulation for gene expression, signal transduction, immune response, oncogenesis and viral propagation. The combined physical structure of the pore, biochemical interaction of transport factors with pore components and the presence of the cellular milieu create conditions under which selective and efficient nucleocytoplasmic transport can occur. In this dissertation, I explore the significance of structure and interaction on transport of globular proteins and polymeric mRNA cargo through the crowded pore. In the first part of this work, an agent based modeling software framework is developed and validated for accurately simulating discrete and stochastic reaction-diffusion systems. A simulation environment representing the structure of the nuclear pore complex along with rules for the dynamics of protein movement and interaction was created using in vivo and in vitro reported parameters. This setup was then used to perform in silico experiments on the role of pore-cargo affinity in optimizing transport efficiency. These experiments demonstrate the pore's sensitivity to cargo affinity in maintaining efficient transport and suggest that a higher affinity binding site at the side of the pore where transport is terminated increases efficiency by reducing futile shuttling of cargo complexes. In the final part of this dissertation, I extend my agent based modeling framework to look at aspects of mRNA export that have remained unaddressed in experimental works. Variations in the number and spacing of transport receptors bound to the mRNA are shown to play a critical role in transport efficiency. In these experiments, a single transport receptor at the 5' end appeared insufficient for facilitating export. Increasing transport receptor coverage along the length of the mRNA improved the chances of successful export. Additionally, it was observed that the presence of a transport receptor near either the 5' or 3' terminus is required for successful export as it likely promotes the emergence of a favorable threading conformation. Finally, it was observed that the use of a single fluorescent tag to track and report mRNA export time, as is standard in current experimental work, is likely to underestimate true transport times. These findings have implications in the design of targeted delivery and export of polymeric molecules into and out the nucleus.
Delivery of therapeutic proteomics and genomics represent an important area of drug delivery research. Genomics and proteomics approaches could be used to direct drug development processes by unearthing pathways involved in disease pathogenesis where intervention may be most successful. This book describes the basics of genomics and proteomics and highlights the various chemical, physical and biological approaches to protein and gene delivery. Covers a diverse array of topics from basic sciences to therapeutic applications of proteomics and genomics delivery Of interest to researchers in both academia and industry Highlights what’s currently known and where further research is needed
Volume 122 of Methods in Cell Biology describes modern tools and techniques used to study nuclear pore complexes and nucleocytoplasmic transport in diverse eukaryotic model systems (including mammalian cells, Xenopus, C. elegans, yeast). The volume enables investigators to analyze nuclear pore complex structure, assembly, and dynamics; to evaluate protein and RNA trafficking through the nuclear envelope; and to design in vivo or in vitro assays appropriate to their research needs. Beyond the study of nuclear pores and transport as such, these protocols will also be helpful to scientists characterizing gene regulation, signal transduction, cell cycle, viral infections, or aging. The NPC being one of the largest multiprotein complexes in the cell, some protocols will also be of interest for people currently characterizing other macromolecular assemblies. This book is thus designed for laboratory use by graduate students, technicians, and researchers in many molecular and cellular disciplines. Describes modern tools and techniques used to study nuclear pore complexes and nucleocytoplasmic transport in diverse eukaryotic model systems (mammalian cells, Xenopus, C. elegans, yeast) Chapters are written by experts in the field Cutting-edge material
Pharmacoepigenetics, Volume Eleven provides a comprehensive volume on the role of epigenetics and epigenomics in drug discovery and development, providing a detailed, but accessible, view of the field, from basic principles, to applications in disease therapeutics. Leading international researchers from across academia, clinical settings and the pharmaceutical industry discuss the influence of epigenetics and epigenomics in human pathology, epigenetic biomarkers for disease prediction, diagnosis, and treatment, current epigenetic drugs, and the application of epigenetic procedures in drug development. Throughout the book, chapter authors offer a balanced and objective discussion of the future of pharmacoepigenetics and its crucial contribution to the growth of precision and personalized medicine. Fully examines the influence of epigenetics and epigenomics in human pathology, epigenetic biomarkers for disease prediction, diagnosis, treatment, current epigenetic drugs and the application of epigenetic procedures in drug development Features chapter contributions from leading international researchers in academia, clinical settings and the pharmaceutical industry Instructs researchers, students and clinicians on how to better interpret and employ pharmacoepigenetics in drug development, efficiency and safety Provides a balanced and objective discussion of the future of pharmacoepigenetics and its crucial role in precision medicine