Pamela A. Silver - US grants

No abstract provided

[unreadable] DESCRIPTION (provided by applicant): This proposal addresses issues relevant to normal cell growth and to disease: the spatial organization within the nucleus, and how the nucleus communicates with the cytoplasm and the cell exterior. The focus is on the relationship between the organization of the genome and the processing and export of mRNAs. The movement of mRNAs through the nucleoplasm and out of the nucleus to cytoplasmic locations is an elaborately orchestrated and regulated process. The pathway of mRNA export includes: proper processing, packaging into protein-RNA complexes, targeting and movement through the nuclear pore complex (NPC) and release into the cytoplasm for translation. In some cases, mRNAs are further localized within the cytoplasm. This proposal focuses on the spatial organization of the genome with respect to its interactions with the NPC, nuclear export factors, RNA binding proteins, and the processing and movement of mRNAs out of the nucleus. The Specific Aims are designed to determine: 1) the requirements for gene movement with respect to the nuclear export machinery; 2) the connection between intranuclear gene location, mRNA export and cytoplasmic mRNA location; 3) the interaction of the genome with the nuclear export machinery; and 4) the identification and specificity of recruitment of RNA binding proteins important for mRNA processing and export. The regulation of mRNA dynamics is key to certain genetic diseases, the function of some viral proteins, the response of cells to growth stimuli, and, in some cases, the basis for drug action. We have come to appreciate the complex interplay between gene expression, nuclear organization and transport. This inherent complexity can affect growth status and disease states. Moreover, defects in mRNA processing are associated with a number of diseases including metastatic cancers, muscular dystrophy and amyotrophic lateral sclerosis. The experiments proposed in this grant will not only lead to new basic insights but also to new ways to analyze on a genome-wide level the situation in genetically defective cells and certain cancers. [unreadable] [unreadable] [unreadable]

DESCRIPTION (provided by applicant): This grant requests support for a new Ph.D. training program in systems biology. Our goal is to train a new wave of systems biology faculty who have even broader interdisciplinary research expertise than the first generation of systems biologists. Systems biology is a nascent field with potential for major impact on drug discovery, the development of personalized medicine, and for helping us understand the molecular bases of complex diseases. It also promises to provide an approach to a deeper understanding of fundamental biological processes, such as differentiation, homeostasis, and evolution. It requires integration of concepts from many disciplines, including medicine, biology, computer science, mathematics, physics, chemistry, and engineering. The Program Faculty represents an energetic and committed multidisciplinary team, with extensive teaching and training experience, that takes seriously the challenge of forging a new discipline. Our Program attracts a diverse student group with varied skills and interests;our training approach is therefore a flexible one, including new interdisciplinary courses, course requirements that are tailored to the needs of the individual, and support for dissertation projects that involve collaboration across two or more labs. Our program aims to educate trainees in the current state of the art in systems biology, and to encourage them to reach higher, expanding the usefulness of theoretical and quantitative approaches in biology and medicine.

DESCRIPTION (provided by applicant): Synthetic biology is seen as an emerging discipline for engineering cells more easily and predictably. Several advances have made this possible, such as the increasing numbers of sequenced genomes as raw materials, rapid synthesis of large DNAs, the ability to quantitate the inner workings of single cells, the potential to reprogra entire organisms with new genomes, and a vision that biological design has some analogy to logic circuits. However, myriad studies on cell organization add a degree of complexity and regulation that has not been appreciated in the overall design processes. The overarching goal of this proposal is to harness the multidimensionality of biology to optimize the production of novel pathways, complexes, and cells. A limitation of current synthetic biology is the tendency to engineer biological systems as if they function in a linear, digital computer-like manner. However, cells function in three spatial dimensions and over time, using multi-dimensionality in the form of protein/nucleic acid/membrane complexes and organelles. The proposed work focuses on assembling, in a predictable manner, protein complexes that move in more than one dimension and on different time scales. This work thus encompasses a new direction that will integrate synthetic biology with cell and structural biology, with direct health-relatedness throug its broader implications for development of protein and cell-based therapeutics. The Specific Aims are to: 1) construct memory circuits that record different levels of cytokine signaling; 2) determine the quantitative and spatial requirements for information transmission between the cell surface and the nucleus; and 3) simulate the behavior of proteins that signal from the cell surface to the nucleus. Type I Interferon/STAT signaling will be studied, because it has therapeutic significance, a high signal-noise ratio, and many questions remain about signaling mechanisms. Multi-element gene-based memory circuits that record for later inspection key events in the existence of a cell will be implemented. Prototype targeted cytokines for activity in cell-based assays will be developed; these will be designed to represent synthetic biological constructs and engineered protein therapeutics, as well as natural flexible proteins that use multiple weak interactions to accomplish complex assembly tasks. Finally, a simulation system that will model the spatiotemporal behavior of flexible multi-domain proteins typical of synthetic-biological constructs or candidate therapeutics will be implemented.