The study and implementation of nanotechnology as applied to biology is making substantial progress toward the expansion of the dialogue between synthetic and biological systems. This dialogue leads to a deeper understanding of the origins, manifestations, and characteristics of biological phenomenon that ultimately will lead to improved methods of diagnosing and treating a variety of pathologies. Perhaps the most prevalent application of this new technology is in the field of cancer research, encompassing an array of diagnostic and therapeutic approaches for in vivo utilization. These approaches include novel ways of enhancing tumor imaging for earlier detection or delivering toxic therapeutics directly to the site of action, sparing the systemic damage that so often accompanies cancer treatment. However, it is the combination of these essential and orthogonal functionalities that is the hallmark of the promise of nanotechnology. Such materials, coined as "theranostics" for their therapeutic and diagnostic capabilities, allow for a new depth of understanding of the behavior of nanoparticles in vivo, and in particular their efficacy as therapeutic treatments. This dissertation discusses the development of platforms and materials that may be employed as theranostic cancer agents from two distinct philosophical approaches--what may be called "traditional" and "non-traditional" nanotechnology. The "non- traditional" approach details the development of a novel DNA nanoparticle platform created through an exponential enrichment process for selected cell targeting. The products compose a novel class of nanoparticles that possess all of the naturally advantageous properties of DNA. The remainder of the dissertation presents a more "traditional" approach to hierarchical nanoparticle construction, discussing synthesis, stabilization and functionalization of theranostic materials of iron oxide and gold and their combination into novel nanostructures for more efficacious in vivo imaging agents. Ultimately, the preferred path between traditional non-traditional methods rests on whether biological selection is more powerful for functionality than rational design, or whether the most efficacious route is a combination thereof

The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.