The body as battlefield

There is an immunological arms race happening within our bodies. Bacteria launch defenses in response to antibacterial peptides:

University of Washington (UW) and McGill University researchers have revealed a molecular mechanism whereby bacteria can recognize tiny antimicrobial peptide molecules, then respond by becoming more virulent.
...the same molecules that the body sends out to help destroy salmonella inadvertently launch bacterial defenses. It is as if missiles armed, rather than demolished, the target. The body's antimicrobial peptides bind to an enzyme, PhoQ, that acts as a watchtower and interceptor near the surface of bacteria cell membranes. The peptide binding activates PhoQ, which sets off a cascade of signals. The signals turn on a large set of bacterial genes. Some of genes are responsible for products that fortify the bacterial cell surface and protect the bacteria from being killed.

The human body in turn mobilizes responses to bacterial RNA:

Researchers at the University of Pennsylvania School of Medicine have published the first study to test the role of RNA chemical modifications on immunity. They have demonstrated that RNA from bacteria stimulates immune cells to orchestrate destruction of invading pathogens. Most RNA from human cells is recognized as being self and does not stimulate an immune response to the same extent as invading bacteria or viruses. The researchers hypothesize that if this self-recognition fails, then autoimmune diseases such as systemic lupus erythematosus could result.

This implies two obvious approaches for nanotech-enhanced bioweapons: enhance bacterial virulence and cripple the body's response to bacterial RNA. Similarly, nanotech-enhanced biodefenses might defeat bacterial virulence mechanisms and enhance the body's capacity to recognize and defend against bacterial proteins.