@phdthesis{20470,
  abstract     = {Systems design has classically relied on composable systems, in which individual subsystems
have defined inputs, outputs, and interactions with each other; however, attempts at
designing complex systems in synthetic biology has often run in to issues of crosstalk and
interference, given that these systems must function within the context of the host. In nature,
mobile genetic elements are systems that have evolved to travel between hosts, and thus
appear to be a good candidate with which to evaluate composability. Selecting temperate
phages as a model system, I used mathematical modelling to identify sources of information
that temperate phages should respond to. I found that essential proteins of temperate phages
can interfere with potential hosts, indicating limitations to composability. I also designed a
lysogeny reporter construct and characterize its behavior across various laboratory and
environmental strains, finding differences in phage lambda lysogens, and potential
interference from prophages that already exist within the environmental strains. Although
the information gathered is not conclusive, it suggests that composability is not a key property
of temperate phages, implying that biological systems may not be composable, and that other
system design principles should be considered when designing synthetic systems.},
  author       = {Wu, Bryan},
  issn         = {2663-337X},
  pages        = {102},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{An examination on phages as a naturally composable system}},
  doi          = {10.15479/AT-ISTA-20470},
  year         = {2025},
}