This dissertation summarizes advances made toward understanding of the composition, structure, mechanism, and regulation of the bacterial type VI secretion system (T6SS). The T6SS is a widely conserved bacterial nanomachine used by Gram-negative bacteria to deliver toxic effector proteins into the extracellular environment or into adjacent target cells. Systematic deletion of open reading frames present in the Vibrio cholerae T6SS gene cluster revealed the genes essential for T6SS activity and provided key insights into understanding the mechanism by which this organelle is assembled and its components are recycled. Characterization of one phage-related T6SS component yielded insight into the mechanism by which many effectors associate with the T6SS organelle and are delivered into target cells. This T6SS component serves both to sharpen the tip of the membrane-puncturing T6SS spike complex and as a vehicle for attaching a diverse set of effector proteins. Time-lapse fluorescence microscopy of GFP-labeled T6SS components revealed key insights into the behavior and regulation of the T6SS in Pseudomonas aeruginosa. The T6SS in this organism assembled in response to exogenous T6SS attack by adjacent sister cells as well as heterologous T6SS+ species V. cholerae and Acinetobacter baylyi. This retaliatory T6SS counterattack was precisely aimed and caused no collateral damage to neighboring, non-aggressive bacteria. These counterattacks are mediated by phosphorylation cascade that recognizes exogenous attacks and post-translationally activates the T6SS in P. aeruginosa. Deletion of genes in this pathway eliminated the retaliatory response while retaining T6SS functionality. This pathway also induced T6SS counterattacks in response to mating pair formation associated with type IV secretion system (T4SS)-mediated DNA conjugation as well as treatment with membrane-disrupting natural product polymyxin B, suggesting that the signal needed to induce T6SS activity was mechanical perturbation of the P. aeruginosa cell membrane. Interestingly, these T4SS-induced counterattacks were able to confer resistance to the acquisition of horizontally transferred foreign DNA by selectively killing conjugative donor cells. As such, the T6SS of P. aeruginosa may represent a type of general bacterial innate immune system capable of responding to a wide range of exogenous threats.

Networks, such as the Internet, are comprised of dense information flows with expansive, multi-directional reach that continuously change—and this changeability is what keeps the network active, relative, and vital. I call the form of network exhibiting those dynamic features the vital network. This form of network is not simply the outcome of connectivity and communication between affiliative objects and actors such as cell phones and humans that together convey a sense or feeling of ‘aliveness,’ it is the outcome of software programming goals for communication systems inspired by nonhuman, self-organizing biological life. The biological turn in computation produces an organizing logic for the vital network that self-propagates connections and disconnections, services, collectives, and structures proximal to forms that feel vital and dynamic. The vital network can do things, it has capacities to act, and different material consequences emerge out of the organization and coordination of communication with particular implications for human privacy, autonomy, and network transparency. I examine the biological turn in computing as a feature within a development program for the design of digital network control systems that rely on self-regulation and autonomous communication processes intentionally constructed to be non-transparent. I explore nonhuman models of control as a response to this requirement considered through three objects: microbe, simulation, and control, each understood in process terms that disclose what these things do and how they act. It is appropriate to the concerns of this dissertation to think of these as object-processes occurring within three moments or transverse becomings: first, in terms of Gilles Deleuze’s notion of differentiation from the one to the many; secondly, from organism to simulation through the use of models to describe microbial processes in informatic terms; and finally, from description to control through the progression in computing from an emphasis on structure and descriptive procedures, to processes of control. Given that so much of contemporary life is structured by communication technology, my study points to the need for an ethics of control to imagine how much and how deep control should go when considering the organization appropriate to our shared, technically enabled, sphere of communication. / Thesis (Ph.D, Sociology) -- Queen's University, 2014-01-27 14:57:29.139