Empirical cumulative distribution functions of cavity cross-sectional areas. Each ECDF plotted above represents the cross-sectional area of each microcolony detected in each fluorescence micrograph in a set of z-stack fluorescence micrographs. Microscopy was performed after roughly 24 hrs of incubation following inoculation, unless otherwise indicated. The ECDFs represent cross-sectional areas from all sampled imaging planes, not only those that maximize the cross-sectional area of a cavity.
The bioenabled material under development is a combination of three components: a microchip, a polymer hydrogel, and a community of genetically engineered bacteria. In this approach, the bacterial component must be optimized under the physical constraints of the polymer matrix and the metabolic demands of the synthetic transgenes. Research activity in this period was directed toward improving our understanding of the spatiotemporal dynamics of cell-cell signaling and the impact of hydrogel stiffness on cell growth and protein expression. These priorities were selected in response to uncertainty regarding the compatibility of the available polymer choices with high performing engineered bacteria and interest in pursuing a division-of-labor approach to the biological component of the device. Questions regarding polymer choice and spatial organization of the biological components will be answered using data collected from the work described in this report.
Design of bacteria whose gene expression can be controlled by electricity. Bacteria can interpret electrical signals by distinguishing between oxidation states of chemical compounds. Altering the oxidation states of these compounds through electrochemistry can therefore lead to changes in bacterial gene expression. We will adapt the well-studied SoxR/SoxS redox-responsive gene circuit in E. coli to establish a digitally-controllable bacterial strain.
Amplification of redox signal via long-distance, pulsatile cell-cell signaling. Cells embedded in a solid media will have diffusion-limited access to molecules oxidized or reduced at the electrode surface. To achieve uniform response to electrical signals, cells nearer to the electrode must communicate with distant cells. We will augment the redox-sensitive cells with a long-distance signaling circuit, previously studied by our lab, to promote a uniform bacterial reaction to electrical input.
Characterizing cell-silicon interface and cell-cell communication under various operating conditions. The rate of redox reactions at the electrode surface, as well as the complementary conversion within bacteria, will depend on electrode design, media composition, and construction of the silicon-hydrogel device itself. In order to best support subsequent modeling and design efforts, we will construct and characterize the performance of devices varying in electrode composition and size, hydrogel density and size, and media composition.