Modular design of biological systems

Abstract

The focus of my research is the development of technology for building compound biological systems from simpler pieces. I designed BioScaffold parts, a family of variable regions that can be inserted into a DNA sequence so that at a later time another set of pieces can be substituted for each variable. The variable regions are selective so that a particular piece can be targeted to each region. I have used this technique to assemble protein domains, tune the expression levels of proteins and remove BioBrick scars. BioScaffold parts can be used in combination with BioBrick Standard Biological Parts to create and store devices with tunable components. I developed simplified methods to produce and examine SbpA, a protein that can either self associate into two-dimensional crystals or bring together fused enzymes when divalent cations such as calcium are added to the protein monomers. My fast and easy purification protocol allows SbpA to be produced under non-denaturing conditions as well as examination of the native state of the protein monomers before crystallization. The absence of a white precipitate when calcium is added to SbpA monomers concentrated to 1 mg/ml provides a simple visual screen that indicates that the protein has failed to crystallize. I also developed a protocol to embed SbpA crystallized on lipid monolayers in trehalose for electron microscopy, allowing creation of a 7 Å resolution map for SbpA. I created a cells-on-paper system to compose, isolate, and subsequently destack and examine different cell types grown in sheets of ordinary filter paper and maintained in a humidified incubation chamber. I found that E coli diluted in LB broth and then applied to filter paper grew at rates similar to the same culture spotted on agar plates. Track etch membranes could be used to isolate different cell types, while still allowing chemical communication between the layers. Use of plasmids that contain fluorescent proteins allowed the behaviour of cells to be tracked using a scanner after destacking of the layers. The cells-on-paper system can be used both to test and construct modular synthetic systems composed of bacterial ensembles and to create and examine the behavior of compositions of cell types typically found in biofilms.