One of Synberc’s four primary research efforts is device and device family design and composition.
Leader: Christopher Voigt
Massachusetts Institute of Technology
Department of Biological Engineering
A device is an engineered genetic object designed to perform a specific function under specific conditions. Researchers build devices by combining one or more standard biological parts. In the practice of synthetic biology, individual investigators typically respond to the needs of different applications or interests by building devices on an ad hoc basis. However, for synthetic biology research to scale up, we need to lay the foundation for “plug and play” genetic devices and establish a defined set of standard device families.
At Synberc, we are doing just that. Our Devices and Device Composition (DDC) thrust supports testbed device engineering via the development of device family specifications. Our DDC work also focuses on creating foundational methods and tools. The DDC thrust complements the work being done in the Parts and Parts Composition Thrust, so that we can better understand how parts might be engineered to better support devices composition. We are also expanding the Device thrust’s emphasis on measurement and modeling, noting our ongoing need to participate in the creation of a professionally-staffed production facility for producing a repository of high quality synthetic biological devices (see also BIOFAB – see http://www.biofab.org/).
A device family is a set of devices that are designed for use in combination with one another. Synberc PIs build in both physical and functional compatibility, and ensure that the material encoding and instantiating the devices can be connected. PIs also ensure that the signal carrier(s) between devices is independent of the internal workings of each device, and that the signal levels and timing between devices are matched. Though it’s possible to invent unlimited sets of devices, we focus on those device families that we believe will be most generally useful to the development of synthetic biology. These include:
Gene expression devices:
An existing family of devices that send and receive signals as levels of gene expression, or that process information and materials via the regulation of gene expression.
A proposed family of devices that send and receive signals via the state of enzymes that modify proteins (e.g., protein kinases), or that process information and materials via the regulation of protein state or location (e.g., nuclear export).
Cell signaling devices:
An existing family of devices that send and receive information from one cell to the next via small molecules, peptides, nucleic acids, or other chemicals. As currently defined, cell signaling devices often include device-specific sender and receiver units that convert device-specific signal carriers (e.g., N-Acyl homoserine lactones) into device-independent signal carriers (e.g., gene expression level).
Metabolic and material devices:
A proposed family of devices that process or manipulate chemicals and materials. Metabolic and material devices will accept device-independent signals from other device families (e.g., gene expression), but provide device-specific control of chemical (and other) signals (e.g., metabolic feedback).
We have already begun to make good initial progress on describing “gene expression” and “cell signaling” devices. Canton et al presents much of our early work, including a first “datasheet” for a formally engineered synthetic biological device (“formal” in the sense that thedevice interacts with other devices via a common signal carrier, and is itself assembled from standardized biological parts). Additional examples of recent accomplishments include modeling, analysis, and preliminary specification of gene expression device signal levels (R. Shetty, MIT Dissertation, 2008), scaffold-based approaches to developing enhanced biosynthetic devices (J. Dueber et al., UC Berkeley, Nature/Biotechnology, submitted), and engineered phosphoregulation of nuclear cytoplasmic shuttling in yeast (S. Sutton, MIT Dissertation, 2008; and submitted).