CHE.496/2008/Schedule/Engineering principles

CHE.496: Biological Systems Design Seminar

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Engineering principles

Synthetic biology - putting engineering into biology link
- Purpose: This article articulates the technical aspect of synthetic biology (i.e., scientific principles that enable the engineering of biological systems). In addition, examples of artifical genetic networks are described. These systems are just the beginning of synthetic biology. As the enabling technologies are perfected (in particular DNA synthesis, standardized cloning, genome engineering of a suitable cellular chassis, and increased modeling capabilities), synthetic biology will move from foundational work to applications (e.g., novel proteins, more complex artificial gene networks).
- Review standardization, abstraction, heirarchy (see Assignment 2 notes)
- Use of standards already in place
  - Standardization
  - Abstraction
  - Modularity
  - Predictability
  - Reliability
  - Uniformity
- Important tools
  - Standardized cloning
  - De novo DNA synthesis
  - Providing chassis
- Use of Devices
  - Oscillators
  - Switches
  - Logic gates
- Problems of joining two modules together

Synthetic biology: new engineering rules for an emerging discipline link
- Reiteration of biological devices
- Assessment of overall system
  - Must consider that all things are happening in the cell
- Types of Modules:
  - Cascades
  - Cell to cell signaling
- Important notes
  - Natural evolution works!
  - Must examine overall population

Brain-storming exercise
- Last time, we touched on the logistical significance of starting a team. We came up with some good ideas on team management, but we didn't touch on the actual project very much. To get the gears rolling a bit, discuss possible pathways to create hydrogen in a cell. What types of organisms should we start looking? What kind of environment will we need to grow the cells in? How are we going to measure hydrogen production? This isn't meant to be a final plan, so you don't need to do any background research. The goal is just to brainstorm some ideas to 'plant the seeds' for the project.