History of this page: In March 2003, the MIT Synthetic Biology Working Group had brainstorming sessions to determine the potential applications of synthetic biology. The information here has been compiled from our wiki at that time.
Additions, suggestions, and improvements are very welcome!
Applications can be organized in various ways. We saw there being 2 orthogonal dimensions for categorizing applications: the level of engineering and area of interest.
Here are the Levels of Resolutions that a Synthetic Biologist could focus on.
The numbers in parenthesis represent the relevant courses at MIT that we think are associated with the particular area.
The number of bacterial cells in your body at this very moment is equivalent to the total population of your own cells. For the most part they are beneficial, preventing infection, aiding digestion, and perhaps even producing useful chemicals. These commensals, as they are called, have evolved with humans in a strongly symbiotic relationship. Clearly, our body is already conditioned to hold a vast army of prokaryotes to do its bidding. How can synthetic biology harness this potential?
Imagine a time in the not-too distant future. Elliott wakes up in the morning to get ready for work. After taking a shower, he examines his clean, clear face in the mirror, deciding that he can probably wait another month before re-applying the bio-spray that keeps his skin pores clean and renders shaving unnecessary. The spray contains skin surface bacteria engineered to eat dirt, oil, and dead skin, as well as dissolve the keratin in facial hair, while keeping the skin intact. They also prevent colonization by foreign bacteria that can cause infection of pores in skin, preventing acne. He looks at his old toothbrush in the medicine cabinet, and decides to throw it away. Ever since the dentist gave him the oral wash earlier in the year, he has had no use for it. The wash contained a population of bacterial cells programmed to vigorously eat and break down any stains or food residue, and dissolve plaque buildup. They also created a special biofilm which prevents other bacteria from colonizing, eliminating halitosis and gingivitis. Elliott decided to change his breath scent, and picked up a small pen light which he set to yellow and flashed in his mouth. A few minutes later he checked his breath. Faintly sweet and citrusy, very pleasant. The bacteria had been programmed to produce different aromatic compounds depending on the detection of specific pulses of light; the type Elliott had washed with gave him 7 popular scents to choose from.
Elliott walked downstairs to the table for breakfast. He had a bowl of cereal and milk, along with a spicy southwest omelette and some sausages. Eating was always an enjoyable experience. Elliott used to be wary of many foods, as he was prone to frequent indigestion, especially from spicy foods or dairy products. But since his visit to the dietician earlier this year, those problems were a thing of the past. After analyzing his symptoms, the doctor selected a digestive commensal from the Biobricks 3000 catalog which had been programmed for his needs. Now lactose and the irritating chemicals in most spicy foods were broken down with ease in his stomach, before they could cause any distress . An added benefit was that he no longer had to worry about food poisoning. The new commensals specifically targeted and killed any pathogens from a long list of possible food contaminants, and could even neutralize the toxins these bacteria produced. Elliott relished his new state of permanent gastrointestinal bliss.
Elliott then left for his exciting job at the screw factory. Little did he know that the PDKLHS (People's Democratic Republic for Lefthanded Screws) had sinister plans this very day. (to be continued)
Such consumer product applications require a significant amount of metabolic engineering, combined with tightly restricted control systems. The chassis for these systems are already in existance, as harmless commensal bacterial species already inhabit these areas of our bodies. Taking these as a starting point, we need to design metabolic pathways and physiology which defines a solution-specific molecular input/output. for example, the toothpaste bacteria must have a metabolism which is geared toward the "food" we designate; in this case, plaque or materials that can cause cavities. These metabolic systems need to be tightly controlled by regulatory and logic systems that allow for feasability; i.e., sufficient energy and nutrients must exist and be managed in the pathway for the bacteria to happily make its living, without the buildup of harmful intermediates or any other metabolic "dead ends". Finally, the system must be designed so that waste products are optimal for function. For example, sweet smelling molecules for fresh breath, or other harmless outputs. The thermodynamics and molecular economy of the cell will have to be tightly constrained to accomplish this.
Replication is one problem that will need to be overcome. How to keep the number of organisms at an optimum, so as not to elicit immune response or get any "buildup", while still reaping the benefits? one possible solution would be incorporating quorom sensing. Other problems involve restriction of growth. You do not want an anti-shaving bacteria to start munching on your eyebrows. Therefore somehow spacial control must be strictly maintained, and I am unsure how this would be accomplished.
Many bacteria grow into colonies which form surfaces with specific properties, called biofilms. These films themselves can be viewed as dynamic materials which can be designed for various functions. One possible function that has been suggested is to generate a biofilm that forms an airtight sphere. The bacteria in this spherical biofilm matrix would secrete hydrogen gas into the sphere, producing a "balloon" which could float. I suggest that such free-floating biofilm spheres would be the perfect cleaners for air pollution. In highly polluted environments, the bacteria would scavenge the particulate sulfur, nitrogen, and carbon compounds out of the air, using them for energy and growth. Waste products would include hydrogen gas, which would be excreted to the inside of the sphere, keeping it afloat.
These structures would start as a typical bacterial mat-like structure. As hydrogen is generated and secreted in between the layers, it will begin to swell until bouyancy takes over, and the mat floats away as a sphere. Questions:
How big will the biofilm structure have to be? it is biologically realistic? How will the spheres replicate? Is there enough energy and materials present in pollutants to power a Hydrogen producing metabolism, or will photosynthesis be required? Can a biofilm be engineered that can prevent the escape of hydrogen?
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