Difference between revisions of "20.109(F10): Mod 2 Day 1 Testing an engineered biological system"
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If synthetic biology is to become a practical and useful engineering discipline, then it will likely need to employ engineering methodologies that characterize more mature engineering disciplines such as mechanical and electrical engineering. For example some, but not all, engineering disciplines employ well-characterized interchangeable parts. As applied to biology, interchangeable parts could mean the refinement of sequences to enable their rapid assembly (think back to how long it took us to delete 32 amino acids from the N-terminal end of GFP...a lot longer and considerably more expertise than it takes to twist a nut on a bolt!). Standardized parts might also describe families of proteins that behave in predictable ways, both individually and in combination with other protein families and sequence motifs. | If synthetic biology is to become a practical and useful engineering discipline, then it will likely need to employ engineering methodologies that characterize more mature engineering disciplines such as mechanical and electrical engineering. For example some, but not all, engineering disciplines employ well-characterized interchangeable parts. As applied to biology, interchangeable parts could mean the refinement of sequences to enable their rapid assembly (think back to how long it took us to delete 32 amino acids from the N-terminal end of GFP...a lot longer and considerably more expertise than it takes to twist a nut on a bolt!). Standardized parts might also describe families of proteins that behave in predictable ways, both individually and in combination with other protein families and sequence motifs. | ||
− | [[Image:2CS basic.png|thumb|right| General scheme for Two Component Signaling]] Fortunately evolution appears to work with motifs and many of these motifs behave in a reasonably modular fashion. Re-used and modular motifs from nature seem sensible places to start building a library of synthetic biological parts. We'll more fully explore the idea of [http://www.partsregistry.org/Main_Page a parts registry] later in the [ | + | [[Image:2CS basic.png|thumb|right| General scheme for Two Component Signaling]] Fortunately evolution appears to work with motifs and many of these motifs behave in a reasonably modular fashion. Re-used and modular motifs from nature seem sensible places to start building a library of synthetic biological parts. We'll more fully explore the idea of [http://www.partsregistry.org/Main_Page a parts registry] later in the [http://openwetware.org/wiki/20.109(F10):_Mod_2_Day_3_Tools_for_system_engineering | module.] |
The response of bacterial cells to changing environmental conditions is one example of a modular and re-used natural theme. Hundreds of "two component signaling systems" (2CS) have been discovered in a wide range of prokaryotic cells, enabling the response of the cells to environmental changes, be they physical or chemical. Generally speaking, two component systems consist of a "sensor" protein that spans the membrane, detecting an environmental cue on its exposed face, and transducing that information to the inside of the cell through a changed activity of its cytoplasmic face. The second component of traditional two component systems is a "responder" protein, usually a transcription factor that accepts the signal from the sensor protein and consequently regulates a set of genes to provide the cell with the proper response to the external stimuli. Examples of two component signaling systems include those that regulate chemotaxis, osmoregulation, density-dependent bioluminescence, and virulence. The mechanism of two component signal transduction will be considered in depth next time. Today we'll look at how one system, the two component system that's responsive to osmolarity changes, was used to build a charismatic and novel biological system, the bacterial photography system. | The response of bacterial cells to changing environmental conditions is one example of a modular and re-used natural theme. Hundreds of "two component signaling systems" (2CS) have been discovered in a wide range of prokaryotic cells, enabling the response of the cells to environmental changes, be they physical or chemical. Generally speaking, two component systems consist of a "sensor" protein that spans the membrane, detecting an environmental cue on its exposed face, and transducing that information to the inside of the cell through a changed activity of its cytoplasmic face. The second component of traditional two component systems is a "responder" protein, usually a transcription factor that accepts the signal from the sensor protein and consequently regulates a set of genes to provide the cell with the proper response to the external stimuli. Examples of two component signaling systems include those that regulate chemotaxis, osmoregulation, density-dependent bioluminescence, and virulence. The mechanism of two component signal transduction will be considered in depth next time. Today we'll look at how one system, the two component system that's responsive to osmolarity changes, was used to build a charismatic and novel biological system, the bacterial photography system. | ||
===Bacteria as pixels=== | ===Bacteria as pixels=== | ||
− | ''E. coli'' do not normally respond to light but [http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html a recent publication ] describes a combination of genes that lead to light-responsive expression of | + | ''E. coli'' do not normally respond to light but [http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html a recent publication ] describes a combination of genes that lead to light-responsive expression of |