Davidson College Synthetic Biology Seminar (Fall 2007)
Davidson College Synthetic Biology Seminar, Fall 2007
Click here to access the class webpage
Synthetic Biology Defined
Synthetic Biology: A Brief Introduction
In 1978, the Nobel Prize in Medicine went to Werner Arber, Daniel Nathans, and Hamilton O. Smith for discovering restriction enzymes (www.nobelprize.org), which launched recombinant DNA technology. Scientists were able to splice open segments of DNA at specific restriction sites and add or take away different DNA segments, seeing how these DNA changes affected cell function. Recombinant DNA technology marks the beginning of the field of synthetic biology.
Using restriction enzymes and recombinant DNA, scientists focused on areas as diverse as biofuels, cellular memory, and directed evolution. Synthetic biology now captures a wide range of disciplines that all hold one thing in common: engineering genomes using preexisting and new biological systems and components. Mathematical modeling informs the design of the synthetic system, device, or circuit, which is implemented in wet lab experiments. Results from experimentation enhance the model. The ultimate goal of synthetic biology, therefore, is not only building novel biological systems, but creating a better understanding of existing ones.
Synthetic Biology in the Media
Here we could link to some articles accessible to the general public...
Students in Dr. Campbell's Fall 2007 Synthetic Biology Seminar each wrote a paper on a specific topic within the field of synthetic biology. With our selections, we do not claim to cover all aspects of synthetic biology, but instead hope to provide an overview on subjects we found interesting. The topics we chose can be classified under three broader areas of synthetic biology research:
- Designng and Optimizing Tools. Mike, Laura, Hunter
- Small Parts and Devices. Erin, Emma, Danielle
- Broader Applications. Samantha, Will
Stochasticity in Gene Expression- Mike Waters
My paper will cover a characterization, implications, and ways to manipulate stochastic processes during gene expression.
Using regulatory RNA, gene expression can now be controlled at the stage after transcription but before translation.
Synthetic cellular memory refers to the engineering of living organisms to produce "a protracted response to a transient stimulus" (Ajo-Franklin, 2007). The construction of such rationally designed memory mechanisms in living organisms provides a more thorough understanding of naturally occurring gene networks. In the future, modular cellular memory networks will likely be a key component of many synthetic biological designs, ranging from biocomputing to engineered cell differentiation (Gardner, 2000).
Medical applications of synthetic biology range from treating cancer, creating low-cost medication, protecting from DNA damage, and using biological vectors as vaccines. My paper explores these current collaborations between medicine and synthetic biology, and the challenges and benefits to come in the future.
Logic gates are computing units that perform a logical function on one or more inputs to produce a single output. Synthetic biologists use various cellular regulation mechanisms (transcription, translation, etc.) to create modular gene expression devices that can be combined in order to engineer cells that perform increasingly complex tasks.
Key to the construction of gene circuits and biosensors are promoter and reporter genes, which control how a cell's genes are transcribed when the cell's environment changes. In addition to using promoters and reporters as available to build cellular machines, synthetic biologists can also alter, redesign, or engineer these genetic components in order to refine biological design.
Ribozymes, or RNA enzymes, serve an important role in cellular function both by acting as carriers of genetic infomation and as catalysts for chemical reactions. These enzymes, which represent important ways of regulating genes, that have yet to be fully discovered. Synthetic biology attempts to understand these complex interactions by creating artificial ribozymes and placing them into existing systems. This modular method of gene regulation could open new ways of solving existing promoter and reporter interactions.
Directed evolution is a method of cellular engineering that uses Darwinian selection to evolve proteins and RNA with desirable properties not found in nature. The reliance of this method on the randomness of mutation and nature's selective properties sharply contrasts to the logical modeling and reasoning associated with traditional synthetic methods. Some might say that the lack of planning involved with directed evolution means it is constitutionally different than synthetic biology. Regardless, the method has been shown to be effective in achieving desired results in a number of cases, and could prove instrumental in the optimization of synthetically-designed constructs.
Other Interesting Areas of Research
Here we could put a brief summary of some other areas of synthetic biology research that are not covered in by any of our papers. These might include:
- Engineering the minimal cell. Scientists are trying to identify or build a cell that contains only those elements necessary to be able to classify it as "living." Bot top-down (Venter) and bottom-up (Luisi) approaches are being used. This research could shed light on the earliest origins of life, as well as provide a vessel (chassis? I don't know correct use of this word...) for engineering synthetic biological functions that avoids the variables typically encountered when introducing a synthetic pathway into a cell.
- Other ideas?