Revision as of 02:11, 6 December 2007

A Review of Synthetic Biology

Synthetic Biology: A Brief Introduction

In 1978, the Nobel Prize in Medicine went to Werner Arber, Daniel Nathans, and Hamilton O. Smith for the discovery of restriction enzymes [1]. This discovery marked the beginning of recombinant DNA technology and genetic engineering. Researchers now had the ability to modify the genomes of organisms by cutting and pasting segments of their DNA. For years, genetic engineers have made slight genome modifications in organisms, either by the insertion or deletion of one or two genes, in order to observe phenotypic changes. More recently, as our knowledge of biological systems has grown, the new field of synthetic biology has begun to steal the spotlight. This field builds on the principles of genetic engineering, but attempts to modify genomes on a much larger scale. Instead of inserting or deleting one or two genes, synthetic biologists use recombinant DNA technology and (increasingly) artificial DNA synthesis to introduce whole gene networks into organisms. Because of its complex nature, synthetic biology brings together many different disciplines (biology, math, engineering, chemistry, etc.) to try to successfully engineer genomes using preexisting and new biological systems and components. The possible areas of influence for such biological devices are seemingly infinite, ranging from the production of reusable biofuels to the treatment of some or all cancers. However, the ultimate goal of synthetic biology is not only to build novel biological systems, but to create a better understanding of existing ones.

Synthetic Biology in the Media

1. 2006 Scientist of the Year: Jay Keasling - Discover Magazine
   
2. Genetic Engineers Who Don't Just Tinker - The New York Times
3. How to Make Life - Esquire
   
4. Making Gasoline from Bacteria - Technology Review
   
5. From God to Darwin to Synthetic Biology - The Tech Chronicles
   
6. In the Business of Synthetic Life - Scientific American
   

Our Papers

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:

Optimizing Existing Biological Parts

1. Stochasticity in Gene Expression- Mike Waters
   My paper will cover a characterization, implications, and ways to manipulate stochastic processes during gene expression.
2. Promoters and Reporters in Synthetic Biology - Laura Voss
   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.
3. Directed Evolution and Synthetic Biology - Hunter Stone
   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.

Designing New Parts

1. Post-transcriptional Regulation Technologies - Erin Zwack
   Using regulatory RNA, gene expression can now be controlled at the stage after transcription but before translation.
2. Logic Gates - Emma Garren
   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.
3. Applications of Ribozymes in Synthetic Systems - Danielle Jordan
   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.

Constructing Biological Devices

1. Synthetic Cellular Memory - Will DeLoache
   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).
2. Medical Applications of Synthetic Biology - Samantha Simpson
   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.

Other Areas of Research

• Biofuels: The construction of organisms that are capable of producing biofuels is one of the hottest areas of synthetic biology research. Reusable energy produced in this manner may one day provide a solution to the energy crisis. Unfortunately, it is difficult to find publications on this topic (likely due to patent protection), so no one in the class was able to write about it.
• Engineering the minimal cell: Scientists are trying to build a cell that contains only those elements necessary to function. Top-down and bottom-up approaches are being used. This research could shed light on the earliest origins of life, as well as provide a simple chassis for engineering novel biological functions.
• Nanotechnology: Utilizing nanotechnology to gain greater control of biological systems could provide more powerful and predictable functionality to engineered biological devices.