Team:MoWestern Davidson/conclusion

Laying the Foundation for an Innovative Project

Our iGEM team worked across disciplinary and institutional boundaries to conceive of an innovative approach to the use of bacterial cells to evaluate the satisfiability, or SAT, problem. We designed a unique system for the project and carried out a number of mathematical analyses in support of the design. We designed and built parts that enabled us to demonstrate the basic molecular mechanism for the project, frameshift suppression. The important milestone that we have achieved is that we have laid the foundation for a very innovative approach to the use of bacterial computers that can evaluate an important class of logical problems.

Parts Contributed to the Registry

Our team contributed 66 parts to the Registry this year. The methods by which we constructed basic parts included direct synthesis by DNA oligonucleotides, site directed mutagenesis of existing parts, and PCR amplification from genomic sources. Our new basic parts that should prove to be of general use, including 5 base suppressor tRNAs and cognate reporter genes to test their function. We also constructed a number of intermediate from combinations of new and existing parts and several devices designed to test frameshift suppression.

Training of Undergraduate Researchers

An important goal of our iGEM team was to enable us as undergraduate students to have a valuable education experience. By taking ownership of the conception, design, construction, and presentation of our project, we learned valuable lessons about conducting scientific research. We learned to work as a team on significant challenges, to communicate across disciplines and distance, to troubleshoot experimental methods, and to communicate our progress in diverse ways.

Exploration of BioMath Connections

Our iGEM is mentored by faculty with backgrounds in both Biology and Mathematics and is composed of students from each of these disciplines. From the beginning of the year, we sought to explore BioMath Connections in the choice of a project and in the way we pursued it. We have found synthetic biology and the iGEM experience to be a very effective way to carry out this type of multidisciplinary research. Mathematical modeling of the satsifiability problem in general and of our specific approach to carrying out SAT problems in bacterial cells informed our biological designs. We also made significant connections between mathematics and biology in the design and construction of physical models of our frameshift suppressor tRNA molecules.

Human Practice

The multidisciplinary nature of our iGEM team is also illustrated by a part of our project in which students at Davidson College researched public opinion of synthetic biology based on provided summaries of the field. Citizens in North Carolina were randomly assigned to one of two groups. One group used the word "create" and similar terms to see if this had an impact on their view of synthetic biology. The other group used words such as "build", "construct", etc.

We also measured each person's "religiosity" and analyzed the impact religiosity had on the manipulation. We found that more religious people were more likely to view synthetic biology in a favorable light which was not what we had predicted.

Faculty at high schools and colleges/universities from across the country were asked how much they presently know about synthetic biology and its implementation in course curricula. The survey revealed that 16% of college faculty reported adequate knowledge of synthetic biology while only 8% of high school teachers reported adequate knowledge of the field. Surveys given to general public were used to study public opinion based on the influence of different descriptions of synthetic biology.

Presentations to a Broader Audience

During 2009, our iGEM team members have presented their project and synthetic biology in general at the following local, regional, and national venues.

• Truman State University Mathematical Biology Seminar, January 2009
• Mathematical Association of America Missouri Section, April 2009
• Genome Consortium for Active Teaching (GCAT) workshop, July 2009
• Missouri Western Summer Research Institute Symposium, July 2009
• Davidson Research Initiative Symposium, September 2009
• Association of College and University Biology Educators (ACUBE), October 2009
• Foundation for the Carolinas, November 2009
• Undergraduate Research Conference at the Interface Between Biology and Mathematics, October 2009

Upcoming presentations include:

• Missouri Western Computer Science, Math, and Physics Colloquium, November 2009
• National Academies Keck Future Initiatives (NAKFI) Conference on Synthetic Biology, November 2009
• National Joint Meetings of the American Mathematics Society, Mathematical Association of America, and the Society for Industrial and Applied Mathematics, January 2010

Directions for Future Research

We have developed a design for the use of frameshift suppression to enable bacterial cells to analyze and report the results of a SAT problem. We have develeped mathematical models for our system that can be used to inform our choices for constructing SAT problems in bacteria. We have constructed the frameshift suppressor tRNA genes that will serve as inputs for the SAT problem and have tested their ability to provide frameshift suppression resulting in expression of reporter genes. Our next step is to determine the ability of bacterial cells to accommodate multiple frameshift suppressor tRNAs and to test combinations of them in cells. Then we will design and construct reporter genes that will carry out simple OR logical operations, which can then be combined in to a 2-SAT problem with multiple reporters for multiple clauses. The following task will be to encode 3-SAT problems in a similar fashion.