A Foray Into Synthetic Biology

Fall 2013

Faculty Sponsor: Professor Kyongbum Lee, Chemical Engineering Department Chair

Course Description:

Biology and the life sciences have experienced major innovations over the last half century. Today, the genome of any organism can be affordably sequenced. We also have the ability to write in the code of life, for about 20 cents per A,T,C, or G. Overall, the genetic engineering toolbox has become much larger while getting significantly cheaper at the same time. The falling costs and greater accessibility of these tools have sparked interest standardizing and streamlining genetic engineering to work with off-the shelf parts. Investigators involved in tackling tangible problems by this approach have dubbed this nascent field “synthetic biology.” Their creations are of incredible breadth, from detecting landmines to synthesize cost-effective antimalarials for the developing world. The International Genetically Engineered Machine Competition (iGEM) was founded in order to foster interest in this emerging discipline while engaging young investigators.

Our goal has been to establish an undergraduate team of researchers who will work closely with select faculty to take part in this annual competition and run a conference on genetically modified organisms in the second semester. We believe the best way to intellectually prime and train undergraduates who want to take part in this highly independent research project is through a class which exposes them not only to the technical aspects of the molecular biology techniques involved but also to the social, legal, and ethical implications of synthetic biology.

Intellectual Goals

To impart familiarity and a thorough understanding of the components involved in the research, design, development, and experimentation associated with synthetic biology, in a competition based setting, for real world experience and application. Bioethics and security is examined. Community outreach to local high schools and networking opportunities with local biotechnology companies are also explored.

Specific Topics:

- Fundamental molecular biology techniques
- Current methods for genomic modification
- Regulations surrounding synthetic biology
- (Bio) Ethical considerations of research
- Human practices
- Brief interludes within related fields, such as: Metabolic Engineering, Developmental Biophysics, Molecular Sensing, etc.

Course Goals & Expectations

This course will be run mainly through guided, independent study in the pursuit of several, interrelated goals. Our aims are multifaceted and it is expected that each member of the course will be involved with several, but have a primary focus in one. - A paper describing the popular beliefs and scientific accuracies and inaccuracies associated with biosecurity and bioethics (Tufts Institute for Global Leadership (IGL)).
- The design of several possible synthetic biology projects to be pursued by the Tufts iGEM team in future years (Professor Nikhil Nair).
- The summation, expansion, and review of the Bdellovibrio bacteriovorous (Bb) project pursued during the summer of 2013.
To ensure the success of these goals, we expect the following:
- A commitment to a, minimum, once weekly general meeting and awareness that additional, supplemental, meetings may be required at various points during the semester.
- The completion of assigned tasks in a timely manner.
- Attendance during all guest lectures which do not conflict with a separate course and to be informed if attendance is not possible.
o Involvement: Before guest lectures, the class will receive papers and summaries of papers written by the visiting lecturer. Discussion will take place as a question and answer session at the end of each guest lecture.
- And a final paper with associated presentation, to be undertaken individually or in groups.
This said, we are highly excited for the opportunity to shape this course with you moving forward and greatly look forward to developing our mutual knowledge.

Project

To be decided more concretely further into the semester, but in the form of a final paper and presentation detailing a project proposal for a possible synthetic biology project as well as a brief paper detailing your experience in the course, pursued topics, and results knowledge gained.
Presentations
At the end of the semester, and with flexible timing, each individual/group will be responsible for a brief presentation regarding their experience in the course and their final paper.

Schedule

This course will be run mainly through guided, independent study with, at minimum, once weekly meetings to review and discuss results. The date of these meetings is tentatively timed for Friday at 3:30 PM.
During our first meeting, we will go present the results of the project undertaken during the summer of 2013 and an overview of the expectations and goals moving forward and highlighted below. We will also discuss the commitments of our members and recommended readings, including, but not limited to, those listed above.
In addition to the course projects and independent study, guest lecturers have been invited from both within and without the Tufts community with expertise in biology, bioethics, biotechnology, venture capitalism, and other fields. Before each guest lecture, additional, supplemental material will be provided. At this time, the below professors have committed to speak, with the location to be determined.

October 15th, 2013 (11AM) – Professor Michael Levin – Developmental Biophysics
October 18th, 2013 (1PM) – Professor Kyongbum Lee – Metabolic Engineering

Recommended Readings

1. Bohannon, J. (2011). The Life Hacker. Science, 1236-1237.
2. Brent, E., Singh, R., & Winters, P. (2011). Synthetic Biology: Regulating Industry Uses of New Biotechnologies. Science, 1254-1256.
3. Church, G. (2012). Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves. Basic Books.
4. David, G. (2009). The Machinery of Life. Copernicus.
5. Enriquez, J. (2005). As the Future Catches You. Crown Business.
6. Khalil, A., & Collins, J. (2010). Synthetic biology: Applications Come of Age. Nature , 367-379.
7. Schwille, P. (2011). Bottom-Up Synthetic Biology: Engineering in a Tinkerer’s World. Science, 1252-1254.
8. Steven, B., & Sismour, M. (2005). Synthetic biology. Nature Reviews Genetics, 533-543.