Team:Johns Hopkins-Wetware/humanpractice

The Human Practices component of iGEM has led to a wealth of online materials available to anyone interested in learning about synthetic biology. Educational resources include lecture presentations, discussions on the ethics of synthetic biology, and lab resources such as animations or protocols.

A major principle underlying the field of synthetic biology is the concept of standardization. While this concept is widely applied in our experimental approaches, we discovered a noticeable absence of standardization with respect to educational resources. More specifically, we are currently lacking a standardized lab course that can be implemented in any biology lab to teach the basics of synthetic biology. To this end, we decided to develop a lab-based module that can be integrated into a general biology curriculum - either in an advance high school classroom setting or at the undergraduate level. We decided to provide a broad educational experience, targeted towards both biology majors as well as the student who do not plan on majoring in the STEM (Science/Technology/Engineering/Mathematics) fields.

Our lab-based module is called "The Yeast Golden Gate Parts Course" and comes complete with lecture materials, protocols, required reagents, and discussion questions. We envision lab instructors integrating this module into pre-existing lab courses in order to introduce a synthetic biology perspective into their molecular biology lab lessons. The lecture materials introduce major synthetic biology principles such as abstraction and standardization. The lab-based component gives the students a chance to subclone parts that will be contributed to a large repository, the Yeast Standardized Collection of Parts for Expression (yeast SCoPE) housed at Johns Hopkins University. In this way, students will be engaged intellectually by the topic of synthetic biology and will also be able to contribute to a larger research goal by participating in populating the Yeast ScOPE with new parts. Overall, our goal is to introduce the synthetic biology field to a broader range of students, not just those planning to major in a biological science or engineering field and we hope to provide a solid educational grounding in synthetic biology concepts.

At the design stage, we engaged our advisors, including Dr. Jef Boeke, a professor at Johns Hopkins University, who is currently leading a project to design and construct a fully synthetic version of a eukaryotic genome. For the synthetic genome project, Dr. Boeke and our other advisors have developed a synthetic biology course at JHU called "Build-A-Genome", and thus provided critical feedback in developing our standardized lab course. With their assistance, we defined a plan for the Yeast Golden Gate Parts Course.

Our goals included:

1. Encourage students to learn the language of synthetic biology.

2. Teach basic molecular biology lab techniques in the context of a synthetic biology application.

3. Discuss current synthetic biology research.

4. Discuss ethical issues in the framework of the project.

Examining general biology lab manuals, it seemed the best way to accomplish these goals would be to have students work on a project utilizing the pre-existing molecular biology lab techniques taught in class.

With this idea in mind, we established a workflow in which students were assigned a set number of parts for construction and starting from PCR amplification would construct these parts, by sub-cloning and sequence verifying the final part constructs.

Having set the defined the workflow and developed an outline of the curriculum, JHU Wetware iGEM team members took the opportunity to test Yeast Golden Gate Parts Course over the month of June in order to troubleshoot and optimize protocols. Importantly, this experience served as an opportunity to provide less experienced iGEM team members with instruction and advice on basic molecular biology techniques. Further, we invited a student from Baltimore Polytechnic High School to participate in the trial run through of the course to verify the concept was applicable to the high school level.

We asked Dr. Karen Zeller, the instructor for the Build-A-Genome synthetic biology course at JHU, to serve as an instructor for the initial offering of the Yeast Golden Gate Parts Course. The syllabus is here (insert link to pdf). Since part of the assumption in designing the course was that students would also be attending general biology lectures, Dr. Zeller provided basic lessons on molecular biology as well as presentations on molecular biology lab techniques. In addition, scientists from the Boeke Lab gave presentations explaining how they would use the parts.

The trial run gave us a chance to modify the protocol and make adjustments to our syllabus, lab manual, and software. Through this experience, we learned a lot, have developed an important educational resource, and in the process generated almost 900 parts (link to parts page) that we have contributed to the Yeast SCoPE here at JHU. Our high school student informed us at the end of the course that it was exciting to contribute to an actual research project. Furthermore, this gave him a concrete example of the concepts underlying synthetic biology.

The team submitted RFC88: Yeast Golden Gate: Standardized Assembly of S. Cerevisiae Transcription Units. This describes the assembly standard which the parts made during the course conform to. Our vision is that the Yeast Golden Gate Parts Course and the Yeast SCoPE, which will contain all of the parts generated, will allow the academic community improved access to a standardized assembly of yeast transcriptional units.

We are in the process of developing a database for that will work seamlessly with the Parts Course and the Yeast SCoPE, allowing instructors to choose parts for their classes to construct and alert the JHU staff when parts are ready for sequencing. This will also be a resource for instructors. We envision parts used for projects to have a link or description to the project the part will contribute to. This will allow students to see their participation in a scientific endeavor and also provide instructors an opportunity to discuss advanced synthetic biology projects or concepts.