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Latest revision as of 03:23, 28 October 2010

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Johns Hopkins iGEM 2010 Human Practice

Open Source Biology

We encourage the Open Source philosophy in the iGEM competition and the entire Synthetic Biology community. To exercise this philosophy, we will make all the genetic material and software we build open source and available to any qualified user in academia or industry and perhaps even DIYBIO.

Together with previous iGEM teams from Johns Hopkins, we have submitted over 100 parts to the Registry, and we still have several hundreds Building Blocks from the synthetic yeast genome project ready to go. We will make all of these parts/BBs available without Intellectual Property (IP) entanglements to anyone who requests it. Moreover, we seek to engage the larger community as a workforce to produce the synthetic yeast genome under the up-front condition that they will not exercise any IP rights on the material or their derivatives. We have developed a unique strategy for doing this, which is to approach the Genetics Society of America to serve as owner of all materials made by the project (in any university), and allow for low cost distribution to all interested parties without restriction. The GSA has informally expressed interest in playing this role. As far as we know we are the only SynBio group taking this approach.

Johns Hopkins iGEM teams have also been involved in the development of several Synthetic Biology software under supervision of Drs. Jef Boeke and Joel Bader and Sarah Richardson. Those software include GeneDesign (http://www.genedesign.org), BioStudio and CloneQC (http://j.mp/cloneqc). We make all of these software applications open source under a BSD license.

Safety

While synthetic biology has huge promise for many diverse applications, there is the concern that because the materials we are manipulating and building with are the key components of life that we could create a potentially very dangerous or uncontrollable organism. We believe that our project does not constitute a significant safety risk to researchers, the public, or the ecosystem.

Our experiments fall under Section III-F-6, “Exempt Experiments,” of the NIH Guidelines for Research Involving Recombinant DNA Molecules by virtue of being in a Saccharomyces chassis (see Appendix C-III of the NIH Guidelines). The NIH Guidelines suggest Biosafety Level 1 (BSL 1) containment, and our procedures were conducted at BSL 1. “Typical” yeast is commonly used in both brewing and baking and are not typically dangerous. Even yeast infections, which are rare, are not very dangerous--albeit harder to eliminate, as both human cells and yeast cells are eukaryotic. Even so, we followed sterile procedure in our laboratory work to prevent our yeast from escaping. This included the use personal protection (gloves and lab coats), careful disposal of waste (autoclaving containers and use of properly marked biohazard bins) and thorough disinfection of surfaces (using ethanol).

Our yeast would not have additional genes that could produce toxins and will not produce any potential harmful agents(besides ethanol which people already knowingly and willingly ingest). As an added safety measure our yeast lacked functional genes for seven essential amino acids, ensuring their limiting their growth to highly supplemented growth media. Furthermore, the genes we added are extremely unlikely to provide a selective advantage to our engineered yeast in the wild, since the functionality they provide--fluorescence in response to voltage or calcium shock--is useless in their niche. In fact, the genes that were knocked out to enhance the function of our parts reduced the cells’ ability to adapt to environmental stress. Thus, we believe that our project is neither high risk nor high hazard.

There are many guidelines to regulate the safe utilization of recombinant DNA on organizational, local, state and national level. From the Hopkins medical school Biosafety Department to keep track of the recombinant DNA being used in the laboratories to the NIH guidelines, there are many safeguards in place to prevent unintentional (or intentional) damage to people or the environment.

Attribution and Contributions

The Johns Hopkins iGEM 2010 team is completely student-driven. The team members formed the team, conceived the research project, raised funding from various sources, found advisors and lab spaces, sought out advice from knowledgeable scholars in the field, and delivered the research project on their own.

The research project presented here is completely not relevant to the research being done in the advisors' laboratories. The advisors provides feedback, advise and encouragement to the team. We sincerely thank our advisors, Dr. Yizhi Cai, Dr. Jef Boeke, and Dr. Marc Ostermeier for their time, advice, and A LOT of patience! We would also like to thank Adam Kim and Dr. Kyle Cunningham for their knowledge, time, and the occasional reagent.