Difference between revisions of "Team:BostonU/Mammalian synbio/Solutions"

Revision as of 18:38, 18 September 2015

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Proposed Solutions

After identifying some difficulties iGEM teams could face when trying to work with mammalian chassis, our team came up with some potential solutions for these issues. Our team is proposing these broad solutions in an effort to inspire discussion in the iGEM community, and ultimately lead to more creative ways to increase research in mammalian chassis.

The three major challenges that we identified were: cost, parts, and awareness.

1. Cost

   We believe that cost is the largest barrier for most teams, and also the most difficult limitation to overcome. While the combination of increasing interest in mammalian synthetic biology along with technological advances should lower cost over time, our team was interested in thinking of more short-term proactive solutions.

   We recognize that one of the most costly factors in doing research in mammalian chassis is the initial cost of equipment like tissue culture hoods and CO2-regulated incubators. Therefore, our team thought about creating an avenue to connect iGEM teams that are based in institutions or labs in which research in mammalian cells is actively done with teams that do not have access to this equipment at the home institutions. Teams with proper facilities could volunteer to be on a “MammoBoard”, and teams without facilities could perform primary cloning and ship their constructs to MammoBoard teams in order to get testing done in mammalian chassis.

   

   Another option is to request facility space at local companies - this might be difficult and only a promising solution for teams located very close to certain biotech companies, but we think it is a good starting point for discussion.

   In terms of cost of reagents, we think that teams with proper facilities in place can identify companies that provide reagents and request donations (suggestion courtesy of Natalie Farny, an instructor from WPI). We purchased our reagents this summer from Fisher Scientific, and there are other companies that supply mammalian products such as Sigma Aldrich and Promega . We suggest that future mammalian teams speak with some of these companies for reagent donations in subsequent years.

   In future years, companies that are interested in supporting mammalian synthetic biology research in iGEM can help develop a “MammoKit”, which could include a starter cell line, media, trypsin, and TC plates. One example of a company interested in supporting mammalian teams across is Agilent Technologies, who offered a cool vector assembly kit to all iGEM teams this year. They developed an easy way to create mammalian expression backbones (in addition to E. coli and yeast) and even sent us their free starter kit this year! This gives us some promise that companies would be receptive to such an idea.

   

   In addition to a “MammoKit”, teams would need the know-how to use these resources effectively. Our team made an effort in this area, as we have documented our detailed protocols and experimental pipeline for working with HEK293T cells. We hope that future teams that work with this cell line help improve these protocols, and also that other teams working with alternative chasses can make their protocols and experimental pipelines available as well.

2. Parts

   We previously discussed how part availability and submission can be difficult for mammalian teams.

   While the MammoBlocks method proposed by MIT iGEM 2010 and 2011 is a great first step for a suitable mammalian part submission method, this standard may not be practical for all mammalian chassis teams. Gateway cloning is proprietary technology from Invitrogen, and asking teams to use these backbones and reagents is costly.

   While the MammoBlocks method proposed by MIT iGEM 2010 and 2011 is a great first step for a suitable mammalian part submission method, this standard may not be practical for all mammalian chassis teams. Gateway cloning is proprietary technology from Invitrogen, and asking teams to use these backbones and reagents is costly.

   Although, current BioBrick submission requirements have been the foundation of the iGEM registry, it may be possible to tweak the criteria so that it is more suitable for larger parts. For example, requiring only one enzyme site in the BioBrick prefix and one site in the suffix (rather than 2 in each) could turn BioBrick part submission into an easier requirement to accomplish. With an easier submission requirement, mammalian teams (and teams with larger parts in general) may be more likely to submit their parts to the registry, since these will more easily follow requirements. Although this solution would eliminate the ability to assemble parts using BioBrick cloning, there are other, new ways to clone parts that do not require BioBrick assembly or restriction enzyme requirements - for example, Gibson cloning.

   Although, current BioBrick submission requirements have been the foundation of the iGEM registry, it may be possible to tweak the criteria so that it is more suitable for larger parts. For example, requiring only one enzyme site in the BioBrick prefix and one site in the suffix (rather than two in each) could turn BioBrick part submission into an easier requirement to accomplish. With an easier submission requirement, mammalian teams (and teams with larger parts in general) may be more likely to submit their parts to the registry, since these will more easily follow requirements. Although this solution would eliminate the ability to assemble parts using BioBrick cloning, there are other, new ways to clone parts that do not require BioBrick assembly or restriction enzyme requirements - for example, Gibson cloning.

   We think that it would be interesting if there was a way to redefine some of the classic BioBrick submission criteria, such that it was more permissive towards submission of larger parts.

3. Awareness

   We hope that future iGEM teams will be inspired to consider projects in mammalian synthetic biology, given more awareness about current efforts in the field. Below are some key Principal Investigators that do cutting-edge mammalian synthetic biology research, and we have included links to their lab websites. We hope that some of the research questions these labs are exploring can spark interest in future iGEM teams.

   Ahmad Khalil, BU http://www.bu.edu/khalillab/

   Wilson Wong, BU http://wilsonwonglab.org/

   Feng Zhang, MIT http://zlab.mit.edu/

   Ron Weiss, MIT http://groups.csail.mit.edu/synbio/

   Pam Silver, Harvard https://silver.med.harvard.edu/

   Christina Smolke, Stanford http://smolkelab.weebly.com/

   Timothy Lu, MIT http://www.rle.mit.edu/sbg/

   Wendell Lim, UCSF http://limlab.ucsf.edu/

   We hope that making some of this information available can inspire future iGEM teams when they are formulating interesting project ideas!

   With regards to incentivizing work done in alternate chassis in iGEM, we think it would be interesting if iGEM could create a special medal or award for teams that are able to work with proper chassis (for ex. “Best Use of Alternate Chassis” award). This could support teams that go out of their way to do interesting research in a non-typical chassis.