Judging/Variance/Peking

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Revision as of 17:22, 8 October 2008

Request

Dear iGEM Judges, I'm writing on behalf of 2008 Peking University iGEM Team to ask for permission to send non-biobrick parts to the registry for the jamboree.

As we can not find effective vectors for yeast expression in the registry, our team has been using the pGREG series of plasmids for yeast protein expression. We have to use the promoter which is sensitive to lacI or Gal4, so those yeast plasmids in the registry can not serve this function. For the same reason our parts can not flank the four standard restriction sites since our vector contains these four or at least some of these four. Of course, we are trying to standardize the parts we have constructed but it seems the time is limited. We wonder if we can send those plasmids based on PGREG backbone.

Moreover, since our project has something to do the precise spot mutation of gal4, those plasmids contain gal4 or gal4 delta gene can not be standardized. As gal4 gene also contain some of the four restriction sites.

Another thing that should be mentioned is that our gene hAIDsc is a codon optimized gene kindly offered by Pro. Youri. I am not sure whether he permits us to send this part to open source.

Thank you very much!

Zhou Zhou College of Life Sciences, Peking University Beijing, 100871 P.R.China mikezzchina@gmail.com

Response

Dear Zhou,

It seems like there are three separate issues you are inquiring about.

The first issue is a problem with the limited number of yeast vectors in the registry, and the need for one that is compatible with your lacI and Gal4 sensitive promotor. The best solution to that would be to add a new vector to the registry, which we would welcome with appropriate documentation. You chose the pGREG series of plasmids, but this series contains the standard restriction sites for biobricks, which makes it incompatible with standard registry parts and thus not a great candidate for addition to the registry. There are two solutions to this problem: 1) make the pGREG vector compatible with biobrick parts, possibly (and with luck) by deleting the current biobrick restriction sites from the vector; or 2) create and document a new assembly standard. The Silver lab has done the later, which you might consider: http://openwetware.org/wiki/Silver:_BB_Strategy . The Silver lab approach, with a twist, is being adopted by the iGEM team from Brown University, as described on our judging variance request website: https://2008.igem.org/Judging/Variance/Brown

The second issue, which at least partially derives from the first, is that your parts do not have biobricked ends. If you are proposing a new biobrick part standard, then you will need to carefully document that standard and propose it to the registry. In that absence of a new standard proposal, you should move your parts to a standard biobrick vector for submission. While we recognize that time is now short, this is not a new issue for your team, and should have been obvious as soon as you began working on your design.

Finally, please do try to obtain permission to submit hAIDsc to the registry as an open source part. If permission is not provided, then you should not submit that part. A core principle of iGEM is that we all gain by sharing, and the registry cannot maintain or distribute parts that are not open source/open access.

Please provide additional information about issues 1) and 2) if you plan to propose new assembly or part standards. While this will be a challenge, it is also a great opportunity to make a contribution to the community.

Sincerely,

iGEM judging team

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 It seems like there are three separate issues you are inquiring about.
-The first issue is a problem with the limited number of yeast vectors in the registry, and the need for one that is compatible with your lacI and Gal4 sensitive promotor. The appropriate solution to that would be to add a new vector to the registry, which we would welcome. You chose the pGREG series of plasmids, but this series contains the standard restriction sites for biobricks, which makes it incompatible with standard registry parts.  There are two solutions to this problem: 1) make the pGREG vector compatible with biobricking, possibly (and with luck) by deleting those biobrick restriction sites from the vector; or 2) create and document a new assembly standard. The Silver lab has done the later, which you might consider: http://openwetware.org/wiki/Silver:_BB_Strategy .  The Silver lab approach, with a twist, is being adopted by the iGEM team from Brown University, as described on our judging variance request website:
+The first issue is a problem with the limited number of yeast vectors in the registry, and the need for one that is compatible with your lacI and Gal4 sensitive promotor. The best solution to that would be to add a new vector to the registry, which we would welcome with appropriate documentation. You chose the pGREG series of plasmids, but this series contains the standard restriction sites for biobricks, which makes it incompatible with standard registry parts and thus not a great candidate for addition to the registry.  There are two solutions to this problem: 1) make the pGREG vector compatible with biobrick parts, possibly (and with luck) by deleting the current biobrick restriction sites from the vector; or 2) create and document a new assembly standard. The Silver lab has done the later, which you might consider: http://openwetware.org/wiki/Silver:_BB_Strategy .  The Silver lab approach, with a twist, is being adopted by the iGEM team from Brown University, as described on our judging variance request website:
 https://2008.igem.org/Judging/Variance/Brown
-The second issue, which at least partially derives from the first, is that your parts do not have biobricked ends.  If you are proposing a new biobrick part standard, then you will need to carefully document that standard and propose it to the registry. In that absence of a new standard proposal, submitting parts that are not in biobrick format will not be useful to the registry.
+The second issue, which at least partially derives from the first, is that your parts do not have biobricked ends.  If you are proposing a new biobrick part standard, then you will need to carefully document that standard and propose it to the registry. In that absence of a new standard proposal, you should move your parts to a standard biobrick vector for submission.  While we recognize that time is now short, this is not a new issue for your team, and should have been obvious as soon as you began working on your design.
-Finally, please try to obtain permission to submit hAIDsc to the registry as an open source part.  If permission is not provided, then you should not submit that part.
+Finally, please do try to obtain permission to submit hAIDsc to the registry as an open source part.  If permission is not provided, then you should not submit that part.  A core principle of iGEM is that we all gain by sharing, and the registry cannot maintain or distribute parts that are not open source/open access.
 Please provide additional information about issues 1) and 2) if you plan to propose new assembly or part standards.  While this will be a challenge, it is also a great opportunity to make a contribution to the community.